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<strong>MediaWiki has been installed.</strong>
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<strong>Welcome to the U-M Big Data Summer Institute 2019 Wiki!</strong>
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== Reading Material ==
  
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Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
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=== Machine Learning Group ===
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====Research Lecture Slides ====
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*[https://drive.google.com/file/d/1HF9cD0cnBEShUVn2Lq9vQYpRxT2ZZ8DJ/view?usp=sharing Introduction]
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*[https://drive.google.com/file/d/1LdxCkiFDmWGHcBYsHUw_W54cM6RETp8T/view?usp=sharing Explore MIMIC]
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*[https://drive.google.com/file/d/15yChJcEgzHjrn_bhYF7wqaaLh5NMCkzA/view?usp=sharing Getting x and y]
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*[https://drive.google.com/file/d/17BCOb3-t5ZJ3eE0Yy9rjlOGn0cn36PUp/view?usp=sharing Some tips]
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*[https://drive.google.com/file/d/1T8PEwWfi7PA8uMnuA9_kF6BSz69A6VKM/view?usp=sharing Sample Pipeline]
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*[https://drive.google.com/file/d/1OBckV_yjuYrl36tOF1lAKiOcWJA8-q34/view?usp=sharing Training Pipleline]
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*[https://drive.google.com/file/d/1i1nel98HYV1mSpro5SaDoMdOqMH5i5Gr/view?usp=sharing CNN]
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*[https://drive.google.com/file/d/1y14n4kl9u4LBQ9M5AnP6knFZpfwgOUAW/view?usp=sharing LSTM]
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*[https://drive.google.com/file/d/1XF-P43lIhYXU0HnS0pyGrIvPzF4HiB0B/view?usp=sharing Structuring]
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*[https://drive.google.com/file/d/12HgspYuZAVVSU49c8AEs8FPqZyoF3c1E/view?usp=sharing Dataset and DataLoader]
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*[https://drive.google.com/file/d/1vnUj-Stf5arWNyLguCPuCm1OYRwZGGr1/view?usp=sharing pytorch models]
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*[https://drive.google.com/file/d/1-r9sC3GMH_qVL3SCsPBgkDh9upS3hfEM/view?usp=sharing Model Development]
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*[https://drive.google.com/file/d/1n2md6F3XQ85WOgMV_20G_DgFqmmBgU3k/view?usp=sharing Population]
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*[https://drive.google.com/file/d/1HEAWEbwP7R1o-UZ1NcrMp2C0Ub3ivAzK/view?usp=sharing Benchmark Features]
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*[https://drive.google.com/file/d/1QpFDYzmyQBvvT9tk4Nr7EYIbh8mMmMOr/view?usp=sharing Inclusion Exclusion]
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====Readings====
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*[https://drive.google.com/file/d/1dvEdmapBY-jgdLOCZLdPwDgbybTWEni9/view?usp=sharing ARF Epidemiology]
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*[https://drive.google.com/file/d/1EzJxIVlXgkGGge20eHGC5HGtl-E7CPO_/view?usp=sharing CNN for Sentence Clarification]
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*[https://drive.google.com/file/d/1rdUGIYh7WkI4qbaJEQjaIXxaXtYYDvQN/view?usp=sharing Learning from Heterogenous Temporal Data]
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*[https://drive.google.com/file/d/12aIplGTH982iBvR7Kao6UBk2lY9Q3311/view?usp=sharing MIMC 3]
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*[https://drive.google.com/file/d/1jQVuZfnbrxzu79ujr_uKYQGvJVmkoJGy/view?usp=sharing MIMIC Benchmarks and Multitask RNN]
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*[https://drive.google.com/file/d/1uh5U_-3NIoUUM7aItA39iTGNkgwI01M7/view?usp=sharing RNNs for Multivariate Time Series]
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*[https://drive.google.com/file/d/1r1y4gez3o46mbqkaWP3umHJv6o6uvzf-/view?usp=sharing TREWScore for Septic Shock]
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*[https://drive.google.com/file/d/1EZnegIgxpmKNLorKwtkh8Veh5kIJu-lV/view?usp=sharing TREWScore Supplement]
  
