Kasper D. Hansen - Publications

Affiliations: 
2009 University of California, Berkeley, Berkeley, CA 

34 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2016 Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B. Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. Bioinformatics (Oxford, England). PMID 27153614 DOI: 10.1093/bioinformatics/btw177  0.76
2015 Vandiver AR, Idrizi A, Rizzardi L, Feinberg AP, Hansen KD. DNA methylation is stable during replication and cell cycle arrest. Scientific Reports. 5: 17911. PMID 26648411 DOI: 10.1038/srep17911  0.76
2015 Pacis A, Tailleux L, Morin AM, Lambourne J, Maclsaac JL, Yotova V, Dumaine A, Danckaert A, Luca F, Grenier JC, Hansen KD, Gicquel B, Yu M, Pai A, He C, et al. Bacterial infection remodels the DNA methylation landscape of human dendritic cells. Genome Research. PMID 26392366 DOI: 10.1101/gr.192005.115  0.76
2015 Fortin JP, Hansen KD. Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data. Genome Biology. 16: 180. PMID 26316348 DOI: 10.1186/s13059-015-0741-y  0.76
2015 Vandiver AR, Irizarry RA, Hansen KD, Garza LA, Runarsson A, Li X, Chien AL, Wang TS, Leung SG, Kang S, Feinberg AP. Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biology. 16: 80. PMID 25886480 DOI: 10.1186/s13059-015-0644-y  0.76
2015 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, et al. Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nature Communications. 6: 6304. PMID 25710614 DOI: 10.1038/ncomms7304  0.76
2015 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, et al. Orchestrating high-throughput genomic analysis with Bioconductor. Nature Methods. 12: 115-21. PMID 25633503 DOI: 10.1038/nmeth.3252  0.76
2015 Ziller MJ, Hansen KD, Meissner A, Aryee MJ. Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nature Methods. 12: 230-2, 1 p following. PMID 25362363 DOI: 10.1038/nmeth.3152  0.76
2015 Huber W, Carey V, Davis S, Hansen KD, Morgan M. The Bioconductor channel in F1000Research F1000research. 4. DOI: 10.12688/f1000research.6758.1  0.76
2014 Fortin JP, Labbe A, Lemire M, Zanke BW, Hudson TJ, Fertig EJ, Greenwood CM, Hansen KD. Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biology. 15: 503. PMID 25599564 DOI: 10.1186/s13059-014-0503-2  0.76
2014 Bjornsson HT, Benjamin JS, Zhang L, Weissman J, Gerber EE, Chen YC, Vaurio RG, Potter MC, Hansen KD, Dietz HC. Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome. Science Translational Medicine. 6: 256ra135. PMID 25273096 DOI: 10.1126/scitranslmed.3009278  0.76
2014 Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (Oxford, England). 30: 1363-9. PMID 24478339 DOI: 10.1093/bioinformatics/btu049  0.76
2014 Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT. Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics (Oxford, England). 15: 413-26. PMID 24398039 DOI: 10.1093/biostatistics/kxt053  0.76
2014 Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, Klein E, Salamon D, Feinberg AP. Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Research. 24: 177-84. PMID 24068705 DOI: 10.1101/gr.157743.113  0.76
2014 Ladd-Acosta C, Hansen KD, Briem E, Fallin MD, Kaufmann WE, Feinberg AP. Common DNA methylation alterations in multiple brain regions in autism. Molecular Psychiatry. 19: 862-71. PMID 23999529 DOI: 10.1038/mp.2013.114  0.76
2014 Fortin JP, Fertig E, Hansen K. shinyMethyl: Interactive quality control of Illumina 450k DNA methylation arrays in R F1000research. 3. DOI: 10.12688/f1000research.4680.2  0.76
2013 Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. illuminaio: An open source IDAT parsing tool for Illumina microarrays. F1000research. 2: 264. PMID 24701342 DOI: 10.12688/f1000research.2-264.v1  0.76
