{"id":25176076,"url":"https://github.com/quantgen/lab-fall-2016","last_synced_at":"2026-01-18T16:32:18.555Z","repository":{"id":92124951,"uuid":"66956868","full_name":"QuantGen/LAB-FALL-2016","owner":"QuantGen","description":null,"archived":false,"fork":false,"pushed_at":"2016-12-03T05:10:46.000Z","size":27,"stargazers_count":0,"open_issues_count":0,"forks_count":2,"subscribers_count":20,"default_branch":"master","last_synced_at":"2025-04-04T01:29:43.731Z","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":"2016-08-30T16:08:47.000Z","updated_at":"2020-01-14T17:14:00.000Z","dependencies_parsed_at":"2023-03-13T17:33:48.304Z","dependency_job_id":null,"html_url":"https://github.com/QuantGen/LAB-FALL-2016","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/QuantGen/LAB-FALL-2016","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2016","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2016/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2016/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2016/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/QuantGen","download_url":"https://codeload.github.com/QuantGen/LAB-FALL-2016/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/QuantGen%2FLAB-FALL-2016/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28541572,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T14:59:57.589Z","status":"ssl_error","status_checked_at":"2026-01-18T14:59:46.540Z","response_time":98,"last_error":"SSL_read: 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":"2025-02-09T13:16:00.696Z","updated_at":"2026-01-18T16:32:18.550Z","avatar_url":"https://github.com/QuantGen.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# Lab Meetings QuantGen Group Fall 2016\n\n[Group's Website](http://quantgen.github.io/)\n\nThis semester we will be covering  papers from outside the group, a few presentations on ongoing research from our group and have a vew invited presenters.\n\n**Advisors**: Each of the students presenting must pick an advisor, possible advisors are: Sudha, Hwasoon, Ana and Gustavo.\n\n**Papers**: Choose one paper from the list below or propose one. Papers should: (a) introduce novel methodology that is relevant to the research interests of the group, or (b) be relevant to the particular applications you are working on. \n\n\n## Schedule\n\n * **Date**: Friday, Sep 9, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Organizational Meeting\n * **Topic(s)**: Discuss plan for the Fall, including lab meeting and papers in progress.\n * **Materials**:\n\n---\n\n * **Date**: Friday, Sep 16, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Marigel Perez-Cabal\n * **Topic(s)**: Use of spectra data for prediction of reproductive outcomes.\n * **Materials**: [Bastin et al., 2016](http://ac.els-cdn.com/S0022030215009492/1-s2.0-S0022030215009492-main.pdf?_tid=f3bc7c68-75df-11e6-8e48-00000aab0f6b\u0026acdnat=1473351720_88db4273f2180f161c1a358d9edac92c). Just focus on the Introduction, the Postpartum changes in milk composition (fat, protein, and fatty acids) and have an overview on the genetic association between MIR spectra and fertility. [Searching for signals from metabolites for reproductive outcomes](https://www.dropbox.com/s/mx3ytysh92vets0/Searching%20for%20signals%20from%20metabolites%20for%20reproductive%20outcomes.pdf?dl=0).\n * **Note**: Chris Schön will give her seminar *Genomic Prediction with Model Training Across Multiple Breeding Cycles Significantly Improves Prediction Accuracy* on Friday Sept 16, 9:00-10:00am in Room 168 Plant Biology Building. [Flyer](https://www.dropbox.com/s/v71qe6zv2ieupt2/ChrisSch%C3%B6nSeminar.pdf?dl=0). All of us are encouraged to attend her seminar.