https://github.com/quantgen/lab-fall-2016
https://github.com/quantgen/lab-fall-2016
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- Host: GitHub
- URL: https://github.com/quantgen/lab-fall-2016
- Owner: QuantGen
- Created: 2016-08-30T16:08:47.000Z (almost 10 years ago)
- Default Branch: master
- Last Pushed: 2016-12-03T05:10:46.000Z (over 9 years ago)
- Last Synced: 2025-04-04T01:29:43.731Z (about 1 year ago)
- Size: 26.4 KB
- Stars: 0
- Watchers: 20
- Forks: 2
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# Lab Meetings QuantGen Group Fall 2016
[Group's Website](http://quantgen.github.io/)
This 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.
**Advisors**: Each of the students presenting must pick an advisor, possible advisors are: Sudha, Hwasoon, Ana and Gustavo.
**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.
## Schedule
* **Date**: Friday, Sep 9, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Organizational Meeting
* **Topic(s)**: Discuss plan for the Fall, including lab meeting and papers in progress.
* **Materials**:
---
* **Date**: Friday, Sep 16, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Marigel Perez-Cabal
* **Topic(s)**: Use of spectra data for prediction of reproductive outcomes.
* **Materials**: [Bastin et al., 2016](http://ac.els-cdn.com/S0022030215009492/1-s2.0-S0022030215009492-main.pdf?_tid=f3bc7c68-75df-11e6-8e48-00000aab0f6b&acdnat=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).
* **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.
---
* **Date**: Friday, Sep 23, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Yeni Bernal
* **Topic(s)**: Understanding genetic structure of human populations
* **Materials**: [Novembre et al 2014. Genes mirror within Europe](http://www.nature.com/nature/journal/v456/n7218/abs/nature07331.html)
---
* **Date**: Friday, Sep 30, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Agustin Gonzalez Reymundez
* **Topic(s)**: Introduction to Epigenetics
* **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&token2=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)
---
* **Date**: Friday, Oct 7, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Canceled due to two seminars in the morning
* **Topic(s)**:
* **Materials**:
---
* **Date**: Friday, Oct 14, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Raka Mandal
* **Topic(s)**: The E-MS Algorithm: Model Selection With Incomplete Data
* **Materials**: [Jiang et al., JASA, 2015](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.948545)
---
* **Date**: Friday, Oct 21, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Topic(s)**: Informal discussion about the HPCC and citation management software (Mendeley & Zotero)
---
* **Date**: Friday, Oct 28, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Marco Lopez-Cruz
* **Topic(s)**: Incorporating LD information in Genomic Prediction with Sequence Data
* **Materials**: Paper: [Carlsen et al., Genetics, 2016](http://www.genetics.org/content/202/2/411)
---
* **Date**: Friday, Nov 4, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Deniz Akdemir
* **Title**: A subjective tour of topics in statistical genetics
* **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.
---
* **Date**: Friday, Nov 11, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Sudha
* **Topic(s)**: Defense Practice
* **Materials**:
---
* **Date**: Friday, Nov 18, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Canceled
* **Topic(s)**:
* **Materials**:
---
* **Date**: Friday, Dec 2, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Hwasoon Kim
* **Topic(s)**: Contribution of genetic and common shared environoment to common disease using the UK-Biobank
* **Materials**: [Muñoz et al., Nat. Gen., 2016] (http://www.nature.com/ng/journal/v48/n9/full/ng.3618.html)
---
* **Date**: Friday, Dec 9, 2016
* **Time**: 1:00-2:00pm
* **Room**: 909 Fee Rd, 6th floor, Central Conference Room
* **Presenter(s)**: Scott Funkhouser
* **Topic(s)**: Genetic Architectures of Quantitative Variation in RNA Editing Pathways
* **Materials**: [Tongjun et al.](http://www.genetics.org/content/202/2/787)
## Suggested Papers (feel free to add more!)
### Perspectives/Reviews
* Protein Variation in Natural Populations and Quantitative Genetic Variation ([Hubby et al., Genetics, 2016](http://www.genetics.org/content/203/4/1497))
* The History of the Y-Chromosome in man ([Hughes & Page, Nat. Gen., 2016](http://www.nature.com/ng/journal/v48/n6/pdf/ng.3580.pdf))
* What do you mean "Epigenetic"? ([Deans & Maggert, Genetics, 2015](http://www.genetics.org/content/199/4/887))
### Methods
* Exact Post-Selection Inference for Sequential Regression Procedures ([Tibshirani et al., JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1108848))
* Fast, Exact Bootstrap Principal Component Analysis for p > 1 Million ([Fisher et al., JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1062383))
* Sparse Regression Incorporating Graphical Structure Among Predictors ([Yu & Liu, JASA, 2016](http://www.tandfonline.com/doi/full/10.1080/01621459.2015.1034319))
* Incorporating LD information in Genomic Prediction with Sequence Data([Carlsen et al., Genetics, 2016](http://www.genetics.org/content/202/2/411))
* 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))
* 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))
### Research and Case Study Articles
* Genetic Variation of Gene Editing ([Tongjun et al., Genetics, 2016](http://www.genetics.org/content/202/2/787))
* Cis- and Trans-Gene Inactivation Caused by Heterochromatin in Drosophila ([Yuriy et al., Genetics, 2016](http://www.genetics.org/content/202/1/93))
* 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))
* 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))
* 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))
* Clonal evolution of glioblastoma under therapy ([Wang et al., Nat Gen., 2016](Clonal evolution of glioblastoma under therapy))
* 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))
* Genetic profiling of anthropometric traits using big data ([Canela-Xandri et al.](http://biorxiv.org/content/early/2015/12/01/033134.abstract))
* 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))
* 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))
* Bolt-REML ([Loh et al., NG, 2015](http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html))
* Testing for Nodal Dependence in Relational Data Matrices ([Volfovsky et al., JASA, 2015](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.965777))
* 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))
* Estimation and Accuracy after Model Selection ([Efron, JASA, 2014](http://www.tandfonline.com/doi/full/10.1080/01621459.2013.823775#abstract))
* A Gene Regulatory Program in Human Breast Cancer ([Li et al., Genetics, 2015](http://www.genetics.org/content/201/4/1341))
* 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))
* Epigenetic Aging Signatures Are Coherently Modified in Cancer ([Qiong Lin, PLoS Genetics](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005334))
* 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))
* 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))
* 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))