2012 Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biology. 13: R83. PMID 23034175 DOI: 10.1186/gb-2012-13-10-r83  0.76
2012 Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nature Neuroscience. 15: 1371-3. PMID 22983211 DOI: 10.1038/nn.3218  0.76
2012 Tung J, Barreiro LB, Johnson ZP, Hansen KD, Michopoulos V, Toufexis D, Michelini K, Wilson ME, Gilad Y. Social environment is associated with gene regulatory variation in the rhesus macaque immune system. Proceedings of the National Academy of Sciences of the United States of America. 109: 6490-5. PMID 22493251 DOI: 10.1073/pnas.1202734109  0.76
2012 Munshaw S, Hwang HS, Torbenson M, Quinn J, Hansen KD, Astemborski J, Mehta SH, Ray SC, Thomas DL, Balagopal A. Laser captured hepatocytes show association of butyrylcholinesterase gene loss and fibrosis progression in hepatitis C-infected drug users. Hepatology (Baltimore, Md.). 56: 544-54. PMID 22331678 DOI: 10.1002/hep.25655  0.76
2012 Hansen KD, Irizarry RA, Wu Z. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (Oxford, England). 13: 204-16. PMID 22285995 DOI: 10.1093/biostatistics/kxr054  0.76
2011 Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nature Biotechnology. 29: 572-3. PMID 21747377 DOI: 10.1038/nbt.1910  0.76
2011 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. Increased methylation variation in epigenetic domains across cancer types. Nature Genetics. 43: 768-75. PMID 21706001 DOI: 10.1038/ng.865  0.76
2011 Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR. Conservation of an RNA regulatory map between Drosophila and mammals. Genome Research. 21: 193-202. PMID 20921232 DOI: 10.1101/gr.108662.110  0.76
2010 Langmead B, Hansen KD, Leek JT. Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology. 11: R83. PMID 20701754 DOI: 10.1186/gb-2010-11-8-r83  0.76
2010 Hansen KD, Brenner SE, Dudoit S. Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Research. 38: e131. PMID 20395217 DOI: 10.1093/nar/gkq224  0.76
2010 Bullard JH, Purdom E, Hansen KD, Dudoit S. Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. Bmc Bioinformatics. 11: 94. PMID 20167110 DOI: 10.1186/1471-2105-11-94  0.76
2009 Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE. Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. Plos Genetics. 5: e1000525. PMID 19543372 DOI: 10.1371/journal.pgen.1000525  0.76
2008 Lee A, Hansen KD, Bullard J, Dudoit S, Sherlock G. 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. Plos Genetics. 4: e1000299. PMID 19096707 DOI: 10.1371/journal.pgen.1000299  0.76
2008 Andersen JH, Harhoff M, Grimstrup S, Vilstrup I, Lassen CF, Brandt LP, Kryger AI, Overgaard E, Hansen KD, Mikkelsen S. Computer mouse use predicts acute pain but not prolonged or chronic pain in the neck and shoulder. Occupational and Environmental Medicine. 65: 126-31. PMID 17681996 DOI: 10.1136/oem.2007.033506  0.76
2004 Danø H, Jacobsen R, Hansen KD, Petersen JK, Lynge E. Use of census data for construction of fertility history for Danish women. Scandinavian Journal of Public Health. 32: 435-41. PMID 15762028 DOI: 10.1080/14034940410028163  0.76
2004 Nybo Andersen AM, Hansen KD, Andersen PK, Davey Smith G. Advanced paternal age and risk of fetal death: a cohort study. American Journal of Epidemiology. 160: 1214-22. PMID 15583374 DOI: 10.1093/aje/  0.76
2004 Danø H, Hansen KD, Jensen P, Petersen JH, Jacobsen R, Ewertz M, Lynge E. Fertility pattern does not explain social gradient in breast cancer in denmark. International Journal of Cancer. Journal International Du Cancer. 111: 451-6. PMID 15221976 DOI: 10.1002/ijc.20203  0.76
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