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== Getting started ==
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=== Genomics Group ===
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
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===== Lectures =====
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* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
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*[https://drive.google.com/open?id=19jBLxGLRKtJD-5Id-H3d0AK0Vu_dfGko BDSI Genomics Intro]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
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*[https://drive.google.com/file/d/1nZkKKbwgRWkfEeyEGzsueJ8Dh_Zjahpv/view?usp=sharing PopGen Intro]
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* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
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===== Intro Exercises =====
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*[https://drive.google.com/open?id=1Wl1JensClieYfVNIcTWzJVxN_N7Tugte Single Cell Exercise]
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*[https://drive.google.com/open?id=18yGPNL0ZhxJR6Rya4K1IDnH1E8Yz6sjS Single Cell R Code]
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*[https://drive.google.com/file/d/1hFlCoxcw758XGfm_LrY6T9kuH6c0R6pJ/view?usp=sharing Intro Integrative]
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===== Papers =====
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====== Population Genetics ======
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*[https://drive.google.com/file/d/1UF6ADS9oc8zOh8R5zvuoRo72viYvMKoA/view?usp=sharing 1000 Genomes Project]
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*[https://drive.google.com/file/d/1ppsbWyfDzwoi_zA-9F6mt05YV3B3y173/view?usp=sharing Cavalli SforzaHGDP 2005]
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*[https://drive.google.com/file/d/1sULpGhl34Cn-TiDtctu78VnLR92oYVh6/view?usp=sharing LiHGDP 2008]
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*[https://drive.google.com/file/d/1NACFUWFfl9ojMl_R6fGOV-YvBbnJkjlb/view?usp=sharing NovembreNature 2008]
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======Single Cell RNA ======
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*[https://drive.google.com/file/d/1Tzv1s58R0GVJBS0xYi2RiSYb4al25go_/view?usp=sharing Macosko_MouseRetinaDropSeq]
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*[https://drive.google.com/file/d/1vg15r6G7jrXSgZXOxsnWKFwbBQnzr8iB/view?usp=sharing Single cell makes big data]
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======Transcriptomics ======
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*[https://drive.google.com/file/d/1SctF-SUft870PGg-43caqyN-B9sWxMh_/view?usp=sharing GamazonPrediXCan 2015]
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*[https://drive.google.com/file/d/1ioY2blWyZxDKonibl9baSXHAiUO2jNEU/view?usp=sharing GusevTWAS 2006]
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 +
==== Online videos to better understand genetics and genomics ====
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===== ''Genetics'' =====
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* [https://www.youtube.com/watch?v=ubq4eu_TDFc&list=PLF9969C74FAAD2BF9 Introduction to Genetics by 23andMe (5 videos)]
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* [https://www.youtube.com/watch?v=Mehz7tCxjSE TED-Ed : How Mendel's pea plants helped us understand genetics - Hortensia Jiménez Díaz]
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* [https://www.youtube.com/watch?v=TU44tR0hJ8A Genetic Recombination and Gene Mapping by Bozeman Science]
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* [https://www.youtube.com/user/UsefulGenetics/playlists Useful Genetics : A college-level comprehensive genetics course with 292 lectures offered by Rosie Redfield at UBC]
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===== ''Useful 3D Animations'' =====
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* [https://www.youtube.com/watch?v=gG7uCskUOrA From DNA to protein - 3D Animation]
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* [https://www.youtube.com/watch?v=SMtWvDbfHLo DNA Transcription - 3D Animation]
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* [https://www.youtube.com/watch?v=aVgwr0QpYNE DNA splicing - 3D Animation]
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* [https://www.youtube.com/watch?v=TfYf_rPWUdY mRNA Translation - 3D Animation]
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* [https://www.youtube.com/watch?v=gbSIBhFwQ4s How DNA is packaged - 3D Animation]
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* [https://www.youtube.com/watch?v=J3HVVi2k2No The Central Dogma - 3D Animation]
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===== ''Gene Regulation and Epigenetics'' =====
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* [https://www.youtube.com/watch?v=kp1bZEUgqVI Epigenetics Lecture by SciShow]
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* [https://www.youtube.com/watch?v=dES-ozV65u4 Hi-C Technique : A 3D map of the Human Genome]
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* [https://www.youtube.com/watch?v=TwXXgEz9o4w The ENCODE Project]
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* [https://www.youtube.com/watch?v=cK-OGB1_ELE RNAi by Nature Video]
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===== ''Sequencing Technologies'' =====
 +
* [https://www.youtube.com/watch?v=AhsIF-cmoQQ TED-Ed : The race to sequence the human genome - Tien Nguyen]
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* [https://www.youtube.com/watch?v=vL7ptq2Dcf0 DropSeq - Droplet-based Single Cell Sequencing by McCarroll Lab]
 +
 
