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Computational Biology

AC Frazee, S Sabunciyan, KD Hansen, RA Irizarry, JT Leek†.
Differential expression analysis of RNA-seq data at single-base resolution.
Biostatistics 2013. DOI PMID

ML Smith†, KA Baggerly, H Bengtsson, ME Ritchie, KD Hansen†.
illuminaio: An open source IDAT parsing tool for Illumina microarrays.
F1000 Research 2013. Awaiting peer review. DOI

KD Hansen∗, S Sabunciyan∗, B Langmead, N Nagy, R Curley, G Klein, E Klein, D Salamon, AP Feinberg†.
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization.
Genome Research 2013. DOI PMID

C Ladd-Acosta, KD Hansen, E Briem, MD Fallin, WE Kaufmann, AP Feinberg†.
Common DNA methylation alterations in multiple brain regions in autism.
Molecular Psychiatry 2013. DOI PMID

KD Hansen∗,†, B Langmead∗†, RA Irizarry†.
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Genome Biology 2012, 13(10):R83. DOI PMID
Highly accessed

BR Herb∗, F Wolschin∗, KD Hansen, MJ Aryee, B Langmead, RA Irizarry, GV Amdam†, AP Feinberg†.
Reversible switching between epigenetic states in honeybee behavioral subcastes.
Nature Neuroscience 2012, 15(10):1371-1373. DOI PMID
  Coverage by Nature News URL
  Coverage by LA Times URL
  Coverage by The New Republic URL
  Coverage by the Guardian UK URL
  Coverage by Discover Magazine URL
  Coverage by The Scientist URL

J Tung†, LB Barreiro, ZP Johnson, KD Hansen, V Michopoulos, D Toufexis, K Michelini, ME Wilson, Y Gilad†.
Social environment is associated with gene regulatory variation in the rhesus macaque immune system.
PNAS 2012, 109(17):6490-6495. DOI PMID
  Faculty of 1000 reviews f1000
  Coverage by NY times URL
  Coverage by Genomeweb URL
  Coverage by Videnskab.db URL

S Munshaw, HS Hwang, M Torbenson, J Quinn, KD Hansen, J Astemborski, SH Mehta, SC Ray, DL Thomas, A Balagopal†.
Laser captured hepatocytes show association of association of butyrylcholinesterase gene loss and fibrosis progression
 in hepatitis C infected drug users.
Hepatology 2012, 56(2):544-554. DOI PMID

KD Hansen, RA Irizarry, and Z WU†.
Removing technical variability in RNA-Seq data using conditional quantile normalization.
Biostatistics 2012, 13(2):204-216. DOI PMID

KD Hansen∗, W Timp∗, H Corrada Bravo∗, S Sabunciyan∗, B Langmead∗, OG McDonald, B Wen, H Wu, Y Liu, D Diep,
 E Briem, K Zhang, RA Irizarry†, and AP Feinberg†.
Increased methylation variation in epigenetic domains across cancer types.
Nature Genetics 2011, 43:768-775. DOI PMID
  Faculty of 1000 reviews f1000
  Comment by JP Issa in Nat Genet, Epigenetic variation and cellular Darwinism. DOI PMID
  Described in Cell DOI
  Coverage by Genomeweb URL

KD Hansen, Z Wu, RA Irizarry†, and JT Leek†.
Sequencing technology does not eliminate biological variability.
Nature Biotechnology 2011, 29:572-573. DOI PMID

AN Brooks∗, L Yang∗, MO Duff, KD Hansen, JW Park, S Dudoit, SE Brenner†, and BR Graveley†.
Conservation of an RNA regulatory map between Drosophila and mammals.
Genome Research 2011, 21(2):193-202. DOI PMID

The modENCODE Consortium, et al.
Identification of functional elements and regulatory circuits by Drosophila modENCODE.
Science 2010, 330:1787-1797. DOI PMID

B Langmead, KD Hansen, and JT Leek†.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Genome Biology 2010, 11:R83. DOI PMID
Highly accessed

KD Hansen†, SE Brenner, and S Dudoit.
Biases in Illumina transcriptome sequencing caused by random hexamer priming.
Nucleic Acids Research 2010, 38(12):e131. DOI PMID

JH Bullard∗,†, EA Purdom∗, KD Hansen, and S Dudoit.
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.
BMC Bioinformatics 2010, 11:94. DOI PMID
Highly accessed

KD Hansen∗, LF Lareau∗, M Blanchette, RE Green, Q Meng, J Rehwinkel, FL Gallusser, E Izaurralde, DC Rio, S Dudoit, and SE Brenner†.
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila.
PLoS Genetics 2009, 5(6):e1000525. DOI PMID

A Lee∗, KD Hansen∗, J Bullard∗, S Dudoit, and G Sherlock†.
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 2008, 4(12):e1000299. DOI PMID

Computational Biology, Preprints

KD Hansen, RA Irizarry, and Z WU†.
Removing technical variability in RNA-Seq data using conditional quantile normalization.
Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 227. PREPRINT

JH Bullard∗, EA Purdom∗, KD Hansen, S Durinck, and S Dudoit.
Statistical Inference in mRNA-Seq: Exploratory Data Analysis and Differential Expression.
Working Paper 247, U.C. Berkeley, Division of Biostatistics, 2009. URL

H Bengtsson†, K Simpson, J Bullard, and KD Hansen.
aroma.affymetrix: A generic framework in R for analyzing small to very large Affymetrix data sets in bounded memory.
Technical Report 745, Department of Statistics, University of California, Berkeley, 2008. PDF

Other

JH Andersen†, M Harhoff, S Grimstrup, I Vilstrup, CF Lassen, LPA Brandt, AI Kryger, E Overgaard, KD Hansen, and S Mikkelsen.
Computer mouse use predicts acute pain but not prolonged or chronic pain in the neck and shoulder.
Occup Environ Med 2008, 65(2):126-131. DOI PMID

A-M Nybo Andersen†, KD Hansen, PK Andersen, and G Davey Smith.
Advanced paternal age and risk of fetal death: a cohort study.
American Journal of Epidemiology 2004, 160(12):1214-1222. DOI PMID

H Danø†, KD Hansen, P Jensen, JH Petersen, R Jacobsen, M Ewertz, and E Lynge.
Fertility pattern does not explain social gradient in breast cancer in Denmark.
International Journal of Cancer 2004, 111(3):451-456. DOI PMID

H Danø†, R Jacobsen, KD Hansen, JK Petersen, and E Lynge.
Use of census data for construction of fertility history for danish women.
Scandinavian Journal of Public Health 2004, 32:435-441. DOI PMID

K Schultz-Larsen, S Kreiner, S Hanning, N Støvring, KD Hansen, and S Lendal.
Den danske ældrepleje under forandring ("An Evaluation of the quality of the danish elder care").
Govermental report, 2004.

KD Hansen and E Hansen.
Opgaver i videregående sandsynlighedsregning ("Exercises in Advanced Probability").
University of Copenhagen (HCØ Tryk), 2000.

∗ indicates equal contribution
† indicates corresponding author