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reading_list.txt
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Add some papers here:
Suggestions for Journal Club Papers - STA426 HS2015
===================================================
[The papers listed here are just suggestions. Find a "methods"
paper that is related to microarray or sequencing data.
See Lecture 1 Notes - STA426_intro.pdf 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