http://bigdatasummerinst.sph.umich.edu/wiki2018/api.php?action=feedcontributions&feedformat=atom&user=Davina+Barron U-M Big Data Summer Institute Wiki - User contributions [en] 2026-05-23T23:23:19Z User contributions MediaWiki 1.29.2 http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=82 Main Page 2018-07-05T15:18:00Z <p>Davina Barron: /* Recorded Lectures */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/open?id=1XMYhAs8WnxhC4vb7u1Eup4aWh0N-1pH1 Reproducible Research - Jedidiah Carlson]<br /> *[https://drive.google.com/open?id=1vWCGrLCYETLlA3Z_91QLHPtr1b1tmnBq Data Processing] - Jed Carlson<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research] - J. Carlson<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Study design and Inference] - R. Little<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> *[https://drive.google.com/open?id=17gGeKY7lj0nE9Z5rVSS1xTgVbKzhV2HH R intro file] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1x56tLgsucEp8fZdCyGoZKx2AJiC9cheY R intro Lecture] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1Lsf3XverXb20zv8uuJiYdGh2qAc04HwZ Linear Algebra] - Klemmer<br /> *[https://drive.google.com/open?id=1AvMWjfQMaDPBe90tLElJqyIEqMQkFXFN Matrix Algebra Lecture] - Klemmer<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=564ba8aa-7e11-4acb-9acc-a90500f3b197 Big Data pt. 2] - Roderick Little, PhD<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=72425167-56ed-4016-a0a3-a905014b2154 Linear Algebra] - Klemmer<br /> <br /> ==== Day 4: June 21 ====<br /> *[https://drive.google.com/file/d/1iihBno6cnaKJD_jy1hZjW55HAZGR-7jz/view?usp=sharing Linear Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/open?id=1N4DVT3RQfnlWpdLrYs9NyK3bcaQepwqv Logistic Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/file/d/1Is4wRzwpi9qjEgdRLaaiH5pnqAJV952s/view?usp=sharing R dplyr Slides] - Matthew Flickinger<br /> *[https://drive.google.com/file/d/1U_djfdZ1l4Ladh7flByTJt0yBKj2_OBp/view?usp=sharing dplyr R code] - Flickinger<br /> *[https://drive.google.com/file/d/1JajnEQi5V366UYMhHZu9O_Btt9miz0G5/view?usp=sharing dplyr R Flights] - Flickinger<br /> *[https://drive.google.com/file/d/1ytD46IcZbBwZNAORxK_6dbqsDZ_JM7O3/view?usp=sharing dplyr OCSLS] - Flickinger<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17b825db-efc1-4062-8fd4-a90600d75981 dplyr] - Matthew Flickinger<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f86c1be8-32ba-427b-82e6-a90600f41994 Logistic Regression] - Matthew Zawistowski<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e7d5c8c2-5774-46e9-a39e-a906014c1cc4 Linear Regression] - Matthew Zawistowski<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/file/d/1zPvY7rTxaZtO4qNazEqM8UD4I3k-r0gS/view?usp=sharing State of Institute Slides] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1Zf0yIVFTESB1NokCKrAPZRqZ65BeZHiE/view?usp=sharing Big Data 3 Slides] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/11LnfEnT2po2SLJmodkaQfyrM8vUnjJPf/view?usp=sharing ggPlot 2 Slides] - Matthew Flickinger, PhD<br /> *[https://drive.google.com/file/d/1riMRVCd5_hQQRlGr4F6PkR8L2JIWG25t/view?usp=sharing Dplyr_Sms]<br /> *[https://drive.google.com/file/d/15Qy8K-r1KmpU8elEMIY4a0SUCaOdyo8G/view?usp=sharing ggplot2]<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=3af6f347-406f-4d8b-9c0b-a90700f2f700 Parameter Estimation] - Rod Little<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=45312fc9-60b5-41ca-935c-a907011267a4 Journey Lecture] - Sanchez<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> *[https://drive.google.com/file/d/1FBj8Uet0cJ02aMP6MHWvFeOuA2bkim4j/view?usp=sharing Matrix Computations] - Peisong Han<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection] - Lauren Beesley<br /> *[https://drive.google.com/open?id=145d1lrONgCGX-CO_sx0o1hj5P4CMxg7o Python Lecture 1] - Max Smith<br /> *[https://drive.google.com/file/d/1DUZRkidMf9qhH5pfomY7POcsDrkZ7n8L/view?usp=sharing Python Notebook 1] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=61694d5a-30a4-41d3-81bc-a90a00d60405 Matrix Computations] - Han<br /> <br /> ==== Day 7: June 26 ====<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection II] - Lauren Beesley<br /> *[https://drive.google.com/open?id=11LzWvnANtEtKASP0IsDYUuuQw4zhi8WD Machine Learning] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1yyRBiZrI5itTNmPdQBXR66wjC7sEwHzL/view?usp=sharing Python Lecture 2] - Max Smith<br /> *[https://drive.google.com/file/d/1Uk7woOZ-Kyq2nkfNoLxjvG1iB8dnULUb/view?usp=sharing Python Notebook 2] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=a35972c1-e7f9-40ea-b0b0-a90b00f3c36b Model Selection Lecture Recording]<br /> <br /> ==== Day 8: June 27 ====<br /> *[https://drive.google.com/open?id=1byHN_lXS7FCiLl-qMqjd6HQlsUFVdKo2 Clustering] - Danai Koutra<br /> *[https://drive.google.com/open?id=1z-TFLyWuQ6KqHFk5YZf59ystG6WPzgP2 Machine Learning II] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1vi5ChOdY49GFL4YKWgf1uEztZpx4an5r/view?usp=sharing Python Lecture 3] - Max Smith<br /> *[https://drive.google.com/file/d/1sBh6yue4tQyQYEyJGZgYymCRLLDyCMLE/view?usp=sharing Python Notebook 3] - Max Smith<br /> <br /> ==== Day 9: June 28 ====<br /> *[https://drive.google.com/file/d/1TJnGSuebCW53CPmeMa2LQbeum8mPZu61/view?usp=sharing Casual Interference Slides] - Zhenke Wu<br /> *[https://drive.google.com/file/d/1hj_Kkg3AnmgQktYOua5PcZNE0gb2ldGg/view?usp=sharing Clustering Part 2 Slides] - Danai Koutra<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c2e8ad3-a066-4186-a5d8-a90d00f3ec3f Interference Lecture Recording] - Wu<br /> <br /> ==== Day 10: June 29 ====<br /> *[https://drive.google.com/file/d/1JcPNpmpy2pMEx4ZDGYrSw9D4OAHAZ2dR/view?usp=sharing R Loops Slides] - Flickinger<br /> *[https://drive.google.com/file/d/1MwFiZdbdsN5LunGuJengUIqW8DC9VNyt/view?usp=sharing dplyr NYC Flights]<br /> *[https://drive.google.com/file/d/16WAFuS6QZLMm3p_wxQR1QUWf8ilWjNB0/view?usp=sharing dplyr OCSLS]<br /> *[https://drive.google.com/file/d/196bEVAtY7pI72UhY_i3BawtMel0zx13C/view?usp=sharing dplyr sms]<br /> *[https://drive.google.com/file/d/1VXohDZ2kVc_zsPaaP2ikTGJXx0oXmcnQ/view?usp=sharing