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Using CisGenome to analyze ChIP-chip and ChIP-seq data.
Ji H, Jiang H, Ma W, Wong WH. Ji H, et al. Curr Protoc Bioinformatics. 2011 Mar;Chapter 2:Unit2.13. doi: 10.1002/0471250953.bi0213s33. Curr Protoc Bioinformatics. 2011. PMID: 21400695 Free PMC article.
Aligning short sequencing reads with Bowtie.
Langmead B. Langmead B. Curr Protoc Bioinformatics. 2010 Dec;Chapter 11:Unit 11.7. doi: 10.1002/0471250953.bi1107s32. Curr Protoc Bioinformatics. 2010. PMID: 21154709 Free PMC article.
Increased methylation variation in epigenetic domains across cancer types.
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Briem E, Zhang K, Irizarry RA, Feinberg AP. Hansen KD, et al. Nat Genet. 2011 Jun 26;43(8):768-75. doi: 10.1038/ng.865. Nat Genet. 2011. PMID: 21706001 Free PMC article.