{"id":25176061,"url":"https://github.com/quantgen/lab-spring-2020","last_synced_at":"2026-02-11T21:03:35.147Z","repository":{"id":92125013,"uuid":"233892380","full_name":"QuantGen/LAB-SPRING-2020","owner":"QuantGen","description":null,"archived":false,"fork":false,"pushed_at":"2020-04-13T17:44:32.000Z","size":1372,"stargazers_count":0,"open_issues_count":2,"forks_count":1,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-09-08T23:43:38.927Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/QuantGen.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-01-14T17:04:46.000Z","updated_at":"2020-04-13T17:44:34.000Z","dependencies_parsed_at":"2023-03-13T17:33:47.387Z","dependency_job_id":null,"html_url":"https://github.com/QuantGen/LAB-SPRING-2020","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/QuantGen/LAB-SPRING-2020","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2020","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2020/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2020/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2020/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/QuantGen","download_url":"https://codeload.github.com/QuantGen/LAB-SPRING-2020/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2020/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29345430,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-11T20:11:40.865Z","status":"ssl_error","status_checked_at":"2026-02-11T20:10:41.637Z","response_time":97,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-02-09T13:15:57.467Z","updated_at":"2026-02-11T21:03:35.131Z","avatar_url":"https://github.com/QuantGen.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Lab Meetings QuantGen Group Spring 2020\n\n## Where? IQ (775 Woodlot Dr), Room 1000\n\n## When? Fridays 12-1\n\n[Group's Website](http://quantgen.github.io/)\n\n| Date           | Presenter(s)     |  Topic(s)        |  Materials    |\n| -------------  | ---------------- | ---------------- | ------------- |\n| 1/17 | Gustavo de los Campos | Introduction |  [link](https://www.nature.com/articles/nmeth.1439#Sec2) |\n| 1/24 | SCIENCE AT THE EDGE DAY | Dr. Mulle (Human Genetics) | 11:30 in 1400 Biomedical \u0026 Physical Sciences Building |\n| 1/31 | Todd Lucas | General Introduction; Racial disparities in kidney transplants | [Paper 1](http://europepmc.org/article/MED/26952001#free-full-text), [Paper 2](https://reader.elsevier.com/reader/sd/pii/S0955470X02800040?token=F35CD9DC0DBAED12AC0AACD40C8F63DD7F7CAD97B07B65F83D12676984DF1B779CA8EB951FD5A6D072765E78332E8D47), [Paper 3](https://onlinelibrary-wiley-com.proxy2.cl.msu.edu/doi/pdfdirect/10.1111/ajt.15526) |\n| 2/7 | Miguel Perez Enciso | Microbiability and methane emissions in dairy cows | [Difford et al.](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007580) |\n| 2/14 | Laura Zingaretti | Deep learning shallow for genomic prediction? | [Zingaretti et al.](https://www.frontiersin.org/articles/10.3389/fpls.2020.00025/full) |\n| 2/28 | Marco Lopez-Cruz | Tensor Graphical LASSO (TeraLASSO) |  |\n| 3/13 |  |  |  |\n| 3/20 | Agustin Gonzalez Reymundez | Cancer detection via multi-analyte plasma biomarkers | [Cohen et al.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6080308/pdf/nihms982921.pdf) |\n| 3/27 | Harold Wu | Tests of Hardy–Weinberg Equilibrium to Structured Populations | [Paper 1](https://www.genetics.org/content/213/3/759) |\n| 4/3 |  Filipe Couto| Wavelet-Based Genetic Association Analysis of Functional Phenotypes Arising From High-Throughput Sequencing Assays |  |\n| 4/10 | Alexa Lupi |  |  |\n| 4/17 | Paulino Perez | Fast parallelized sampling of Bayesian regression models for whole-genome prediction | [Paper 1](https://link.springer.com/article/10.1186/s12711-020-00533-x) |\n| 4/24 | Fernando Aguate | Nonlinear Mixed Effects Models for Repeated Measures Data | [Paper 1](https://www.jstor.org/stable/2532087?seq=1) |\n\n\n### Ideas for articles\n\nIf you have a paper you would like to present, use that one, otherwise feel free to choose one from this list\n* [Bayesian Graphical Regression (JASA, 2019)](https://amstat.tandfonline.com/doi/full/10.1080/01621459.2017.1389739#.XjBHKRdJlUM)\n* [Cell type–specific gene expression differences in complex tissues.](https://www.nature.com/articles/nmeth.1439#Sec2) Shen-Orr et al.\n* [Wavelet-Based Genetic Association Analysis of Functional Phenotypes Arising From High-Throughput Sequencing Assays.](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5795621/) Shim et al.\n* [False discovery rates: a new deal.](https://academic.oup.com/biostatistics/article/18/2/275/2557030) Stephens\n* [The conditional permutation test for independence while controlling for confounders](https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12340) Berrett et al.\n* [Tensor graphical lasso (TeraLasso)](https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12339) Greenewald et al.\n* [A Multi-tissue Transcriptome Analysis of Human Metabolites Guides Interpretability of Associations Based on Multi-SNP Models for Gene Expression](https://www.cell.com/ajhg/fulltext/S0002-9297(20)30003-3) Ndungu et al.\n* [Learning representations of microbe–metabolite interactions](https://www.nature.com/articles/s41592-019-0616-3) Morton et al.\n* [UK Biobank Whole-Exome Sequence Binary Phenome Analysis with Robust Region-Based Rare-Variant Test](https://www.cell.com/ajhg/fulltext/S0002-9297(19)30433-1) Zhao et al.\n* [Genomic Medicine Year in Review: 2019](https://www.cell.com/ajhg/fulltext/S0002-9297(19)30427-6) Manolio et al.\n* [Making the Most of Clumping and Thresholding for Polygenic Scores](https://www.cell.com/ajhg/fulltext/S0002-9297(19)30422-7) Prive et al.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-spring-2020","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantgen%2Flab-spring-2020","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-spring-2020/lists"}