ggplot MPG]<br /> *[https://drive.google.com/file/d/1ALpHsZE3OLSCssBSPmxLFEj0EYMMW90_/view?usp=sharing ggplot NYC Flights]<br /> *[https://drive.google.com/file/d/1BQdcx-nO9DuwTaGbh6j344HUwKh9uJKa/view?usp=sharing R Simulations] <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fe2eaaf5-c6ed-49a2-81ed-a90e00d6637d Reading Like A Scientist] - Griffiths<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c35e5178-7bde-4f0c-b626-a90e00f3cb3f R and Loops] - Flickinger<br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523fba18-c518-4adb-8a33-a91100d68d51 Data Mining] - Najarian<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=624967a6-e082-4cb4-b762-a91100f3129c Information Visualization] - Kay<br /> <br /> ==== Day 12: July 3 ====<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d5e31bac-36a4-4fd0-9ea3-a91200d65459 Data Mining 2] - Najarian<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b25cbf29-0c99-4923-8ff7-a91200f2ea45 Bayesian Statistics] - Wen<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]<br /> * [[https://drive.google.com/file/d/15pPcBQrTBj9ze9VthpTZLmkEa3yRaz8T/view?usp=sharing Daily Schedule]] - Last update July 3, 2018</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=81 Main Page 2018-07-05T15:17:38Z <p>Davina Barron: /* Recorded Lectures */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/open?id=1XMYhAs8WnxhC4vb7u1Eup4aWh0N-1pH1 Reproducible Research - Jedidiah Carlson]<br /> *[https://drive.google.com/open?id=1vWCGrLCYETLlA3Z_91QLHPtr1b1tmnBq Data Processing] - Jed Carlson<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research] - J. Carlson<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Study design and Inference] - R. Little<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> *[https://drive.google.com/open?id=17gGeKY7lj0nE9Z5rVSS1xTgVbKzhV2HH R intro file] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1x56tLgsucEp8fZdCyGoZKx2AJiC9cheY R intro Lecture] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1Lsf3XverXb20zv8uuJiYdGh2qAc04HwZ Linear Algebra] - Klemmer<br /> *[https://drive.google.com/open?id=1AvMWjfQMaDPBe90tLElJqyIEqMQkFXFN Matrix Algebra Lecture] - Klemmer<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=564ba8aa-7e11-4acb-9acc-a90500f3b197 Big Data pt. 2] - Roderick Little, PhD<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=72425167-56ed-4016-a0a3-a905014b2154 Linear Algebra] - Klemmer<br /> <br /> ==== Day 4: June 21 ====<br /> *[https://drive.google.com/file/d/1iihBno6cnaKJD_jy1hZjW55HAZGR-7jz/view?usp=sharing Linear Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/open?id=1N4DVT3RQfnlWpdLrYs9NyK3bcaQepwqv Logistic Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/file/d/1Is4wRzwpi9qjEgdRLaaiH5pnqAJV952s/view?usp=sharing R dplyr Slides] - Matthew Flickinger<br /> *[https://drive.google.com/file/d/1U_djfdZ1l4Ladh7flByTJt0yBKj2_OBp/view?usp=sharing dplyr R code] - Flickinger<br /> *[https://drive.google.com/file/d/1JajnEQi5V366UYMhHZu9O_Btt9miz0G5/view?usp=sharing dplyr R Flights] - Flickinger<br /> *[https://drive.google.com/file/d/1ytD46IcZbBwZNAORxK_6dbqsDZ_JM7O3/view?usp=sharing dplyr OCSLS] - Flickinger<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17b825db-efc1-4062-8fd4-a90600d75981 dplyr] - Matthew Flickinger<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f86c1be8-32ba-427b-82e6-a90600f41994 Logistic Regression] - Matthew Zawistowski<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e7d5c8c2-5774-46e9-a39e-a906014c1cc4 Linear Regression] - Matthew Zawistowski<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/file/d/1zPvY7rTxaZtO4qNazEqM8UD4I3k-r0gS/view?usp=sharing State of Institute Slides] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1Zf0yIVFTESB1NokCKrAPZRqZ65BeZHiE/view?usp=sharing Big Data 3 Slides] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/11LnfEnT2po2SLJmodkaQfyrM8vUnjJPf/view?usp=sharing ggPlot 2 Slides] - Matthew Flickinger, PhD<br /> *[https://drive.google.com/file/d/1riMRVCd5_hQQRlGr4F6PkR8L2JIWG25t/view?usp=sharing Dplyr_Sms]<br /> *[https://drive.google.com/file/d/15Qy8K-r1KmpU8elEMIY4a0SUCaOdyo8G/view?usp=sharing ggplot2]<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=3af6f347-406f-4d8b-9c0b-a90700f2f700 Parameter Estimation] - Rod Little<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=45312fc9-60b5-41ca-935c-a907011267a4 Journey Lecture] - Sanchez<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> *[https://drive.google.com/file/d/1FBj8Uet0cJ02aMP6MHWvFeOuA2bkim4j/view?usp=sharing Matrix Computations] - Peisong Han<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection] - Lauren Beesley<br /> *[https://drive.google.com/open?id=145d1lrONgCGX-CO_sx0o1hj5P4CMxg7o Python Lecture 1] - Max Smith<br /> *[https://drive.google.com/file/d/1DUZRkidMf9qhH5pfomY7POcsDrkZ7n8L/view?usp=sharing Python Notebook 1] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=61694d5a-30a4-41d3-81bc-a90a00d60405 Matrix Computations] - Han<br /> <br /> ==== Day 7: June 26 ====<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection II] - Lauren Beesley<br /> *[https://drive.google.com/open?id=11LzWvnANtEtKASP0IsDYUuuQw4zhi8WD Machine Learning] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1yyRBiZrI5itTNmPdQBXR66wjC7sEwHzL/view?usp=sharing Python Lecture 2] - Max Smith<br /> *[https://drive.google.com/file/d/1Uk7woOZ-Kyq2nkfNoLxjvG1iB8dnULUb/view?usp=sharing Python Notebook 2] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=a35972c1-e7f9-40ea-b0b0-a90b00f3c36b Model Selection Lecture Recording]<br /> <br /> ==== Day 8: June 27 ====<br /> *[https://drive.google.com/open?id=1byHN_lXS7FCiLl-qMqjd6HQlsUFVdKo2 Clustering] - Danai Koutra<br /> *[https://drive.google.com/open?id=1z-TFLyWuQ6KqHFk5YZf59ystG6WPzgP2 Machine Learning II] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1vi5ChOdY49GFL4YKWgf1uEztZpx4an5r/view?usp=sharing Python Lecture 3] - Max Smith<br /> *[https://drive.google.com/file/d/1sBh6yue4tQyQYEyJGZgYymCRLLDyCMLE/view?usp=sharing Python Notebook 3] - Max Smith<br /> <br /> ==== Day 9: June 28 ====<br /> *[https://drive.google.com/file/d/1TJnGSuebCW53CPmeMa2LQbeum8mPZu61/view?usp=sharing Casual Interference Slides] - Zhenke Wu<br /> *[https://drive.google.com/file/d/1hj_Kkg3AnmgQktYOua5PcZNE0gb2ldGg/view?usp=sharing Clustering Part 2 Slides] - Danai Koutra<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c2e8ad3-a066-4186-a5d8-a90d00f3ec3f Interference Lecture Recording] - Wu<br /> <br /> ==== Day 10: June 29 ====<br /> *[https://drive.google.com/file/d/1JcPNpmpy2pMEx4ZDGYrSw9D4OAHAZ2dR/view?usp=sharing R Loops Slides] - Flickinger<br /> *[https://drive.google.com/file/d/1MwFiZdbdsN5LunGuJengUIqW8DC9VNyt/view?usp=sharing dplyr NYC Flights]<br /> *[https://drive.google.com/file/d/16WAFuS6QZLMm3p_wxQR1QUWf8ilWjNB0/view?usp=sharing dplyr OCSLS]<br /> *[https://drive.google.com/file/d/196bEVAtY7pI72UhY_i3BawtMel0zx13C/view?usp=sharing dplyr sms]<br /> *[https://drive.google.com/file/d/1VXohDZ2kVc_zsPaaP2ikTGJXx0oXmcnQ/view?usp=sharing ggplot MPG]<br /> *[https://drive.google.com/file/d/1ALpHsZE3OLSCssBSPmxLFEj0EYMMW90_/view?usp=sharing ggplot NYC Flights]<br /> *[https://drive.google.com/file/d/1BQdcx-nO9DuwTaGbh6j344HUwKh9uJKa/view?usp=sharing R Simulations] <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fe2eaaf5-c6ed-49a2-81ed-a90e00d6637d Reading Like A Scientist] - Griffiths<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c35e5178-7bde-4f0c-b626-a90e00f3cb3f R and Loops] - Flickinger<br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523fba18-c518-4adb-8a33-a91100d68d51 Data Mining] - Najarian<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=624967a6-e082-4cb4-b762-a91100f3129c Information Visualization] - Kay<br /> <br /> ==== Day 12: July 3 ====<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d5e31bac-36a4-4fd0-9ea3-a91200d65459 Data Mining 2] - Najaran<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b25cbf29-0c99-4923-8ff7-a91200f2ea45 Bayesian Statistics] - Wen<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]<br /> * [[https://drive.google.com/file/d/15pPcBQrTBj9ze9VthpTZLmkEa3yRaz8T/view?usp=sharing Daily Schedule]] - Last update July 3, 2018</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=80 Main Page 2018-07-05T15:16:50Z <p>Davina Barron: /* Recorded Lectures */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/open?id=1XMYhAs8WnxhC4vb7u1Eup4aWh0N-1pH1 Reproducible Research - Jedidiah Carlson]<br /> *[https://drive.google.com/open?id=1vWCGrLCYETLlA3Z_91QLHPtr1b1tmnBq Data Processing] - Jed Carlson<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research] - J. Carlson<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Study design and Inference] - R. Little<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> *[https://drive.google.com/open?id=17gGeKY7lj0nE9Z5rVSS1xTgVbKzhV2HH R intro file] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1x56tLgsucEp8fZdCyGoZKx2AJiC9cheY R intro Lecture] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1Lsf3XverXb20zv8uuJiYdGh2qAc04HwZ Linear Algebra] - Klemmer<br /> *[https://drive.google.com/open?id=1AvMWjfQMaDPBe90tLElJqyIEqMQkFXFN Matrix Algebra Lecture] - Klemmer<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=564ba8aa-7e11-4acb-9acc-a90500f3b197 Big Data pt. 2] - Roderick Little, PhD<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=72425167-56ed-4016-a0a3-a905014b2154 Linear Algebra] - Klemmer<br /> <br /> ==== Day 4: June 21 ====<br /> *[https://drive.google.com/file/d/1iihBno6cnaKJD_jy1hZjW55HAZGR-7jz/view?usp=sharing Linear Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/open?id=1N4DVT3RQfnlWpdLrYs9NyK3bcaQepwqv Logistic Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/file/d/1Is4wRzwpi9qjEgdRLaaiH5pnqAJV952s/view?usp=sharing R dplyr Slides] - Matthew Flickinger<br /> *[https://drive.google.com/file/d/1U_djfdZ1l4Ladh7flByTJt0yBKj2_OBp/view?usp=sharing dplyr R code] - Flickinger<br /> *[https://drive.google.com/file/d/1JajnEQi5V366UYMhHZu9O_Btt9miz0G5/view?usp=sharing dplyr R Flights] - Flickinger<br /> *[https://drive.google.com/file/d/1ytD46IcZbBwZNAORxK_6dbqsDZ_JM7O3/view?usp=sharing dplyr OCSLS] - Flickinger<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17b825db-efc1-4062-8fd4-a90600d75981 dplyr] - Matthew Flickinger<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f86c1be8-32ba-427b-82e6-a90600f41994 Logistic Regression] - Matthew Zawistowski<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e7d5c8c2-5774-46e9-a39e-a906014c1cc4 Linear Regression] - Matthew Zawistowski<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/file/d/1zPvY7rTxaZtO4qNazEqM8UD4I3k-r0gS/view?usp=sharing State of Institute Slides] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1Zf0yIVFTESB1NokCKrAPZRqZ65BeZHiE/view?usp=sharing Big Data 3 Slides] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/11LnfEnT2po2SLJmodkaQfyrM8vUnjJPf/view?usp=sharing ggPlot 2 Slides] - Matthew Flickinger, PhD<br /> *[https://drive.google.com/file/d/1riMRVCd5_hQQRlGr4F6PkR8L2JIWG25t/view?usp=sharing Dplyr_Sms]<br /> *[https://drive.google.com/file/d/15Qy8K-r1KmpU8elEMIY4a0SUCaOdyo8G/view?usp=sharing ggplot2]<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=3af6f347-406f-4d8b-9c0b-a90700f2f700 Parameter Estimation] - Rod Little<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=45312fc9-60b5-41ca-935c-a907011267a4 Journey Lecture] - Sanchez<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> *[https://drive.google.com/file/d/1FBj8Uet0cJ02aMP6MHWvFeOuA2bkim4j/view?usp=sharing Matrix Computations] - Peisong Han<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection] - Lauren Beesley<br /> *[https://drive.google.com/open?id=145d1lrONgCGX-CO_sx0o1hj5P4CMxg7o Python Lecture 1] - Max Smith<br /> *[https://drive.google.com/file/d/1DUZRkidMf9qhH5pfomY7POcsDrkZ7n8L/view?usp=sharing Python Notebook 1] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=61694d5a-30a4-41d3-81bc-a90a00d60405 Matrix Computations] - Han<br /> <br /> ==== Day 7: June 26 ====<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection II] - Lauren Beesley<br /> *[https://drive.google.com/open?id=11LzWvnANtEtKASP0IsDYUuuQw4zhi8WD Machine Learning] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1yyRBiZrI5itTNmPdQBXR66wjC7sEwHzL/view?usp=sharing Python Lecture 2] - Max Smith<br /> *[https://drive.google.com/file/d/1Uk7woOZ-Kyq2nkfNoLxjvG1iB8dnULUb/view?usp=sharing Python Notebook 2] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=a35972c1-e7f9-40ea-b0b0-a90b00f3c36b Model Selection Lecture Recording]<br /> <br /> ==== Day 8: June 27 ====<br /> *[https://drive.google.com/open?id=1byHN_lXS7FCiLl-qMqjd6HQlsUFVdKo2 Clustering] - Danai Koutra<br /> *[https://drive.google.com/open?id=1z-TFLyWuQ6KqHFk5YZf59ystG6WPzgP2 Machine Learning II] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1vi5ChOdY49GFL4YKWgf1uEztZpx4an5r/view?usp=sharing Python Lecture 3] - Max Smith<br /> *[https://drive.google.com/file/d/1sBh6yue4tQyQYEyJGZgYymCRLLDyCMLE/view?usp=sharing Python Notebook 3] - Max Smith<br /> <br /> ==== Day 9: June 28 ====<br /> *[https://drive.google.com/file/d/1TJnGSuebCW53CPmeMa2LQbeum8mPZu61/view?usp=sharing Casual Interference Slides] - Zhenke Wu<br /> *[https://drive.google.com/file/d/1hj_Kkg3AnmgQktYOua5PcZNE0gb2ldGg/view?usp=sharing Clustering Part 2 Slides] - Danai Koutra<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c2e8ad3-a066-4186-a5d8-a90d00f3ec3f Interference Lecture Recording] - Wu<br /> <br /> ==== Day 10: June 29 ====<br /> *[https://drive.google.com/file/d/1JcPNpmpy2pMEx4ZDGYrSw9D4OAHAZ2dR/view?usp=sharing R Loops Slides] - Flickinger<br /> *[https://drive.google.com/file/d/1MwFiZdbdsN5LunGuJengUIqW8DC9VNyt/view?usp=sharing dplyr NYC Flights]<br /> *[https://drive.google.com/file/d/16WAFuS6QZLMm3p_wxQR1QUWf8ilWjNB0/view?usp=sharing dplyr OCSLS]<br /> *[https://drive.google.com/file/d/196bEVAtY7pI72UhY_i3BawtMel0zx13C/view?usp=sharing dplyr sms]<br /> *[https://drive.google.com/file/d/1VXohDZ2kVc_zsPaaP2ikTGJXx0oXmcnQ/view?usp=sharing ggplot MPG]<br /> *[https://drive.google.com/file/d/1ALpHsZE3OLSCssBSPmxLFEj0EYMMW90_/view?usp=sharing ggplot NYC Flights]<br /> *[https://drive.google.com/file/d/1BQdcx-nO9DuwTaGbh6j344HUwKh9uJKa/view?usp=sharing R Simulations] <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fe2eaaf5-c6ed-49a2-81ed-a90e00d6637d Reading Like A Scientist] - Griffiths<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c35e5178-7bde-4f0c-b626-a90e00f3cb3f R and Loops] - Flickinger<br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=523fba18-c518-4adb-8a33-a91100d68d51 Data Mining] - Najaran<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=624967a6-e082-4cb4-b762-a91100f3129c Information Visualization] - Kay<br /> <br /> ==== Day 12: July 3 ====<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d5e31bac-36a4-4fd0-9ea3-a91200d65459 Data Mining 2] - Najaran<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b25cbf29-0c99-4923-8ff7-a91200f2ea45 Bayesian Statistics] - Wen<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]<br /> * [[https://drive.google.com/file/d/15pPcBQrTBj9ze9VthpTZLmkEa3yRaz8T/view?usp=sharing Daily Schedule]] - Last update July 3, 2018</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=78 Main Page 2018-07-03T13:48:26Z <p>Davina Barron: /* Additional Resources */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/open?id=1XMYhAs8WnxhC4vb7u1Eup4aWh0N-1pH1 Reproducible Research - Jedidiah Carlson]<br /> *[https://drive.google.com/open?id=1vWCGrLCYETLlA3Z_91QLHPtr1b1tmnBq Data Processing] - Jed Carlson<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research] - J. Carlson<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Study design and Inference] - R. Little<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> *[https://drive.google.com/open?id=17gGeKY7lj0nE9Z5rVSS1xTgVbKzhV2HH R intro file] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1x56tLgsucEp8fZdCyGoZKx2AJiC9cheY R intro Lecture] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1Lsf3XverXb20zv8uuJiYdGh2qAc04HwZ Linear Algebra] - Klemmer<br /> *[https://drive.google.com/open?id=1AvMWjfQMaDPBe90tLElJqyIEqMQkFXFN Matrix Algebra Lecture] - Klemmer<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=564ba8aa-7e11-4acb-9acc-a90500f3b197 Big Data pt. 2] - Roderick Little, PhD<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=72425167-56ed-4016-a0a3-a905014b2154 Linear Algebra] - Klemmer<br /> <br /> ==== Day 4: June 21 ====<br /> *[https://drive.google.com/file/d/1iihBno6cnaKJD_jy1hZjW55HAZGR-7jz/view?usp=sharing Linear Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/open?id=1N4DVT3RQfnlWpdLrYs9NyK3bcaQepwqv Logistic Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/file/d/1Is4wRzwpi9qjEgdRLaaiH5pnqAJV952s/view?usp=sharing R dplyr Slides] - Matthew Flickinger<br /> *[https://drive.google.com/file/d/1U_djfdZ1l4Ladh7flByTJt0yBKj2_OBp/view?usp=sharing dplyr R code] - Flickinger<br /> *[https://drive.google.com/file/d/1JajnEQi5V366UYMhHZu9O_Btt9miz0G5/view?usp=sharing dplyr R Flights] - Flickinger<br /> *[https://drive.google.com/file/d/1ytD46IcZbBwZNAORxK_6dbqsDZ_JM7O3/view?usp=sharing dplyr OCSLS] - Flickinger<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17b825db-efc1-4062-8fd4-a90600d75981 dplyr] - Matthew Flickinger<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f86c1be8-32ba-427b-82e6-a90600f41994 Logistic Regression] - Matthew Zawistowski<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e7d5c8c2-5774-46e9-a39e-a906014c1cc4 Linear Regression] - Matthew Zawistowski<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/file/d/1zPvY7rTxaZtO4qNazEqM8UD4I3k-r0gS/view?usp=sharing State of Institute Slides] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1Zf0yIVFTESB1NokCKrAPZRqZ65BeZHiE/view?usp=sharing Big Data 3 Slides] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/11LnfEnT2po2SLJmodkaQfyrM8vUnjJPf/view?usp=sharing ggPlot 2 Slides] - Matthew Flickinger, PhD<br /> *[https://drive.google.com/file/d/1riMRVCd5_hQQRlGr4F6PkR8L2JIWG25t/view?usp=sharing Dplyr_Sms]<br /> *[https://drive.google.com/file/d/15Qy8K-r1KmpU8elEMIY4a0SUCaOdyo8G/view?usp=sharing