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84 results
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Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.
Fortin JP, Hansen KD. Fortin JP, et al. Among authors: hansen kd. Genome Biol. 2015 Aug 28;16(1):180. doi: 10.1186/s13059-015-0741-y. Genome Biol. 2015. PMID: 26316348 Free PMC article.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Langmead B, Hansen KD, Leek JT. Langmead B, et al. Among authors: hansen kd. Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11. Genome Biol. 2010. PMID: 20701754 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.
Removing technical variability in RNA-seq data using conditional quantile normalization.
Hansen KD, Irizarry RA, Wu Z. Hansen KD, et al. Biostatistics. 2012 Apr;13(2):204-16. doi: 10.1093/biostatistics/kxr054. Epub 2012 Jan 27. Biostatistics. 2012. PMID: 22285995 Free PMC article.
Reversible switching between epigenetic states in honeybee behavioral subcastes.
Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP. Herb BR, et al. Among authors: hansen kd. Nat Neurosci. 2012 Oct;15(10):1371-3. doi: 10.1038/nn.3218. Epub 2012 Sep 16. Nat Neurosci. 2012. PMID: 22983211 Free PMC article.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Hansen KD, Langmead B, Irizarry RA. Hansen KD, et al. Genome Biol. 2012 Oct 3;13(10):R83. doi: 10.1186/gb-2012-13-10-r83. Genome Biol. 2012. PMID: 23034175 Free PMC article.
Common DNA methylation alterations in multiple brain regions in autism.
Ladd-Acosta C, Hansen KD, Briem E, Fallin MD, Kaufmann WE, Feinberg AP. Ladd-Acosta C, et al. Among authors: hansen kd. Mol Psychiatry. 2014 Aug;19(8):862-71. doi: 10.1038/mp.2013.114. Epub 2013 Sep 3. Mol Psychiatry. 2014. PMID: 23999529 Free PMC article.
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization.
Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Hansen KD, et al. Genome Res. 2014 Feb;24(2):177-84. doi: 10.1101/gr.157743.113. Epub 2013 Sep 25. Genome Res. 2014. PMID: 24068705 Free PMC article.
Differential expression analysis of RNA-seq data at single-base resolution.
Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT. Frazee AC, et al. Among authors: hansen kd. Biostatistics. 2014 Jul;15(3):413-26. doi: 10.1093/biostatistics/kxt053. Epub 2014 Jan 6. Biostatistics. 2014. PMID: 24398039 Free PMC article.
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays.
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Aryee MJ, et al. Among authors: hansen kd. Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28. Bioinformatics. 2014. PMID: 24478339 Free PMC article.
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