 +
=== Data Mining on Large Complex Datasets ===
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*
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====Papers====
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*
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== 2019 Presentations ==
 +
 
 +
=== <u>Week 1</u> ===
 +
==== Day 1: RCRS Training, June 17 ====
 +
* [[Media:Al-Marzouki_s05.pdf|Al-Marzouki]] - The effect of scientific misconduct on the results of clinical trials: A Delphi survey
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* [[Media: Baggerlycoombes.pdf|Baggerly Coombes]] - Deriving  Chemosensitivity from cell lines: forensic bioinformatics and reproducible research in high-throughput biology
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* [[Media: Benjaminisignificance.pdf|Benjamini]] - Redefine statistical significance
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* [[Media: Ethicalguidelines.pdf|Ethical guidelines]] - Ethical Guidelines for Statistical Practice article
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* [[Media: Ethics_review.ppt|Ethics reviews]] - Ethical statistical practice review slides
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* [[Media: Moving_to_a_World_Beyond_p_0_05.pdf|Moving to a World beyond]] - Moving to a World Beyond “p < 0.05”
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* [[Media:On_being_scientist_2009.pdf|On being a scientist]] - On being a scientist article
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* [[Media:On+Being+A+Scientist.pptx|On being a scientist ppt]] - On being a scientist slides
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=====Recorded Lectures=====
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=58d266f3-210d-4d7c-8788-aa6f014a70ec Cluster computing] - Dan Barker
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=65fd73f4-195a-4198-87b7-aa6f01299c4c RCRS Training] - Mukherjee
 +
 
 +
==== Day 2: Reproducible Research, Study Design and Inference, and Linear Regression, June 18 ====
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* [[Media: Bdsi_reproducible_research_2019_06_18.pptx|Reproducible Research]] LeFaive
 +
* [[Media: Little2019-bigdata1.pdf| Study design and Inference]] Little
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* [[Media: LinearRegression-2019slides.pdf|Linear regression]] Hector
 +
=====Recorded Lectures=====
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=82eb9256-bf4c-40a4-8487-aa7000d6d63b Reproducible research] - LeFaive
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4c63a289-5f6a-4706-8627-aa7000f2900e Study designs & Inference] - Little
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=44357ae0-d327-461e-a386-aa70014ddbb0 Linear regression] - Hector
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 +
==== Day 3: Logistic Regression, Observational Data and Bias, and Probability, June 19 ====
 +
* [[Media:LogisticRegression-slides.pdf|Logistic regression]] - Hector
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* [[Media:Little2019-bigdata2.pdf|Observational data and Bias]] - Little
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* [[Media:Probability_Rmd.pdf |Probability]] - Hartman
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1d0dd55a-3464-4a16-b9b5-aa7100d6b216 Logistic regression] - Hector
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=bbdbb94d-6455-4e3d-a0a3-aa7100f2fec2 Observational Data, Bias] - Little
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=a111bacf-7bde-4376-9738-aa71014ebdf6 Probability review] - Hartman
 +
 
 +
==== Day 4: Causal inference, Parameter Estimation/Likelihood, and Linear Algebra, June 20 ====
 +
*[[Media: Causal_Inference.pdf|Causal Inference]] - Wu
 +
*[[Media: Little2019-bigdata3.pdf|Parameter estimation and Likelihood]] - Little
 +
*[[Media: Linear_algebra.pdf|Linear algebra]] - Hartman
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=b9a2f7e1-a2d2-400f-aaf3-aa7200d78be4 Causal Inference] - Wu
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=cd4dba3d-a4dc-4972-bbe8-aa7200f30723 Parameter Estimation / Likelihood] - Little
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0a05bea8-c048-4d52-b193-aa72014f8220 Linear Algebra] - Hartman
 +
 