\n \n---\n\n * **Date**: Friday, Sep 23, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Yeni Bernal\n * **Topic(s)**: Understanding genetic structure of human populations\n * **Materials**: [Novembre et al 2014. Genes mirror within Europe](http://www.nature.com/nature/journal/v456/n7218/abs/nature07331.html)\n\n---\n\n * **Date**: Friday, Sep 30, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Agustin Gonzalez Reymundez\n * **Topic(s)**: Introduction to Epigenetics\n * **Materials**: [Introduction to epigenetics, Ballestar] (http://download.springer.com/static/pdf/261/chp%253A10.1007%252F978-1-4419-8216-2_1.pdf?originUrl=http%3A%2F%2Flink.springer.com%2Fchapter%2F10.1007%2F978-1-4419-8216-2_1\u0026token2=exp=1474476448~acl=%2Fstatic%2Fpdf%2F261%2Fchp%25253A10.1007%25252F978-1-4419-8216-2_1.pdf%3ForiginUrl%3Dhttp%253A%252F%252Flink.springer.com%252Fchapter%252F10.1007%252F978-1-4419-8216-2_1*~hmac=2b80d2e25c5c3f5458c230cecd33f94f80e78544d66a8ae4d93aa2d035dbb62c)\n\n---\n\n * **Date**: Friday, Oct 7, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Canceled due to two seminars in the morning\n * **Topic(s)**: \n * **Materials**: \n\n---\n\n * **Date**: Friday, Oct 14, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Raka Mandal\n * **Topic(s)**: The E-MS Algorithm: Model Selection With Incomplete Data \n * **Materials**: [Jiang et al., JASA, 2015](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.948545)\n\n\n---\n\n * **Date**: Friday, Oct 21, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Topic(s)**: Informal discussion about the HPCC and citation management software (Mendeley \u0026 Zotero)\n\n---\n\n * **Date**: Friday, Oct 28, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Marco Lopez-Cruz\n * **Topic(s)**: Incorporating LD information in Genomic Prediction with Sequence Data\n * **Materials**: Paper: [Carlsen et al., Genetics, 2016](http://www.genetics.org/content/202/2/411)\n\n---\n\n * **Date**: Friday, Nov 4, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Deniz Akdemir \n * **Title**: A subjective tour of topics in statistical genetics\n * **Abstract**: In this presentation, I will be sharing my perspective on a number of problems in statistical genetics and more specifically on genome-wide prediction, association and genomic selection. I will introduce these approaches and talk about some factors affecting their success. I will stress the importance of designing populations for genetic experiments; explain the idea of local epistasis and how it is relevant to association and prediction; and describe an approach to combine genetic data from multiple experiments. Instead of going into the mathematical details I will focus on the ideas, and refer to some statistical software packages I have developed.\n\n---\n\n * **Date**: Friday, Nov 11, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Sudha\n * **Topic(s)**: Defense Practice\n * **Materials**:\n\n---\n\n * **Date**: Friday, Nov 18, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Canceled\n * **Topic(s)**:\n * **Materials**:\n\n---\n\n * **Date**: Friday, Dec 2, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Hwasoon Kim\n * **Topic(s)**: Contribution of genetic and common shared environoment to common disease using the UK-Biobank\n * **Materials**: [Muñoz et al., Nat. Gen., 2016] (http://www.nature.com/ng/journal/v48/n9/full/ng.3618.html)\n\n---\n\n * **Date**: Friday, Dec 9, 2016\n * **Time**: 1:00-2:00pm\n * **Room**: 909 Fee Rd, 6th floor, Central Conference Room\n * **Presenter(s)**: Scott Funkhouser\n * **Topic(s)**: Genetic Architectures of Quantitative Variation in RNA Editing Pathways\n * **Materials**: [Tongjun et al.](http://www.genetics.org/content/202/2/787)\n\n\n## Suggested Papers (feel free to add more!)\n\n### Perspectives/Reviews\n\n * Protein Variation in Natural Populations and Quantitative Genetic Variation ([Hubby et al., Genetics, 2016](http://www.genetics.org/content/203/4/1497))\n * The History of the Y-Chromosome in man ([Hughes \u0026 Page, Nat. Gen., 2016](http://www.nature.com/ng/journal/v48/n6/pdf/ng.3580.pdf))\n * What do you mean \"Epigenetic\"? ([Deans \u0026 Maggert, Genetics, 2015](http://www.genetics.org/content/199/4/887))\n\n### Methods\n\n * Exact Post-Selection Inference for Sequential Regression Procedures ([Tibshirani et al., JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1108848))\n * Fast, Exact Bootstrap Principal