reading_list.txt

Suggestions for Journal Club Papers - STA426 HS2016
===================================================

[The papers listed here are just suggestions.  As mentioned,
 the journal club papers need to be something that relates
 "statistics" and "genomics".  See Lecture 1 Notes for more details about
 expectations of the Journal Club Presentations.  Please discuss
 your chosen paper with Mark/Hubert before signing up.]


RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
Li B, Dewey CN
BMC Bioinformatics. 2011 Aug 4;12:323.
http://www.ncbi.nlm.nih.gov/pubmed/21816040
http://www.biomedcentral.com/1471-2105/12/323


Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.
Van De Wiel MA, Leday GG, Pardo L, Rue H, Van Der Vaart AW, Van Wieringen WN.
Biostatistics. 2013 Jan;14(1):113-28.
http://www.ncbi.nlm.nih.gov/pubmed/22988280


Circular binary segmentation for the analysis of array-based DNA copy number data.
Olshen AB, Venkatraman ES, Lucito R, Wigler M.
Biostatistics. 2004 Oct;5(4):557-72.
http://www.ncbi.nlm.nih.gov/pubmed/15475419


Empirical Bayes Analysis of a Microarray Experiment
Bradley Efron, Robert Tibshirani, John D Storey & Virginia Tusher
Journal of the American Statistical Association
Volume 96, Issue 456, 2001; pages 1151-1160
http://www.tandfonline.com/doi/abs/10.1198/016214501753382129#.VB_QHS6Szpg


Epigenome-wide association studies without the need for cell-type composition
Zou J, Lippert C, Heckerman D, Aryee M, Listgarten J.
Nat Methods. 2014 Mar;11(3):309-11.
http://www.ncbi.nlm.nih.gov/pubmed/24464286
http://www.nature.com/nmeth/journal/v11/n3/full/nmeth.2815.html


Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
Jeffrey T Leek, John D Storey 
http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.0030161


Summarizing and correcting the GC content bias in high-throughput sequencing
Yuval Benjamini and Terence P. Speed
http://www.ncbi.nlm.nih.gov/pubmed/22323520