 +
==== Day 5: Data Wrangling in R with dplyr, Parts I and II, June 21 ====
 +
*[[Media: Bdsi_2019_dplyr.pdf|Dplyr slides]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_dplyr_nycflights.pdf |Dplyr flight practice]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_dplyr_nycflights_answers.pdf |Dplyr flight practice answers]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_dplyr_ocsls.pdf |Dplyr and OCLS practice]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_dplyr_ocsls_answers.pdf |Dplyr and OCLS practice answers]] - Flickinger
 +
*[[Media: Bdsi_dplyr.pdf |Dplyr code]] - Flickinger
 +
*[[Media: Boehnke_Journey_BDSI2019.pptx|Journey lectures]] - Boehnke
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d3e590db-bfe9-4ab5-91b1-aa7300f2ee1f R Workshop dplyr Part II] - Flickinger
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=399865c6-35b3-4eb1-8f36-aa73010fd4ba Journey Lecture] - Boehnke
 +
* No Recording Available (Data Wrangling in R with dplyr - Flickinger)
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 +
=== <u>Week 2</u> ===
 +
====Day 6: Visualization Data in R with ggplot2 - Part I & II and Generalized Linear Models, June 24 ====
 +
*[[Media: Bdsi_2019_ggplot2.pdf|Ggplot2 slides]] - Flickinger
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*[[Media: Bdsi_2019_r_practice_ggplot2_mpg.pdf|Ggplot2 mpg exercise]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_ggplot2_mpg_answers.pdf|Ggplot2 mpg excercise answers]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_ggplot2_nycflights.pdf|Ggplot2 flights exercise]] - Flickinger
 +
*[[Media: Bdsi_2019_r_practice_ggplot2_nycflights_answers.pdf|Ggplot2 flights answers exercise]] - Flickinger
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=4e2adcbb-ae95-454b-a23f-aa7600d69323 Visualizing Data in R Part I] - Flickinger
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d3e2760c-619b-47b7-8eb3-aa7600efc305 Visualizing Data in R - Part II] - Flickinger
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=39a14a1a-4958-49bb-bee2-aa76014dc1da Generalized Linear Models] - Hartman
 +
 
 +
==== Day 7: Machine Learning I & Model Selection, June 25 ====
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*[[Media: BEESLEY BDSI Presentation.pdf|Model selection I & II slides]] - Beesley
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*[[Media: Wiens_ML_Lecture1.pdf|Machine Learning I slides]] - Wiens
 +
=====Recorded Lectures=====
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*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=37a6279a-2657-49bb-b5f8-aa7700f31d9d Model Selection 1] - Beesley
 +
*No recording available (Machine Learning I - Wiens)
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==== Day 8: Machine Learning II & Unsupervised Learning/Clustering I, June 26 ====
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*[[Media: Wiens_ML_Lecture2.pdf|Machine Learning II slides]] - Wiens
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=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=699e8e7c-a33a-4efb-9f90-aa78014dfeda Correlated data models] - Hartman
 +
*No recording available (Machine Learning II - Wiens)
 +
*No recording available (Unsupervised Learning, Clustering I - Koutra)
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==== Day 9: Unsupervised Learning/Clustering II and Model Selection II, June 27 ====
 +
*[[Media:beesley ms2.pdf|Model Selection II slides]] - Beesley
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=1f07dda4-81d9-41b0-bd43-aa7900f30d9e Model Selection Part II] - Beesley
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=84588ff1-9cf8-4f44-b1f4-aa79014de845 Assessment of predictive models] - Boonstra
 +
* No recording available (Unsupervised Learning, Clustering II - Koutra)
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 +
==== Day 10: Python Workshop I and II, June 28 ====
 +
*[[Media:BDSI Python Tutorial.pdf|Python Workshop I and II]] - Kamran
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=d0134ee0-6ba2-4f4c-be10-aa7a00d74e9c Python Workshop] - Kamran
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=e194044c-b797-4a55-b7b1-aa7a00f30604 Python workshop Part II] - Kamran
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8aa9d6ab-7c78-4eb7-8a46-aa7a0113714d Journey Lecture] - Banerjee
 +
 
