https://github.com/quantgen/lab-spring-2020
https://github.com/quantgen/lab-spring-2020
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/quantgen/lab-spring-2020
- Owner: QuantGen
- Created: 2020-01-14T17:04:46.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2020-04-13T17:44:32.000Z (about 6 years ago)
- Last Synced: 2025-09-08T23:43:38.927Z (9 months ago)
- Size: 1.31 MB
- Stars: 0
- Watchers: 19
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Lab Meetings QuantGen Group Spring 2020
## Where? IQ (775 Woodlot Dr), Room 1000
## When? Fridays 12-1
[Group's Website](http://quantgen.github.io/)
| Date | Presenter(s) | Topic(s) | Materials |
| ------------- | ---------------- | ---------------- | ------------- |
| 1/17 | Gustavo de los Campos | Introduction | [link](https://www.nature.com/articles/nmeth.1439#Sec2) |
| 1/24 | SCIENCE AT THE EDGE DAY | Dr. Mulle (Human Genetics) | 11:30 in 1400 Biomedical & Physical Sciences Building |
| 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) |
| 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) |
| 2/14 | Laura Zingaretti | Deep learning shallow for genomic prediction? | [Zingaretti et al.](https://www.frontiersin.org/articles/10.3389/fpls.2020.00025/full) |
| 2/28 | Marco Lopez-Cruz | Tensor Graphical LASSO (TeraLASSO) | |
| 3/13 | | | |
| 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) |
| 3/27 | Harold Wu | Tests of Hardy–Weinberg Equilibrium to Structured Populations | [Paper 1](https://www.genetics.org/content/213/3/759) |
| 4/3 | Filipe Couto| Wavelet-Based Genetic Association Analysis of Functional Phenotypes Arising From High-Throughput Sequencing Assays | |
| 4/10 | Alexa Lupi | | |
| 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) |
| 4/24 | Fernando Aguate | Nonlinear Mixed Effects Models for Repeated Measures Data | [Paper 1](https://www.jstor.org/stable/2532087?seq=1) |
### Ideas for articles
If you have a paper you would like to present, use that one, otherwise feel free to choose one from this list
* [Bayesian Graphical Regression (JASA, 2019)](https://amstat.tandfonline.com/doi/full/10.1080/01621459.2017.1389739#.XjBHKRdJlUM)
* [Cell type–specific gene expression differences in complex tissues.](https://www.nature.com/articles/nmeth.1439#Sec2) Shen-Orr et al.
* [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.
* [False discovery rates: a new deal.](https://academic.oup.com/biostatistics/article/18/2/275/2557030) Stephens
* [The conditional permutation test for independence while controlling for confounders](https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12340) Berrett et al.
* [Tensor graphical lasso (TeraLasso)](https://rss.onlinelibrary.wiley.com/doi/10.1111/rssb.12339) Greenewald et al.
* [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.
* [Learning representations of microbe–metabolite interactions](https://www.nature.com/articles/s41592-019-0616-3) Morton et al.
* [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.
* [Genomic Medicine Year in Review: 2019](https://www.cell.com/ajhg/fulltext/S0002-9297(19)30427-6) Manolio et al.
* [Making the Most of Clumping and Thresholding for Polygenic Scores](https://www.cell.com/ajhg/fulltext/S0002-9297(19)30422-7) Prive et al.