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ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data.
Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H. Wu G, et al. Bioinformatics. 2013 May 1;29(9):1182-9. doi: 10.1093/bioinformatics/btt108. Epub 2013 Mar 1. Bioinformatics. 2013. PMID: 23457041 Free PMC article.
Thawing Frozen Robust Multi-array Analysis (fRMA).
McCall MN, Irizarry RA. McCall MN, et al. BMC Bioinformatics. 2011 Sep 16;12:369. doi: 10.1186/1471-2105-12-369. BMC Bioinformatics. 2011. PMID: 21923903 Free PMC article.
Assessing affymetrix GeneChip microarray quality.
McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. McCall MN, et al. BMC Bioinformatics. 2011 May 7;12:137. doi: 10.1186/1471-2105-12-137. BMC Bioinformatics. 2011. PMID: 21548974 Free PMC article.
Patient-oriented gene set analysis for cancer mutation data.
Boca SM, Kinzler KW, Velculescu VE, Vogelstein B, Parmigiani G. Boca SM, et al. Genome Biol. 2010;11(11):R112. doi: 10.1186/gb-2010-11-11-r112. Epub 2010 Nov 23. Genome Biol. 2010. PMID: 21092299 Free PMC article.
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD Jr, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, J… See abstract for full author list ➔ Shi L, et al. Nat Biotechnol. 2010 Aug;28(8):827-38. doi: 10.1038/nbt.1665. Epub 2010 Jul 30. Nat Biotechnol. 2010. PMID: 20676074 Free PMC article.