 +
=== <u>Week 3</u> ===
 +
==== Day 11: Data Mining I and Visualization I, July 1 ====
 +
*[[Media:bdsi2019-vis-for-data-science-1.pdf|Visualization I slides]] - Kay
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=56ea7d1a-d2df-4d2c-a570-aa7d00d6b518 Data Mining Part I] - Gryak
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=da78299d-aecf-4823-bc5f-aa7d00f39f4b Visualization I] - Kay
 +
 
 +
==== Day 12: Data Mining II and Precision Health, July 2 ====
 +
*[[Media:ClinicalCareMachineLearningBDSI.pptx|Precision Health slides]] - Kheterpal
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=393e57a1-b764-49c0-9a77-aa7e00f21944 Precision Health] - Kheterpal
 +
* No recording available (Data Mining II - Gryak)
 +
 
 +
==== Day 13: Visualization II and Intro to Bayes I, July 3====
 +
*[[Media:bdsi2019-vis-for-data-science-2.pdf|Visualization II slides]] - Kay
 +
*[[Media:Bayes1.pdf|Intro to Bayes I slides]] - Wen
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=91c1bb99-5542-4086-8389-aa7f00f2dab8 Introduction to Bayes] - Wen
 +
* No recording available (Visualization II - Kay)
 +
 
 +
==== Day 14: July 4 - NO CLASS ====
 +
 
 +
==== Day 15: Intro to Bayes II, July 5 ====
 +
*[[Media:Bayes2.pdf|Intro to Bayes II slides]] - Wen
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=279b3f8e-deed-4086-bfab-aa81010fb121 Journey lecture] - Panigrahi
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=ded3c71e-7fd3-4b76-a3a5-aa8100d649e9 Introduction to Bayes II] - Wen
 +
* No recording available (Journey Lectures: Taylor)
 +
* No recording available (State of the Institute: Mukherjee)
 +
 
 +
=== <u>Week 4</u> ===
 +
==== Day 16: From Genomics to Prevention of Cardiovascular Diseases and R Markdown, July 8 ====
 +
*[[Media:BigDataSummerInstitute_Surakka-1.pptx|From Genomics to Prevention of Cardiovascular Diseases slides]] - Surakka
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2f15f9f3-55e5-4450-b562-aa8400d70030 Genomics to Prevention of Cardiovascular Disease] - Surakka
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=285e928a-cf75-49ce-8440-aa8400f3056d R Markdown] - Boonstra
 +
 
 +
==== Day 17: Bayes Computation I and II, July 9 ====
 +
*[[Media:BDSI_Lecture_Slides.pdf|Bayes Computation I and II slides]] - Chen
 +
=====Recorded Lectures=====
 +
*No recordings available (Computation I & II - Chen)
 +
 
 +
==== Day 18: Reading Like a Scientific Writer and Social Network, July 10 ====
 +
*[[Media:Griffiths-BDSI-Reading like a Scientific Writer-2019.pptx|Reading Like a Scientific Writer slides]] - Griffiths
 +
=====Recorded Lectures=====
 +
* No recording available (Reading like a scientific writer - Griffiths)
 +
* No recording available (Social Network - Adar)
 +
* No recording available (Journey Lecture-Bowman)
 +
 
 +
==== Day 19: Stroke Disparities and Human-Centered Computing: Using Speech to Understand Behavior, July 11 ====
 +
*[[Media:Stroke health Disparities Program final 2019-1.pptx|Stroke Disparities slides]] - Lisabeth
 +
*[[Media:EMP_BDSI.pdf|Human-Centered Computing slides]] - Provost
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=96a45868-6793-4579-be17-aa8700d6d01f Stroke disparities] - Lisabeth
 +
* No recording available (Human-Centered Computing: Using Speech to Understand Behavior - Provost)
 +
 
 +
==== Day 20: Spatial Epidemiology, July 12 ====
 +
*[[Media:zelner_bdsi.pdf|Spatial Epidemiology slides]] - Zelner
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=0f0408ed-8286-4412-8cfc-aa88010ed154 Journey Lecture] - Spino
 +
* No recording available (Spatial Epidemiology - Zelner)
 +
* No recording available (State of the Institute - Mukherjee)
 +
 