ggplot2]<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=3af6f347-406f-4d8b-9c0b-a90700f2f700 Parameter Estimation] - Rod Little<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=45312fc9-60b5-41ca-935c-a907011267a4 Journey Lecture] - Sanchez<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> *[https://drive.google.com/file/d/1FBj8Uet0cJ02aMP6MHWvFeOuA2bkim4j/view?usp=sharing Matrix Computations] - Peisong Han<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection] - Lauren Beesley<br /> *[https://drive.google.com/open?id=145d1lrONgCGX-CO_sx0o1hj5P4CMxg7o Python Lecture 1] - Max Smith<br /> *[https://drive.google.com/file/d/1DUZRkidMf9qhH5pfomY7POcsDrkZ7n8L/view?usp=sharing Python Notebook 1] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=61694d5a-30a4-41d3-81bc-a90a00d60405 Matrix Computations] - Han<br /> <br /> ==== Day 7: June 26 ====<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection II] - Lauren Beesley<br /> *[https://drive.google.com/open?id=11LzWvnANtEtKASP0IsDYUuuQw4zhi8WD Machine Learning] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1yyRBiZrI5itTNmPdQBXR66wjC7sEwHzL/view?usp=sharing Python Lecture 2] - Max Smith<br /> *[https://drive.google.com/file/d/1Uk7woOZ-Kyq2nkfNoLxjvG1iB8dnULUb/view?usp=sharing Python Notebook 2] - Max Smith<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=a35972c1-e7f9-40ea-b0b0-a90b00f3c36b Model Selection Lecture Recording]<br /> <br /> ==== Day 8: June 27 ====<br /> *[https://drive.google.com/open?id=1byHN_lXS7FCiLl-qMqjd6HQlsUFVdKo2 Clustering] - Danai Koutra<br /> *[https://drive.google.com/open?id=1z-TFLyWuQ6KqHFk5YZf59ystG6WPzgP2 Machine Learning II] - Jenna Wiens<br /> *[https://drive.google.com/file/d/1vi5ChOdY49GFL4YKWgf1uEztZpx4an5r/view?usp=sharing Python Lecture 3] - Max Smith<br /> *[https://drive.google.com/file/d/1sBh6yue4tQyQYEyJGZgYymCRLLDyCMLE/view?usp=sharing Python Notebook 3] - Max Smith<br /> <br /> ==== Day 9: June 28 ====<br /> *[https://drive.google.com/file/d/1TJnGSuebCW53CPmeMa2LQbeum8mPZu61/view?usp=sharing Casual Interference Slides] - Zhenke Wu<br /> *[https://drive.google.com/file/d/1hj_Kkg3AnmgQktYOua5PcZNE0gb2ldGg/view?usp=sharing Clustering Part 2 Slides] - Danai Koutra<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c2e8ad3-a066-4186-a5d8-a90d00f3ec3f Interference Lecture Recording] - Wu<br /> <br /> ==== Day 10: June 29 ====<br /> *[https://drive.google.com/file/d/1JcPNpmpy2pMEx4ZDGYrSw9D4OAHAZ2dR/view?usp=sharing R Loops Slides] - Flickinger<br /> *[https://drive.google.com/file/d/1MwFiZdbdsN5LunGuJengUIqW8DC9VNyt/view?usp=sharing dplyr NYC Flights]<br /> *[https://drive.google.com/file/d/16WAFuS6QZLMm3p_wxQR1QUWf8ilWjNB0/view?usp=sharing dplyr OCSLS]<br /> *[https://drive.google.com/file/d/196bEVAtY7pI72UhY_i3BawtMel0zx13C/view?usp=sharing dplyr sms]<br /> *[https://drive.google.com/file/d/1VXohDZ2kVc_zsPaaP2ikTGJXx0oXmcnQ/view?usp=sharing ggplot MPG]<br /> *[https://drive.google.com/file/d/1ALpHsZE3OLSCssBSPmxLFEj0EYMMW90_/view?usp=sharing ggplot NYC Flights]<br /> *[https://drive.google.com/file/d/1BQdcx-nO9DuwTaGbh6j344HUwKh9uJKa/view?usp=sharing R Simulations] <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=fe2eaaf5-c6ed-49a2-81ed-a90e00d6637d Reading Like A Scientist] - Griffiths<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=c35e5178-7bde-4f0c-b626-a90e00f3cb3f R and Loops] - Flickinger<br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]<br /> * [[https://drive.google.com/file/d/15pPcBQrTBj9ze9VthpTZLmkEa3yRaz8T/view?usp=sharing Daily Schedule]] - Last update July 3, 2018</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=72 Main Page 2018-06-25T21:17:26Z <p>Davina Barron: /* Recorded Lectures */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/open?id=1XMYhAs8WnxhC4vb7u1Eup4aWh0N-1pH1 Reproducible Research - Jedidiah Carlson]<br /> *[https://drive.google.com/open?id=1vWCGrLCYETLlA3Z_91QLHPtr1b1tmnBq Data Processing] - Jed Carlson<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research] - J. Carlson<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Study design and Inference] - R. Little<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> *[https://drive.google.com/open?id=17gGeKY7lj0nE9Z5rVSS1xTgVbKzhV2HH R intro file] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1x56tLgsucEp8fZdCyGoZKx2AJiC9cheY R intro Lecture] - Matthew Flickinger<br /> *[https://drive.google.com/open?id=1Lsf3XverXb20zv8uuJiYdGh2qAc04HwZ Linear Algebra] - Klemmer<br /> *[https://drive.google.com/open?id=1AvMWjfQMaDPBe90tLElJqyIEqMQkFXFN Matrix Algebra Lecture] - Klemmer<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=564ba8aa-7e11-4acb-9acc-a90500f3b197 Big Data pt. 2] - Roderick Little, PhD<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=72425167-56ed-4016-a0a3-a905014b2154 Linear Algebra] - Klemmer<br /> <br /> ==== Day 4: June 21 ====<br /> *[https://drive.google.com/file/d/1iihBno6cnaKJD_jy1hZjW55HAZGR-7jz/view?usp=sharing Linear Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/open?id=1N4DVT3RQfnlWpdLrYs9NyK3bcaQepwqv Logistic Regression Slides] - Matthew Zawistowski<br /> *[https://drive.google.com/file/d/1Is4wRzwpi9qjEgdRLaaiH5pnqAJV952s/view?usp=sharing R dplyr Slides] - Matthew Flickinger<br /> *[https://drive.google.com/file/d/1U_djfdZ1l4Ladh7flByTJt0yBKj2_OBp/view?usp=sharing dplyr R code] - Flickinger<br /> *[https://drive.google.com/file/d/1JajnEQi5V366UYMhHZu9O_Btt9miz0G5/view?usp=sharing dplyr R Flights] - Flickinger<br /> *[https://drive.google.com/file/d/1ytD46IcZbBwZNAORxK_6dbqsDZ_JM7O3/view?usp=sharing dplyr OCSLS] - Flickinger<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17b825db-efc1-4062-8fd4-a90600d75981 dplyr] - Matthew Flickinger<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=f86c1be8-32ba-427b-82e6-a90600f41994 Logistic Regression] - Matthew Zawistowski<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e7d5c8c2-5774-46e9-a39e-a906014c1cc4 Linear Regression] - Matthew Zawistowski<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/file/d/1zPvY7rTxaZtO4qNazEqM8UD4I3k-r0gS/view?usp=sharing State of Institute