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Results: 1 to 20 of 39

1.

Functional normalization of 450k methylation array data improves replication in large cancer studies.

Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD.

Genome Biol. 2014 Dec 3;15(12):503. doi: 10.1186/s13059-014-0503-2.

PMID:
25599564
[PubMed - in process]
2.

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.

Ziller MJ, Hansen KD, Meissner A, Aryee MJ.

Nat Methods. 2014 Nov 2. doi: 10.1038/nmeth.3152. [Epub ahead of print]

PMID:
25362363
[PubMed - as supplied by publisher]
3.

Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome.

Bjornsson HT, Benjamin JS, Zhang L, Weissman J, Gerber EE, Chen YC, Vaurio RG, Potter MC, Hansen KD, Dietz HC.

Sci Transl Med. 2014 Oct 1;6(256):256ra135. doi: 10.1126/scitranslmed.3009278.

PMID:
25273096
[PubMed - in process]
4.

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.

Bioinformatics. 2014 May 15;30(10):1363-9. doi: 10.1093/bioinformatics/btu049. Epub 2014 Jan 28.

PMID:
24478339
[PubMed - indexed for MEDLINE]
5.

Differential expression analysis of RNA-seq data at single-base resolution.

Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT.

Biostatistics. 2014 Jul;15(3):413-26. doi: 10.1093/biostatistics/kxt053. Epub 2014 Jan 6.

PMID:
24398039
[PubMed - in process]
Free PMC Article
6.

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.

Genome Res. 2014 Feb;24(2):177-84. doi: 10.1101/gr.157743.113. Epub 2013 Sep 25.

PMID:
24068705
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Common DNA methylation alterations in multiple brain regions in autism.

Ladd-Acosta C, Hansen KD, Briem E, Fallin MD, Kaufmann WE, Feinberg AP.

Mol Psychiatry. 2014 Aug;19(8):862-71. doi: 10.1038/mp.2013.114. Epub 2013 Sep 3.

PMID:
23999529
[PubMed - in process]
8.

A comparison of the sensory profile and sensory processing measure home form for children with fetal alcohol spectrum disorders.

Hansen KD, Jirikowic T.

Phys Occup Ther Pediatr. 2013 Nov;33(4):440-52. doi: 10.3109/01942638.2013.791914. Epub 2013 May 13.

PMID:
23663112
[PubMed - indexed for MEDLINE]
9.

illuminaio: An open source IDAT parsing tool for Illumina microarrays.

Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD.

F1000Res. 2013 Dec 4;2:264. doi: 10.12688/f1000research.2-264.v1. eCollection 2013.

PMID:
24701342
[PubMed]
Free PMC Article
10.

Human neural stem cells induce functional myelination in mice with severe dysmyelination.

Uchida N, Chen K, Dohse M, Hansen KD, Dean J, Buser JR, Riddle A, Beardsley DJ, Wan Y, Gong X, Nguyen T, Cummings BJ, Anderson AJ, Tamaki SJ, Tsukamoto A, Weissman IL, Matsumoto SG, Sherman LS, Kroenke CD, Back SA.

Sci Transl Med. 2012 Oct 10;4(155):155ra136. doi: 10.1126/scitranslmed.3004371. Erratum in: Sci Transl Med. 2012 Dec 19;4(165):165er7.

PMID:
23052293
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.

Hansen KD, Langmead B, Irizarry RA.

Genome Biol. 2012 Oct 3;13(10):R83. doi: 10.1186/gb-2012-13-10-r83.

PMID:
23034175
[PubMed - in process]
Free PMC Article
12.

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.

Nat Neurosci. 2012 Oct;15(10):1371-3. doi: 10.1038/nn.3218. Epub 2012 Sep 16.

PMID:
22983211
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Social environment is associated with gene regulatory variation in the rhesus macaque immune system.

Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopoulos V, Toufexis D, Michelini K, Wilson ME, Gilad Y.

Proc Natl Acad Sci U S A. 2012 Apr 24;109(17):6490-5. doi: 10.1073/pnas.1202734109. Epub 2012 Apr 9.

PMID:
22493251
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users.

Munshaw S, Hwang HS, Torbenson M, Quinn J, Hansen KD, Astemborski J, Mehta SH, Ray SC, Thomas DL, Balagopal A.

Hepatology. 2012 Aug;56(2):544-54. doi: 10.1002/hep.25655. Epub 2012 Jul 6.

PMID:
22331678
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Removing technical variability in RNA-seq data using conditional quantile normalization.

Hansen KD, Irizarry RA, Wu Z.

Biostatistics. 2012 Apr;13(2):204-16. doi: 10.1093/biostatistics/kxr054. Epub 2012 Jan 27.

PMID:
22285995
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Sequencing technology does not eliminate biological variability.

Hansen KD, Wu Z, Irizarry RA, Leek JT.

Nat Biotechnol. 2011 Jul 11;29(7):572-3. doi: 10.1038/nbt.1910. No abstract available.

PMID:
21747377
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

An organotypic slice culture model of chronic white matter injury with maturation arrest of oligodendrocyte progenitors.

Dean JM, Riddle A, Maire J, Hansen KD, Preston M, Barnes AP, Sherman LS, Back SA.

Mol Neurodegener. 2011 Jul 5;6:46. doi: 10.1186/1750-1326-6-46.

PMID:
21729326
[PubMed]
Free PMC Article
18.

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.

Nat Genet. 2011 Jun 26;43(8):768-75. doi: 10.1038/ng.865.

PMID:
21706001
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Conservation of an RNA regulatory map between Drosophila and mammals.

Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR.

Genome Res. 2011 Feb;21(2):193-202. doi: 10.1101/gr.108662.110. Epub 2010 Oct 4.

PMID:
20921232
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Cloud-scale RNA-sequencing differential expression analysis with Myrna.

Langmead B, Hansen KD, Leek JT.

Genome Biol. 2010;11(8):R83. doi: 10.1186/gb-2010-11-8-r83. Epub 2010 Aug 11.

PMID:
20701754
[PubMed - indexed for MEDLINE]
Free PMC Article
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