 +
=== <u>Week 5</u> ===
 +
==== Day 21: Natural Language Processing I and II, July 15 ====
 +
*
 +
=====Recorded Lectures=====
 +
*No recording available (Natural Language Processing I & II - Singh)
 +
 
 +
==== Day 22: Optimization I and II, July 16 ====
 +
*[[Media:bdsi_optimization_2019.pdf|Optimization slides]] - Kang
 +
=====Recorded Lectures=====
 +
* No recording available (Optimization I & II - Kang)
 +
 
 +
==== Day 23: Writing from Point A to Point B and Bayesian Data Integration and Precision Medicine, July 17 ====
 +
*[[Media:Writing Clearly--Point A to Point B-2019.pptx|Writing from Point A to Point B slides]] - Griffiths
 +
*[[Media:science-of-writing.pdf|Science of Writing paper]] - Griffiths
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=06dc5e25-839e-4ce9-98ab-aa8d00f14531 Data Integration & Precision Medicine] - Baladandayuthapani
 +
* No recording available (Writing from Point A to Point D: Simple Strategies for Conveying Complex Ideas - Griffiths)
 +
 
 +
==== Day 24: Radiation Oncology and Imaging Analysis and Optimization in Health, July 18 ====
 +
*[[Media:bdsi_talk_radiomics1_2019.pptx|Radiation Oncology slides]] - Rao
 +
*[[Media:Denton_SPH_2019.pdf|Optimization in Health slides]] - Denton
 +
*[[Media:Barnett - 2017.pdf|Two Stage Biomarker Protocols paper]]
 +
*[[Media:Barnett_et_al-2017-Cancer.pdf|Optimizing Active Surveillance Strategies paper]]
 +
*[[Media:Zhang-2012b.pdf|Optimization of Prostate Biopsy Referral Decisions paper]]
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=8f823802-79bb-4893-856f-aa8e00f07b36 Cancer Surveillance] - Denton
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=6fe1b436-61cd-4679-93f1-aa8e00d33e09 Radiation oncology & precision medicine] - Rao
 +
 
 +
==== Day 25: Confessions of a Clinical Researcher, July 19 ====
 +
*
 +
=====Recorded Lectures=====
 +
* No recording available ( Better, Not Just Bigger Data Analytics: Confessions of a Clinical Researcher - Nallamothu)
 +
* No recording available (Journey Lecture - Orozco del Pino)
 +
* No recording available (Journey Lecture - Beesley)
 +
* No recording available (State of the Institute - Zoellner)
 +
 
 +
=== <u>Week 6</u> ===
 +
 
 +
==== Day 26: Preparing for Graduate School and CVs and Resumes, July 22 ====
 +
*[[Media:BDSI- 2019- Prepping for Grad School.pptx|Preparing for Graduate School slides]] - Kidwell
 +
*[[Media:Resumes& CVs_Peer Review_2019_BDSI-1.pptx|CVs and Resumes slides]] - Forbes
 +
*[[Media:RESUME RUBRIC_1 page for students_final-1.pdf|Resume Rubric slides]]
 +
*[[Media:Curriculum Vita Checklist Guide_Summer 2019-1.pdf|CV Guide handout]]
 +
*[[Media:Action verb list.pdf|Action Verb handout]]
 +
*[[Media:Resume Samples Updated Sept. 2018.pdf|Resume Samples handout]]
 +
*[[Media:WORD TRICKS AND TIPS.pdf|Word Tricks handout]]
 +
=====Recorded Lectures=====
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=7a959293-7303-4636-a1ad-aa9500e2a612 CVs & Resumes] - Forbes
 +
*[https://sph.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=3fecb1a7-af27-4b87-8e6e-aa9500e2afcf Preparing for Grad School] - Kidwell
 +
 
 +
==== Day 27: Pick Me!, July 23 ====
 +
*
 +
=====Recorded Lectures=====
 +
* No recording available (TBD - Grifftihs)
 +
 