Slides] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1Zf0yIVFTESB1NokCKrAPZRqZ65BeZHiE/view?usp=sharing Big Data 3 Slides] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/11LnfEnT2po2SLJmodkaQfyrM8vUnjJPf/view?usp=sharing ggPlot 2 Slides] - Matthew Flickinger, PhD<br /> *[https://drive.google.com/file/d/1riMRVCd5_hQQRlGr4F6PkR8L2JIWG25t/view?usp=sharing Dplyr_Sms]<br /> *[https://drive.google.com/file/d/15Qy8K-r1KmpU8elEMIY4a0SUCaOdyo8G/view?usp=sharing ggplot2]<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=3af6f347-406f-4d8b-9c0b-a90700f2f700 Parameter Estimation] - Rod Little<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=45312fc9-60b5-41ca-935c-a907011267a4 Journey Lecture] - Sanchez<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> *[https://drive.google.com/file/d/1FBj8Uet0cJ02aMP6MHWvFeOuA2bkim4j/view?usp=sharing Matrix Computations] - Peisong Han<br /> *[https://drive.google.com/file/d/11cgzTqWhq4-voT1zBIMjS2XvGbMFgQR6/view?usp=sharing Model Selection] - Lauren Beesley<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=61694d5a-30a4-41d3-81bc-a90a00d60405 Matrix Computations] - Han<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=61 Main Page 2018-06-20T19:10:29Z <p>Davina Barron: /* Recorded Lectures */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research] - J. Carlson<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Study design and Inference] - R. Little<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=60 Main Page 2018-06-20T19:09:31Z <p>Davina Barron: /* Recorded Lectures */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/open?id=19qcnGMIdoYZ9mvPwsU2kAvZcqArmd6oO BDSI Lecture]<br /> *[https://drive.google.com/open?id=1gZtk4LjLDcdUSBEsNZ1qTJ2UHRDL--JO Flux Guide]<br /> *[https://drive.google.com/open?id=1XDX7hkicATX0y7cVDb9PDCsPZo1gLdPi Python Guide]<br /> *[https://drive.google.com/open?id=1kueXa-kFk6DiKVqItTEL-sFT_xmHg9Fb Python Tutorial]<br /> <br /> === Genomics Group ===<br /> <br /> ===== Lectures =====<br /> *[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]<br /> <br /> ===== Intro Exercises =====<br /> *[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]<br /> *[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/open?id=1FspYcn_B93e1BVQ6Q2QZxGygADd1khD7 Project Description]<br /> *[https://drive.google.com/open?id=1-5F8sTNcoarpDFhLhyt7ETjx6BKqsokW BDSI Imaging R Tutorial]<br /> *[https://drive.google.com/open?id=1Fikr9tXih99FRlNhktWvqi2XQfePRlmJ Imaging R Code]<br /> <br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7c7f99dc-7179-4420-a583-a903014b92c3 Klemmer Evening Lecture]<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> =====Recorded Lectures=====<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=142b0ba1-795a-4d9c-9c50-a90400d9f85a Reproducible Research - J. Carlson]<br /> *[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=17e02d6f-b195-4370-a354-a90400f37ff9 Big Data - R. Little]<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=54 Main Page 2018-06-18T16:12:19Z <p>Davina Barron: /* Day 5: June 22 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1AxwIOpI9h0iIcJvSJ0mQ7qxt1YTvGjEr/view?usp=sharing Fisher22philtransa] - On the Mathematical Foundations of Theoretical Statistics<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=53 Main Page 2018-06-18T16:09:23Z <p>Davina Barron: /* Day 3: June 20 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=52 Main Page 2018-06-18T16:09:14Z <p>Davina Barron: /* Day 5: June 22 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=51 Main Page 2018-06-18T16:08:51Z <p>Davina Barron: /* Day 5: June 22 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1K5UHDWDv_UyhuYUmt-wYtk6LiLT2mmiB/view?usp=sharing castnejm1989] - Preliminary report<br /> *[https://drive.google.com/file/d/1LvFT7OcgPQKdQoqZuH2LPN-if0Mj-BM8/view?usp=sharing Tocainideahj80] - Prophylaxis of ventricular tachyarrythmias<br /> *[https://drive.google.com/file/d/1Xdxds2fQgebLgauzI_Mfvc2tsZrDimHa/view?usp=sharing wakefieldlancet] - Ileal-lymphoid-nodular hyperplasia, non-specific colitis, and pervasive developmental disorder in children<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=50 Main Page 2018-06-18T15:56:32Z <p>Davina Barron: /* Pappers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=49 Main Page 2018-06-18T15:56:23Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Pappers ====<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=48 Main Page 2018-06-18T15:55:31Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Pappers ====<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=47 Main Page 2018-06-18T15:53:47Z <p>Davina Barron: /* Pappers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Pappers ====<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer: Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=46 Main Page 2018-06-18T15:53:37Z <p>Davina Barron: /* Pappers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Pappers ====<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer:<br /> Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=45 Main Page 2018-06-18T15:53:13Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Pappers ====<br /> *[https://drive.google.com/file/d/1u0uqMh8I8d7BomHSgKxiGwgnk3PE_aDB/view?usp=sharing cameronpaulingpnas1976] - Supplemental ascorbate in the supportive treatment of cancer:<br /> Prolongation of survival times in terminal human cancer.