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Transient reduction of DNA methylation at the onset of meiosis in male mice.

Gaysinskaya V, Miller BF, De Luca C, van der Heijden GW, Hansen KD, Bortvin A.

Epigenetics Chromatin. 2018 Apr 4;11(1):15. doi: 10.1186/s13072-018-0186-0.


Improving Metabolic Health Through Precision Dietetics in Mice.

Barrington WT, Wulfridge P, Wells AE, Rojas CM, Howe SYF, Perry A, Hua K, Pellizzon MA, Hansen KD, Voy BH, Bennett BJ, Pomp D, Feinberg AP, Threadgill DW.

Genetics. 2018 Jan;208(1):399-417. doi: 10.1534/genetics.117.300536. Epub 2017 Nov 20.


Software for the Integration of Multiomics Experiments in Bioconductor.

Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, Mer AS, Riester M, Morgan M, Carey V, Waldron L.

Cancer Res. 2017 Nov 1;77(21):e39-e42. doi: 10.1158/0008-5472.CAN-17-0344.


Ensuring due process in the IACUC and animal welfare setting: considerations in developing noncompliance policies and procedures for institutional animal care and use committees and institutional officials.

Hansen BC, Gografe S, Pritt S, Jen KC, McWhirter CA, Barman SM, Comuzzie A, Greene M, McNulty JA, Michele DE, Moaddab N, Nelson RJ, Norris K, Uray KD, Banks R, Westlund KN, Yates BJ, Silverman J, Hansen KD, Redman B.

FASEB J. 2017 Oct;31(10):4216-4225. doi: 10.1096/fj.201601250R. Epub 2017 Aug 15. Review.


Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.


Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.

Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE.

Nat Methods. 2017 Feb 28;14(3):216-217. doi: 10.1038/nmeth.4187. No abstract available.


Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics.

Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD.

Anal Chem. 2017 Mar 21;89(6):3517-3523. doi: 10.1021/acs.analchem.6b04719. Epub 2017 Mar 7.


Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.


Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.

Fortin JP, Triche TJ Jr, Hansen KD.

Bioinformatics. 2017 Feb 15;33(4):558-560. doi: 10.1093/bioinformatics/btw691.


A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome.

Benjamin JS, Pilarowski GO, Carosso GA, Zhang L, Huso DL, Goff LA, Vernon HJ, Hansen KD, Bjornsson HT.

Proc Natl Acad Sci U S A. 2017 Jan 3;114(1):125-130. doi: 10.1073/pnas.1611431114. Epub 2016 Dec 20.


"Gap hunting" to characterize clustered probe signals in Illumina methylation array data.

Andrews SV, Ladd-Acosta C, Feinberg AP, Hansen KD, Fallin MD.

Epigenetics Chromatin. 2016 Dec 7;9:56. doi: 10.1186/s13072-016-0107-z. eCollection 2016.


Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver.

Li X, Liu Y, Salz T, Hansen KD, Feinberg A.

Genome Res. 2016 Dec;26(12):1730-1741. Epub 2016 Oct 13.


Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B.

Bioinformatics. 2016 Aug 15;32(16):2551-3. doi: 10.1093/bioinformatics/btw177. Epub 2016 Apr 21.


DNA methylation is stable during replication and cell cycle arrest.

Vandiver AR, Idrizi A, Rizzardi L, Feinberg AP, Hansen KD.

Sci Rep. 2015 Dec 9;5:17911. doi: 10.1038/srep17911.


Testing and Validation of Computational Methods for Mass Spectrometry.

Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A.

J Proteome Res. 2016 Mar 4;15(3):809-14. doi: 10.1021/acs.jproteome.5b00852. Epub 2015 Nov 17.


Public data and open source tools for multi-assay genomic investigation of disease.

Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L.

Brief Bioinform. 2016 Jul;17(4):603-15. doi: 10.1093/bib/bbv080. Epub 2015 Oct 12. Review.


Bacterial infection remodels the DNA methylation landscape of human dendritic cells.

Pacis A, Tailleux L, Morin AM, Lambourne J, MacIsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, Tung J, Pastinen T, Kobor MS, Pique-Regi R, Gilad Y, Barreiro LB.

Genome Res. 2015 Dec;25(12):1801-11. doi: 10.1101/gr.192005.115. Epub 2015 Sep 21.


Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.

Fortin JP, Hansen KD.

Genome Biol. 2015 Aug 28;16:180. doi: 10.1186/s13059-015-0741-y.


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.


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.


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.


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.


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.


The Bioconductor channel in F1000Research.

Huber W, Carey V, Davis S, Hansen KD, Morgan M.

Version 2. F1000Res. 2015 Jul 10 [revised 2016 Jan 1];4:217. doi: 10.12688/f1000research.6758.2. eCollection 2015.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


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.


Biases in Illumina transcriptome sequencing caused by random hexamer priming.

Hansen KD, Brenner SE, Dudoit S.

Nucleic Acids Res. 2010 Jul;38(12):e131. doi: 10.1093/nar/gkq224. Epub 2010 Apr 14.


Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.

Bullard JH, Purdom E, Hansen KD, Dudoit S.

BMC Bioinformatics. 2010 Feb 18;11:94. doi: 10.1186/1471-2105-11-94.


Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.

Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE.

PLoS Genet. 2009 Jun;5(6):e1000525. doi: 10.1371/journal.pgen.1000525. Epub 2009 Jun 19.


Novel low abundance and transient RNAs in yeast revealed by tiling microarrays and ultra high-throughput sequencing are not conserved across closely related yeast species.

Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G.

PLoS Genet. 2008 Dec;4(12):e1000299. doi: 10.1371/journal.pgen.1000299. Epub 2008 Dec 19.


Computer mouse use predicts acute pain but not prolonged or chronic pain in the neck and shoulder.

Andersen JH, Harhoff M, Grimstrup S, Vilstrup I, Lassen CF, Brandt LP, Kryger AI, Overgaard E, Hansen KD, Mikkelsen S.

Occup Environ Med. 2008 Feb;65(2):126-31. Epub 2007 Aug 6.


Use of census data for construction of fertility history for Danish women.

Danø H, Jacobsen R, Hansen KD, Petersen JK, Lynge E.

Scand J Public Health. 2004;32(6):435-41.


Advanced paternal age and risk of fetal death: a cohort study.

Nybo Andersen AM, Hansen KD, Andersen PK, Davey Smith G.

Am J Epidemiol. 2004 Dec 15;160(12):1214-22.


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