 +
== Day 29: Symposium ==
 +
'''2019 Professor Lectures Presentations'''
 +
*
 +
'''2019 Student Poster Presentations'''
 +
*[https://umich.app.box.com/s/xwc8ecl2l3gahlpdhobkm0zbx4dvu3qa/file/496616682213 Data Mining Presentation]
 +
*[https://umich.app.box.com/s/xwc8ecl2l3gahlpdhobkm0zbx4dvu3qa/file/496590467731 Machine Learning Presentation]
 +
*[https://umich.app.box.com/s/xwc8ecl2l3gahlpdhobkm0zbx4dvu3qa/file/496560211380 Genomics Presentation]
 +
'''2018 Student Poster Presentations'''
 +
*[https://drive.google.com/file/d/1TGNqkCAV9eBJ_-zHbiU-yo3N4Aowm_HB/view?usp=sharing Imaging Group Presentation]
 +
*[https://drive.google.com/file/d/1S01_WV6wfJ6BE2Op-01byw0WFUZadPjR/view?usp=sharing Machine Learning Group Presentation]
 +
*[https://drive.google.com/file/d/1LlZgR4TAlyYaS88bQ6qgZncWFuS0lFuC/view?usp=sharing Genetics Group Presentation]
 +
*[https://drive.google.com/file/d/1HqWZFGjHgIYOoqqlpQxc0qn9y7PTa4hD/view?usp=sharing Data Mining Presentation]
 +
'''2017 Student Poster Presentations'''
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-WFNPZzd5TndqZ0U/view?usp=sharing Data Mining/ Machine Learning]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-S2xrUFM0ZEI3dGM/view?usp=sharing Electronic Health Records (EHR)]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NEZ1YnQyVW0tREE/view?usp=sharing Genomics]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-cDVJNUtIcjRjcFE/view?usp=sharing Imaging]
 +
=====2017 Symposium Reference Files=====
 +
*[https://drive.google.com/file/d/1zwuVp6_sIRIlKx79-i0uZRp6Gtooi6g8/view?usp=sharing 2017 Symposium Program]
 +
*[https://drive.google.com/file/d/18FfpzqxwPSunJfHM3pHDxYYggAPlKgWX/view?usp=sharing 2017 Symposium Flyer]
 +
======2017 Symposium Projects======
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-Zm5RWHByeWdUd2M/view?usp=sharing A Time-to-Event Analysis of Heart Failure via Electronic Health Records]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-UEIwRVNZaVJXRFk/view?usp=sharing Melanoma Detection by Classifying Skin Lesion Images]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VEk4RExSSkV3NGM/view?usp=sharing Classifying Skin Lesions Images Using Adaptive Boosting]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-RDR1UmtsV3hFUVk/view?usp=sharing Machine Learning Classification of Skin Lesion Images]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-YWs0alJGdTA3UE0/view?usp=sharing Genomics: Genome Storage and Assembly]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-SU1KWFdPcWZzMEk/view?usp=sharing Predicting the Transcriptome from the Genome]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VGhDZlZZeHAyRDQ/view?usp=sharing Classification of Cell Types from Peripheral Mononuclear Blood Cells]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-bzRTUTlQek9JRGM/view?usp=sharing EHR-Based Study of Long-Term Infectious Diseases]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VjRsZkJfalVNbVk/view?usp=sharing Visualizing Lab and Phenotype Associations Using PheWAS and Electronic Health Records]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-NXJoemNibTFxZXc/view?usp=sharing Data Mining: Microenvironment Microarray Spot Based Approach for Cell Prediction]
 +
*[https://drive.google.com/file/d/0B2ht_TCS6xC-VDdJQmtOZHR6RE0/view?usp=sharing Estimating Cell Growth with Machine Learning and Data Mining]
 +
 
 +
== Additional Resources ==
 +
* [[Media:BDSI_2019_Master_Schedule.docx|Daily Schedule]] - Last update June 4, 2019
 +
* [[Media:BDSI_2019_Social_Events.pdf|Social events Schedule]] - Last update June 6, 2019

Latest revision as of 11:13, 6 June 2021

Welcome to the U-M Big Data Summer Institute 2019 Wiki!