<br /> *[https://drive.google.com/file/d/1ICwXElGosi-at-kxP36nS7Vd0Z3XKQU3/view?usp=sharing comroe1977] - Experimental studies designed to evaluate the management of<br /> patients with incurable cancer<br /> *[https://drive.google.com/file/d/1qKKeiQkZQel20OQK-ejhcbpmV8wqwl0E/view?usp=sharing CREAGAN] - Failure of High-Dose Vitamin C therapy to benefit patients with advanced cancer<br /> *[https://drive.google.com/file/d/1IuaVOmt24Sb_OPOfedRz26FOUdakEYzQ/view?usp=sharing neyman34jrss] - On the Two Different Aspects of the Representative Method: The Method of Stratified Sampling and the Method of Purposive Selection<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=44 Main Page 2018-06-18T15:46:20Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=43 Main Page 2018-06-18T15:45:53Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> *[https://drive.google.com/file/d/1362WGLqQJ8mn5HhMmYVpRvqyLfd4XpjS/view?usp=sharing BDSI Life in Ann Arbor] - Stephen Salermo<br /> <br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=42 Main Page 2018-06-18T15:44:34Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1c5ZLytCDbUJ85wracUY5x9x8Xe1cztYW/view?usp=sharing BDSI Event Presentation] - Robert Peng<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=41 Main Page 2018-06-18T14:55:46Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1XhTTNyZR_egX4SyPc14E252FB9xTUQ6D/view?usp=sharing BDSIOrientationSupplement] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=40 Main Page 2018-06-18T14:52:05Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=39 Main Page 2018-06-18T14:51:38Z <p>Davina Barron: /* Day 0: June 17 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=38 Main Page 2018-06-18T14:51:13Z <p>Davina Barron: /* Day 0: June 17 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/open?id=1i-sktSXggJAeHcKrSSEYGArEJmzle1_Y breiman] - Statistical Modeling: The Two Cultures<br /> *[https://drive.google.com/file/d/1BYU00G8x5U4OW2Qhq6gRLQFSZ8ZYOt11/view?usp=sharing breimaninterview] - A conversation with Leo Breiman<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=37 Main Page 2018-06-18T14:24:51Z <p>Davina Barron: /* Day 0: June 17 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=36 Main Page 2018-06-18T13:26:02Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing Training for Responsible Conduct in Research] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=35 Main Page 2018-06-18T13:25:15Z <p>Davina Barron: /* Day 1: June 18 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> *[https://drive.google.com/file/d/1JCdOhE7NhhzjPi7ouqEA-ta81TbQBbWW/view?usp=sharing TRCR] - Training for Responsible Conduct in Research<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=34 Main Page 2018-06-18T13:15:42Z <p>Davina Barron: /* Papers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being a scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=33 Main Page 2018-06-18T13:15:24Z <p>Davina Barron: /* Papers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> *[https://drive.google.com/file/d/1YLUlWXPM4w8cqFROmoUj9npt2dJqb8za/view?usp=sharing ethicalguidelines] Ethical Guidelines for Statistical Practice<br /> *[https://drive.google.com/file/d/1Zue_3Lh-RGAwF6EImm-nHC_7oX8KfwlM/view?usp=sharing ODS] - On being scientist 2009<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=32 Main Page 2018-06-18T13:12:42Z <p>Davina Barron: /* Papers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> *[https://drive.google.com/open?id=1I5sMZBIzijzlvi3Xj13WTuS9AzVpa0Sf baggerlycoombes] - Deriving chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=31 Main Page 2018-06-18T13:10:14Z <p>Davina Barron: /* Papers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> *[https://drive.google.com/file/d/1LL0_i9jjjSQdIxe-NvWdk_z0MTaesbFJ/view?usp=sharing Al-Marzouki_s05] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey<br /> <br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=30 Main Page 2018-06-18T10:59:55Z <p>Davina Barron: /* Transciptomics */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transcriptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=29 Main Page 2018-06-18T10:58:21Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=28 Main Page 2018-06-18T10:57:30Z <p>Davina Barron: /* Day 5: June 22 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/file/d/1JK6uPSWW-YUl9upsGWrIkX58jW16A86d/view?usp=sharing Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Parameter Estimation] - Roderick Little, PhD<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=27 Main Page 2018-06-18T10:56:35Z <p>Davina Barron: /* Day 3: June 20 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/file/d/1JK6uPSWW-YUl9upsGWrIkX58jW16A86d/view?usp=sharing Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> *[https://drive.google.com/open?id=1OVsi449OGgrKqlnOBBsApizpg9gul-9H Observational Data] - Roderick Little, PhD<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=26 Main Page 2018-06-18T10:53:47Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/file/d/1JK6uPSWW-YUl9upsGWrIkX58jW16A86d/view?usp=sharing Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=25 Main Page 2018-06-18T10:51:57Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/file/d/1JK6uPSWW-YUl9upsGWrIkX58jW16A86d/view Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=24 Main Page 2018-06-18T10:47:17Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=1o3HfK3V1V3zoUxzKwEx9d0h_fGAIiP1D Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=23 Main Page 2018-06-18T10:45:49Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Study design and inference. ] - Roderick Little, PhD<br /> <br /> ==== Day 3: June 20 ====<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=22 Main Page 2018-06-18T10:45:16Z <p>Davina Barron: /* Day 2: June 19 */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining Group ===<br /> <br /> ====Papers ====<br /> *[https://drive.google.com/file/d/1UqhVbAUzIdepGyMQBdkjb77kHdME0TL2/view?usp=sharing Data Instructions]<br /> <br /> === Machine Learning Group ===<br /> <br /> === Genomics Group ===<br /> <br /> ===== Papers =====<br /> ====== Population Genetics ======<br /> *[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]<br /> *[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]<br /> *[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]<br /> *[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]<br /> ======Single Cell RNA ======<br /> *[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]<br /> *[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]<br /> ======Transciptomics ======<br /> *[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]<br /> *[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> ====Papers====<br /> *[https://drive.google.com/file/d/1rs5SLylP-GwjYxzyUy5W5XmUJuDRZWj4/view?usp=sharing Intro to Radiomics]<br /> *[https://drive.google.com/file/d/14I7vrN_Ag9YR2zhDf9d8kKXs94IWNLy7/view?usp=sharing Skin Imaging]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ===== Papers =====<br /> ==== Day 2: June 19 ====<br /> *[https://drive.google.com/open?id=11bv6vYqV7NugbRP6668By2F_GB0SRmiX Study design and inference. ] Rod Little<br /> <br /> ==== Day 3: June 20 ====<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron http://bigdatasummerinst.sph.umich.edu/wiki2018/index.php?title=Main_Page&diff=9 Main Page 2018-06-12T20:57:01Z <p>Davina Barron: /* Papers */</p> <hr /> <div>&lt;strong&gt;Welcome to the U-M Big Data Summer Institute 2018 Wiki!