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Results: 1 to 20 of 43

1.

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.

Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP.

Genome Biol. 2015 Apr 16;16:80. doi: 10.1186/s13059-015-0644-y.

2.

Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children.

Hong X, Hao K, Ladd-Acosta C, Hansen KD, Tsai HJ, Liu X, Xu X, Thornton TA, Caruso D, Keet CA, Sun Y, Wang G, Luo W, Kumar R, Fuleihan R, Singh AM, Kim JS, Story RE, Gupta RS, Gao P, Chen Z, Walker SO, Bartell TR, Beaty TH, Fallin MD, Schleimer R, Holt PG, Nadeau KC, Wood RA, Pongracic JA, Weeks DE, Wang X.

Nat Commun. 2015 Feb 24;6:6304. doi: 10.1038/ncomms7304.

3.

Deep subconjunctival injection of gentamicin for the treatment of bacterial conjunctivitis in macaques (Macaca mulatta and Macaca fascicularis).

Gografe SI, Hansen BC, Hansen KD.

Lab Anim (NY). 2015 Mar;44(3):92-6. doi: 10.1038/laban.661.

PMID:
25693106
4.

Orchestrating high-throughput genomic analysis with Bioconductor.

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M.

Nat Methods. 2015 Feb;12(2):115-21. doi: 10.1038/nmeth.3252. Review.

5.

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.

6.

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

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

Nat Methods. 2015 Mar;12(3):230-2, 1 p following 232. doi: 10.1038/nmeth.3152. Epub 2014 Nov 2.

PMID:
25362363
7.

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.

8.

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.

9.

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. Erratum in: Biostatistics. 2014 Jul;15(3):584-5.

10.

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.

11.

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.

12.

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
13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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