Contents

Reading Material

Machine Learning Group

Research Lecture Slides

Readings

Genomics Group

Lectures
Intro Exercises
Papers
Population Genetics
Single Cell RNA
Transcriptomics

Online videos to better understand genetics and genomics

Genetics
Useful 3D Animations
Gene Regulation and Epigenetics
Sequencing Technologies

Data Mining on Large Complex Datasets

Papers

2019 Presentations

Week 1

Day 1: RCRS Training, June 17

Recorded Lectures

Day 2: Reproducible Research, Study Design and Inference, and Linear Regression, June 18

Recorded Lectures

Day 3: Logistic Regression, Observational Data and Bias, and Probability, June 19

Recorded Lectures

Day 4: Causal inference, Parameter Estimation/Likelihood, and Linear Algebra, June 20

Recorded Lectures

Day 5: Data Wrangling in R with dplyr, Parts I and II, June 21

Recorded Lectures

Week 2

Day 6: Visualization Data in R with ggplot2 - Part I & II and Generalized Linear Models, June 24

Recorded Lectures

Day 7: Machine Learning I & Model Selection, June 25

Recorded Lectures

Day 8: Machine Learning II & Unsupervised Learning/Clustering I, June 26

Recorded Lectures
  • Correlated data models - Hartman
  • No recording available (Machine Learning II - Wiens)
  • No recording available (Unsupervised Learning, Clustering I - Koutra)

Day 9: Unsupervised Learning/Clustering II and Model Selection II, June 27

Recorded Lectures

Day 10: Python Workshop I and II, June 28

Recorded Lectures

Week 3

Day 11: Data Mining I and Visualization I, July 1

Recorded Lectures

Day 12: Data Mining II and Precision Health, July 2

Recorded Lectures

Day 13: Visualization II and Intro to Bayes I, July 3

Recorded Lectures

Day 14: July 4 - NO CLASS

Day 15: Intro to Bayes II, July 5

Recorded Lectures

Week 4

Day 16: From Genomics to Prevention of Cardiovascular Diseases and R Markdown, July 8

Recorded Lectures

Day 17: Bayes Computation I and II, July 9

Recorded Lectures
  • No recordings available (Computation I & II - Chen)

Day 18: Reading Like a Scientific Writer and Social Network, July 10

Recorded Lectures
  • No recording available (Reading like a scientific writer - Griffiths)
  • No recording available (Social Network - Adar)
  • No recording available (Journey Lecture-Bowman)

Day 19: Stroke Disparities and Human-Centered Computing: Using Speech to Understand Behavior, July 11

Recorded Lectures
  • Stroke disparities - Lisabeth
  • No recording available (Human-Centered Computing: Using Speech to Understand Behavior - Provost)

Day 20: Spatial Epidemiology, July 12

Recorded Lectures
  • Journey Lecture - Spino
  • No recording available (Spatial Epidemiology - Zelner)
  • No recording available (State of the Institute - Mukherjee)

Week 5

Day 21: Natural Language Processing I and II, July 15

Recorded Lectures
  • No recording available (Natural Language Processing I & II - Singh)

Day 22: Optimization I and II, July 16

Recorded Lectures
  • No recording available (Optimization I & II - Kang)

Day 23: Writing from Point A to Point B and Bayesian Data Integration and Precision Medicine, July 17

Recorded Lectures

Day 24: Radiation Oncology and Imaging Analysis and Optimization in Health, July 18

Recorded Lectures

Day 25: Confessions of a Clinical Researcher, July 19

Recorded Lectures
  • No recording available ( Better, Not Just Bigger Data Analytics: Confessions of a Clinical Researcher - Nallamothu)
  • No recording available (Journey Lecture - Orozco del Pino)
  • No recording available (Journey Lecture - Beesley)
  • No recording available (State of the Institute - Zoellner)

Week 6

Day 26: Preparing for Graduate School and CVs and Resumes, July 22

Recorded Lectures

Day 27: Pick Me!, July 23

Recorded Lectures
  • No recording available (TBD - Grifftihs)

Day 29: Symposium

2019 Professor Lectures Presentations

2019 Student Poster Presentations

2018 Student Poster Presentations

2017 Student Poster Presentations

2017 Symposium Reference Files
2017 Symposium Projects

Additional Resources

Retrieved from "http://bigdatasummerinst.sph.umich.edu/wiki2019/index.php?title=Main_Page&oldid=226"