&lt;/strong&gt;<br /> <br /> Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User&#039;s Guide] for information on using the wiki software.<br /> <br /> == Reading Material ==<br /> <br /> === Data Mining ===<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-Z0s2MzZndzFKb1U/view?usp=sharing Project Outline]<br /> <br /> === Machine Learning Group ===<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-d3lraWpzSmZXa2c/view?usp=sharing Project Outline]<br /> ==== Papers ====<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-bXVkS0d4MW9EcDg/view?usp=sharing Bush et al. (2016) Unravelling the Human Genome]<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-SF9IWlVDZTlkSEE/view?usp=sharing AAndreu-Perez et al. (2015) Big Data for Health]<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-QlozUVZ4bG1NUm8/view?usp=sharing Madigan et al. (2014) A Systematic Approach to Evaluating Evidence from Observational Studies]<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-UnVzSEJGbVNYbG8/view?usp=sharing Collins et al. (2015) A New Initiative on Precision Medicine]<br /> <br /> === Genomics Group ===<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-WWxIVUJ5SDA1MUU/view?usp=sharing Project Outline]<br /> <br /> ==== Papers ====<br /> <br /> ===== &#039;&#039;Population Genetics&#039;&#039; =====<br /> * 1000GenomesProject.pdf<br /> * CavalliSforzaHGDP2005.pdf<br /> * LiHGDP2008.pdf<br /> * NovemberNature2008<br /> <br /> ===== &#039;&#039;Single Cell RNA&#039;&#039; ===== <br /> * Macosko_MouseRetinaDropSeq.pdf<br /> * Single cells make big data.pdf<br /> <br /> ===== &#039;&#039;Transcriptomics&#039;&#039; =====<br /> * GamazonPrediXcan2015.pdf<br /> * GusevTWAS2016.pdf<br /> <br /> ==== Online videos to better understand genetics and genomics ====<br /> <br /> ===== &#039;&#039;Genetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=ubq4eu_TDFc&amp;list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]<br /> * [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel&#039;s pea plants helped us understand genetics - Hortensia Jiménez Díaz]<br /> * [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]<br /> * [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC] <br /> <br /> ===== &#039;&#039;Useful 3D Animations&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]<br /> * [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]<br /> * [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]<br /> * [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]<br /> * [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]<br /> * [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]<br /> <br /> ===== &#039;&#039;Gene Regulation and Epigenetics&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]<br /> * [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]<br /> * [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]<br /> * [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]<br /> <br /> ===== &#039;&#039;Sequencing Technologies&#039;&#039; =====<br /> * [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]<br /> * [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]<br /> <br /> === Imaging Group ===<br /> *[https://drive.google.com/file/d/0B2ht_TCS6xC-QlBuM3l4b0dSdTA/view?usp=sharing Project Outline]<br /> <br /> == 2018 Presentations ==<br /> <br /> === &lt;u&gt;Week 1&lt;/u&gt; ===<br /> ==== Day 0: June 17 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRAZFnG_Ypla2ZBim39VZ__T33ck6uwBGy_eGqQR3pmpp0dDPCqFlx597N7nGC9pqvnw8Vsgg3y9T91/pub?start=false&amp;loop=false&amp;delayms=60000 Orientation Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 1: June 18 ====<br /> *[https://docs.google.com/presentation/d/e/2PACX-1vRQckVN89cMdtjnjaS7_FJ7BJFYvQIHvgUSXw2OTEhRtu56EZ2s9VSgq0I46Dmi7ryfXVmug5a2beLJ/pub?start=false&amp;loop=false&amp;delayms=60000 Welcome Slides 2018] - Bhramar Mukherjee, PhD<br /> <br /> ==== Day 2: June 19 ====<br /> <br /> ==== Day 3: June 20 ====<br /> <br /> ==== Day 4: June 21 ====<br /> <br /> ====Day 5: June 22 ====<br /> <br /> === &lt;u&gt;Week 2&lt;/u&gt; ===<br /> ==== Day 6: June 25 ====<br /> <br /> ==== Day 7: June 26 ====<br /> <br /> ==== Day 8: June 27 ====<br /> <br /> ==== Day 9: June 28 ====<br /> <br /> ==== Day 10: June 29 ====<br /> <br /> <br /> === &lt;u&gt;Week 3&lt;/u&gt; ===<br /> ==== Day 11: July 2 ====<br /> <br /> ==== Day 12: July 3 ====<br /> <br /> ==== Day 13: July 4 (NO CLASS) ====<br /> <br /> ==== Day 14: July 5 ====<br /> <br /> ==== Day 15: July 6 ====<br /> <br /> <br /> === &lt;u&gt;Week 4&lt;/u&gt; ===<br /> ==== Day 16: July 9 ====<br /> <br /> ==== Day 17: July 10 ====<br /> <br /> ==== Day 18: July 11 ====<br /> <br /> ==== Day 19: July 12 ====<br /> <br /> ==== Day 20: July 13 ====<br /> <br /> <br /> === &lt;u&gt;Week 5&lt;/u&gt; ===<br /> ==== Day 21: July 16 ====<br /> <br /> ==== Day 22: July 17 ====<br /> <br /> ==== Day 23: July 18 ====<br /> <br /> ==== Day 24: July 19 ====<br /> <br /> ==== Day 25: July 20 ====<br /> <br /> === &lt;u&gt;Week 6&lt;/u&gt; ===<br /> ==== Day 26: July 23 ====<br /> <br /> ==== Day 27: July 24 ====<br /> <br /> ==== Day 28: July 25 ====<br /> <br /> == Day 29: Symposium ==<br /> <br /> &#039;&#039;&#039;Student Poster Presentations&#039;&#039;&#039;<br /> <br /> == Additional Resources ==<br /> * [[DataCamp Resources]]</div> Davina Barron