{"id":25176068,"url":"https://github.com/quantgen/lab-spring-2016","last_synced_at":"2026-01-15T23:02:01.106Z","repository":{"id":92124973,"uuid":"49529082","full_name":"QuantGen/LAB-SPRING-2016","owner":"QuantGen","description":null,"archived":false,"fork":false,"pushed_at":"2016-04-27T14:16:16.000Z","size":48427,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-04-04T01:29:40.881Z","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":"2016-01-12T21:10:51.000Z","updated_at":"2020-01-14T17:14:14.000Z","dependencies_parsed_at":"2023-03-13T17:33:47.833Z","dependency_job_id":null,"html_url":"https://github.com/QuantGen/LAB-SPRING-2016","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/QuantGen/LAB-SPRING-2016","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2016","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2016/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2016/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2016/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/QuantGen","download_url":"https://codeload.github.com/QuantGen/LAB-SPRING-2016/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-SPRING-2016/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28473974,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-15T22:27:41.514Z","status":"ssl_error","status_checked_at":"2026-01-15T21:54:47.910Z","response_time":62,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 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":"2025-02-09T13:15:59.004Z","updated_at":"2026-01-15T23:02:01.100Z","avatar_url":"https://github.com/QuantGen.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Lab Meetings QuantGen Group Spring 2016\n\n[Group's Website](http://quantgen.github.io/)\n\n\nThis season we will be covering papers from outside the group (~8), sfotware from the group (1-2) and eventually discussion of grant proposals.\n\nPapers: chose one paper from the list below or propose one. Papers should: (a) introduce novel metholdology that is relevant to the topics of research of interest of the group, or (b) be relevant to the particular applications you are working on. \n\nSoftware: we will organize 1-2 sections to share software being developed by the group. \n\nGrant proposals: if time permit we will include on section on grant writing (format to be determined).\n\n\n## Schedule\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday, January 20, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: NA\n * **Topic(s)**: Organizational meeting\n * **Materials**: NA\n\n \n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday, January 27, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Agustin \n * **Topic(s)**: DNA Methylation   \n * **Materials**: \n    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Agustin_Paper_DNA%20Methylation.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Agustin_Slides.pptx)\n\n \n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday, February 3, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Hank\n * **Topic(s)**: Identify Cis-eQTL Target Gene associated with GBM   \n * **Materials**:\n    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Hank_Paper_GBM%20eQTL.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Hank_Slides.pptx)\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday, February 10, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Yeni\n * **Topic(s)**: The Nature of genetic Variation for Complex Traits   \n * **Materials**: \n    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Yeni_Paper_Nature%20of%20Genetic%20Variation%20for%20Complex%20Traits%20Revealed%20by%20GWAS%20and%20Regional%20Heritability%20Mapping%20Analyses.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Yeni_Slides.pdf)\n\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday, February 17, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Prof. Jiayu Zhou\n * **Topic(s)**: Multi-task Learning and its Applications   \n * **Materials**:   \n    * [Homepage](http://jiayuzhou.github.io/)\n\n\n----------------------------------------------------------------------------\n\n * **Date**:  Thursday, February 25, 2016.\n * **Time**:  1:30-3:00pm\n * **Room**:  East Conference Room\n * **Presenter(s)**: Dr. Hsu \u0026 Dr. Ho\n * **Topic(s)**: Genetic architecture and predictive modeling of quantitative traits\n * **Materials**:\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Steve%20Hsu_Slides.pdf)\n    * [Video](http://infoproc.blogspot.com/2015/05/genetic-architecture-and-predictive.html)\n    * [Reference](http://infoproc.blogspot.com/2009/09/some-favorite-posts.html)\n\n\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday,  March 2, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: \n * **Topic(s)**:     \n * **Materials**:    \n\n----------------------------------------------------------------------------\n\n\n *  Wednesday,  March 9, 2016. **(No Lab Meeting, Spring Break)**\n    \n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday,  March 16, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: TBD\n * **Topic(s)**:    \n * **Materials**: \n\n\n---------------------------------------------------------------------------- \n * **Date**:  Wednesday,  March 23, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Felix\n * **Topic(s)**: Modification of the Coiled-Coil domain from the RB gene in transgenic potato using the CRISPR/Cas9 system   \n * **Materials**:\n    * [Review](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Felix_Review_Genome%20Editing.pdf)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Felix_Slides_Genome%20editing.pdf)\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday,  March 30, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Fernando\n * **Topic(s)**:  Use of high-resolution image data for prediction of maize yield \n * **Materials**: \n    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Fernando_short%20article.docx)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Fernando_Slides_Image%20data%20to%20presidict%20maize%20yield.pptx)\n\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday, April 6, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**:  NA\n * **Topic(s)**:  NA\n * **Materials**:   NA\n\n----------------------------------------------------------------------------\n\n\n * **Date**:  Wednesday,  April 13, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Sudha\n * **Topic(s)**:  Modeling genetic heterogeneity and sex differences using random effect interactions   \n * **Materials**: \n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Sudha_Slides.pdf)\n\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday,  April 20, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Mengying\n * **Topic(s)**: Significancy vs prediction power, partition retention method    \n * **Materials**: \n    * [Article](http://www.pnas.org/content/112/45/13892.abstract)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Mengying_Slides.pdf)\n\n----------------------------------------------------------------------------\n\n * **Date**:  Wednesday,  April 27, 2016.\n * **Time**:  1:45-2:45pm\n * **Room**:  Central Conference Room\n * **Presenter(s)**: Scott\n * **Topic(s)**: RNA editing: new sources of genomic variation, software and application   \n * **Materials**: \n    * [Introduction](http://genome.cshlp.org/content/early/2013/12/17/gr.164749.113.abstract)\n    * [Software](https://github.com/funkhou9/editTools)\n    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Scott_Slides.pdf)\n\n----------------------------------------------------------------------------\n\n\n\n## Wishlist (you may either choose a paper from this list or suggest one).\n\n \n* [ Lo et al., Why significant variables aren’t automatically good predictors (PNAS, 2015) ] (http://www.pnas.org/content/112/45/13892.abstract)\n* [ Canela-Xandri et al., Accurate genetic profiling of anthropometric traits using a big data approach.](http://biorxiv.org/content/early/2015/12/01/033134.abstract)\n* [Kumar et al., Limitations of GCTA as a solution to the missing\nheritability problem (PNAS, 2015) ](http://www.pnas.org/content/113/1/E61.full.pdf)\n* [Mancuso et al. The contribution of rare variation to prostate cancer heritability (NG, 2015)](http://www.nature.com/ng/journal/v48/n1/full/ng.3446.html)\n* [Loh et al. \"Bolt-REML\" (NG, 2015)](http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html)\n* [Volfovsky et al., Testing for Nodal Dependence in Relational Data Matrices (JASA, 2015)](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.965777)\n* [Jiang et al., The E-MS Algorithm: Model Selection With Incomplete Data (JASA, 2015)](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.948545)\n* [Efron, Estimation and Accuracy after Model Selection (JASA, 2014)](http://www.tandfonline.com/doi/full/10.1080/01621459.2013.823775#abstract)\n* [Li et al. A Gene Regulatory Program in Human Breast Cancer (Genetics, 2015)](http://www.genetics.org/content/201/4/1341)\n* [Bourke et al. The Double-Reduction Landscape in Tetraploid Potato as Revealed by a High-Density Linkage Map (Genetics, 2015)](http://www.genetics.org/content/201/3/853)\n* [Deans \u0026 Maggert, What do you mean \"Epigenetic\"? (Genetics, 2015)](http://www.genetics.org/content/199/4/887)\n* [Renhua Li,A Gene Regulatory Program in Human Breast Cancer](http://www.genetics.org/content/201/4/1341)\n* [Armando Caballero, The Nature of Genetic Variation for Complex Traits Revealed by GWAS and Regional Heritability Mapping Analyses](http://www.genetics.org/content/201/4/1601)\n* [Nicholas A. Furlotte, Efficient Multiple-Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed Model](http://www.genetics.org/content/200/1/59)\n* [Deniz Akdemir, Locally Epistatic Genomic Relationship Matrices for Genomic Association and Prediction](http://www.genetics.org/content/199/3/857)\n* [Paul Brennan,Genomics of Cancer and a New Era for Cancer Prevention](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005522)\n* [Roderick C. Slieker, DNA Methylation Landscapes of Human Fetal Development](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005583)\n* [Qiong Lin, Epigenetic Aging Signatures Are Coherently Modified in Cancer ](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005334)\n* [Tian Yuan, An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging ](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004996)\n* [Xu Chen, Dominant Genetic Variation and Missing Heritability for Human Complex Traits: Insights from Twin versus Genome-wide Common SNP Models](http://www.cell.com/ajhg/abstract/S0002-9297%2815%2900406-1)\n* [Bjarni J. Vilhjálmsson, Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores](http://www.cell.com/ajhg/abstract/S0002-9297%2815%2900365-1)\n* [Big data mining yields novel insights on cancer](http://www.nature.com/ng/journal/v47/n2/full/ng.3205.html)\n* [Factors underlying variable DNA methylation in a human community cohort](http://www.pnas.org/content/109/Supplement_2/17253.full.pdf?sid=c8beed59-5f0c-471b-a773-14b0ba21ef82)\n* [Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005689)\n[Contrasting genetic architectures of schizophrenia and other complex diseases using fast variance-components analysis](http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html#supplementary-information)\n[Efficient Multiple-Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed Model](http://genetics.org/content/200/1/59)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-spring-2016","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantgen%2Flab-spring-2016","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-spring-2016/lists"}