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https://github.com/quantgen/lab-spring-2016


https://github.com/quantgen/lab-spring-2016

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README 

          
# Lab Meetings QuantGen Group Spring 2016



[Group's Website](http://quantgen.github.io/)



This season we will be covering papers from outside the group (~8), sfotware from the group (1-2) and eventually discussion of grant proposals.



Papers: 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. 



Software: we will organize 1-2 sections to share software being developed by the group. 



Grant proposals: if time permit we will include on section on grant writing (format to be determined).



## Schedule

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 * **Date**:  Wednesday, January 20, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: NA

 * **Topic(s)**: Organizational meeting

 * **Materials**: NA



 

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 * **Date**:  Wednesday, January 27, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Agustin 

 * **Topic(s)**: DNA Methylation   

 * **Materials**: 

    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Agustin_Paper_DNA%20Methylation.pdf)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Agustin_Slides.pptx)



 

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 * **Date**:  Wednesday, February 3, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Hank

 * **Topic(s)**: Identify Cis-eQTL Target Gene associated with GBM   

 * **Materials**:

    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Hank_Paper_GBM%20eQTL.pdf)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Hank_Slides.pptx)



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 * **Date**:  Wednesday, February 10, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Yeni

 * **Topic(s)**: The Nature of genetic Variation for Complex Traits   

 * **Materials**: 

    * [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)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Yeni_Slides.pdf)



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 * **Date**:  Wednesday, February 17, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Prof. Jiayu Zhou

 * **Topic(s)**: Multi-task Learning and its Applications   

 * **Materials**:   

    * [Homepage](http://jiayuzhou.github.io/)



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 * **Date**:  Thursday, February 25, 2016.

 * **Time**:  1:30-3:00pm

 * **Room**:  East Conference Room

 * **Presenter(s)**: Dr. Hsu & Dr. Ho

 * **Topic(s)**: Genetic architecture and predictive modeling of quantitative traits

 * **Materials**:

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Steve%20Hsu_Slides.pdf)

    * [Video](http://infoproc.blogspot.com/2015/05/genetic-architecture-and-predictive.html)

    * [Reference](http://infoproc.blogspot.com/2009/09/some-favorite-posts.html)



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 * **Date**:  Wednesday,  March 2, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: 

 * **Topic(s)**:     

 * **Materials**:    



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 *  Wednesday,  March 9, 2016. **(No Lab Meeting, Spring Break)**

    

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 * **Date**:  Wednesday,  March 16, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: TBD

 * **Topic(s)**:    

 * **Materials**: 



---------------------------------------------------------------------------- 

 * **Date**:  Wednesday,  March 23, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Felix

 * **Topic(s)**: Modification of the Coiled-Coil domain from the RB gene in transgenic potato using the CRISPR/Cas9 system   

 * **Materials**:

    * [Review](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Felix_Review_Genome%20Editing.pdf)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Felix_Slides_Genome%20editing.pdf)



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 * **Date**:  Wednesday,  March 30, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Fernando

 * **Topic(s)**:  Use of high-resolution image data for prediction of maize yield 

 * **Materials**: 

    * [Article](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Fernando_short%20article.docx)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Fernando_Slides_Image%20data%20to%20presidict%20maize%20yield.pptx)



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 * **Date**:  Wednesday, April 6, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**:  NA

 * **Topic(s)**:  NA

 * **Materials**:   NA



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 * **Date**:  Wednesday,  April 13, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Sudha

 * **Topic(s)**:  Modeling genetic heterogeneity and sex differences using random effect interactions   

 * **Materials**: 

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Sudha_Slides.pdf)



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 * **Date**:  Wednesday,  April 20, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Mengying

 * **Topic(s)**: Significancy vs prediction power, partition retention method    

 * **Materials**: 

    * [Article](http://www.pnas.org/content/112/45/13892.abstract)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Mengying_Slides.pdf)



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 * **Date**:  Wednesday,  April 27, 2016.

 * **Time**:  1:45-2:45pm

 * **Room**:  Central Conference Room

 * **Presenter(s)**: Scott

 * **Topic(s)**: RNA editing: new sources of genomic variation, software and application   

 * **Materials**: 

    * [Introduction](http://genome.cshlp.org/content/early/2013/12/17/gr.164749.113.abstract)

    * [Software](https://github.com/funkhou9/editTools)

    * [Slides](https://github.com/QuantGen/LAB-SPRING-2016/blob/master/Scott_Slides.pdf)



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## Wishlist (you may either choose a paper from this list or suggest one).



 

* [ Lo et al., Why significant variables aren’t automatically good predictors (PNAS, 2015) ] (http://www.pnas.org/content/112/45/13892.abstract)

* [ 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)

* [Kumar et al., Limitations of GCTA as a solution to the missing

heritability problem (PNAS, 2015) ](http://www.pnas.org/content/113/1/E61.full.pdf)

* [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)

* [Loh et al. "Bolt-REML" (NG, 2015)](http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html)

* [Volfovsky et al., Testing for Nodal Dependence in Relational Data Matrices (JASA, 2015)](http://www.tandfonline.com/doi/full/10.1080/01621459.2014.965777)

* [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)

* [Efron, Estimation and Accuracy after Model Selection (JASA, 2014)](http://www.tandfonline.com/doi/full/10.1080/01621459.2013.823775#abstract)

* [Li et al. A Gene Regulatory Program in Human Breast Cancer (Genetics, 2015)](http://www.genetics.org/content/201/4/1341)

* [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)

* [Deans & Maggert, What do you mean "Epigenetic"? (Genetics, 2015)](http://www.genetics.org/content/199/4/887)

* [Renhua Li,A Gene Regulatory Program in Human Breast Cancer](http://www.genetics.org/content/201/4/1341)

* [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)

* [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)

* [Deniz Akdemir, Locally Epistatic Genomic Relationship Matrices for Genomic Association and Prediction](http://www.genetics.org/content/199/3/857)

* [Paul Brennan,Genomics of Cancer and a New Era for Cancer Prevention](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005522)

* [Roderick C. Slieker, DNA Methylation Landscapes of Human Fetal Development](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005583)

* [Qiong Lin, Epigenetic Aging Signatures Are Coherently Modified in Cancer ](http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1005334)

* [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)

* [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)

* [Bjarni J. Vilhjálmsson, Modeling Linkage Disequilibrium Increases Accuracy of Polygenic Risk Scores](http://www.cell.com/ajhg/abstract/S0002-9297%2815%2900365-1)

* [Big data mining yields novel insights on cancer](http://www.nature.com/ng/journal/v47/n2/full/ng.3205.html)

* [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)

* [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)

[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)

[Efficient Multiple-Trait Association and Estimation of Genetic Correlation Using the Matrix-Variate Linear Mixed Model](http://genetics.org/content/200/1/59)