Component Analysis for p \u003e 1 Million ([Fisher et al., JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1062383))\n * Sparse Regression Incorporating Graphical Structure Among Predictors ([Yu  \u0026 Liu, JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1034319))\n * Incorporating LD information in Genomic Prediction with Sequence Data([Carlsen et al., Genetics, 2016](http://www.genetics.org/content/202/2/411))\n * Tensor decomposition for multiple-tissue gene expression experiments [Hore et al., Nat. Gen., 2016](http://www.nature.com/ng/journal/v48/n9/full/ng.3624.html))\n * Structured Matrix Completion with Applications to Genomic Data Integration ([Cai et al., JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1021005))\n\n### Research and Case Study Articles\n\n  * Genetic Variation of Gene Editing ([Tongjun et al., Genetics, 2016](http://www.genetics.org/content/202/2/787))\n  * Cis- and Trans-Gene Inactivation Caused by Heterochromatin in Drosophila ([Yuriy et al., Genetics, 2016](http://www.genetics.org/content/202/1/93))\n  * Contribution of genetic and common shared environoment to common disease using the UK-Biobank ([Muñoz et al., Nat. Gen., 2016](http://www.nature.com/ng/journal/v48/n9/full/ng.3618.html))\n  * Integration of eQTL and GWAS results for prediction of complex trait gene targets ([Zhu et al., Nat Genet., 2016](http://www.nature.com/ng/journal/v48/n5/pdf/ng.3538.pdf))\n  * The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis ([Gibson et al., Nat Gen., 2016](http://www.nature.com/ng/journal/v48/n8/full/ng.3602.html))\n  * Clonal evolution of glioblastoma under therapy ([Wang et al., Nat Gen., 2016](Clonal evolution of glioblastoma under therapy))\n  * Variants with large effects on blood lipids and the role of  cholesterol and triglycerides in coronary disease ([Helgadottir et al., Nat. Gen., 2016](http://www.nature.com/ng/journal/v48/n6/pdf/ng.3561.pdf))\n  * Genetic profiling of anthropometric traits using big data ([Canela-Xandri et al.](http://biorxiv.org/content/early/2015/12/01/033134.abstract))\n  * Limitations of GCTA as a solution to the missing heritability problem ([Kumar et al, PNAS, 2015 ](http://www.pnas.org/content/113/1/E61.full.pdf))\n  * The contribution of rare variation to prostate cancer heritability ([Mancuso et al., NG, 2015](http://www.nature.com/ng/journal/v48/n1/full/ng.3446.html))\n  * Bolt-REML ([Loh et al., NG, 2015](http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html))\n  * Testing for Nodal Dependence in Relational Data Matrices ([Volfovsky et al., JASA, 2015](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.965777))\n  * The E-MS Algorithm: Model Selection With Incomplete Data ([Jiang et al., JASA, 2015](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.948545))\n  * Estimation and Accuracy after Model Selection ([Efron, JASA, 2014](http://www.tandfonline.com/doi/full/10.1080/01621459.2013.823775#abstract))\n  * A Gene Regulatory Program in Human Breast Cancer ([Li et al., Genetics, 2015](http://www.genetics.org/content/201/4/1341))\n  * DNA Methylation Landscapes of Human Fetal Development ([Roderick C. Slieker, PLoS Genetics, 2015](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005583))\n  * Epigenetic Aging Signatures Are Coherently Modified in Cancer ([Qiong Lin, PLoS Genetics](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005334))\n  * An Integrative Multi-scale Analysis of the Dynamic DNA Methylation Landscape in Aging ([Tian Yuan, PLoS Genetics, 2015](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1004996))\n  * Factors underlying variable DNA methylation in a human community cohort ([Lam et al., PNAS, 2012](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([Pineda et al., PLoS Genetics, 2015](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005689))\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-fall-2016","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fquantgen%2Flab-fall-2016","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fquantgen%2Flab-fall-2016/lists"}