Publication Repositories

Google Scholar Citations | PubMed | ORCID: 0000-0003-0086-0687 | Europe PMC Citations | Impactstory

Current Preprints

L Rizzardi, P Hickey, V Rodriguez, R Tryggvadottir, C Callahan, A Idrizi, KD Hansen, AP Feinberg.
Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric disease heritability.
bioRxiv 2017.
DOI |

P Wulfridge, B Langmead, AP Feinberg, KD Hansen.
Choice of reference genome can introduce massive bias in bisulfite sequencing data.
bioRxiv, 2016.
DOI |

L Collado-Torres, A Nellore, K Kammers, SE Ellis, MA Taub, KD Hansen, AE Jaffe, B Langmead, JT Leek.
recount: A large-scale resource of analysis-ready RNA-seq expression data.
bioRxiv, 2016.
DOI |

Computational Biology

SC Zheng, S Beck, AE Jaffe, DC Koestler, KD Hansen, AE Houseman, RA Irizarry, and AE Teschendorff.
Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses.
Nature Methods 2017, 14(3):216-217.
DOI | PMID |

L Myint, A Kleensang, L Zhao, T Hartung, and KD Hansen.
Joint bounding of peaks across samples improves differential analysis in mass spectrometry-based metabolomics.
Analytical Chemistry 2017, in press.
DOI | PMID |

JP Fortin, T Triche Jr, KD Hansen.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Bioinformatics 2017, in press.
DOI | PMID |

JS Benjamin, GO Pilarowski, GA Carossoa, L Zhang, DL Huso, LA Goff, HJ Vernon, KD Hansen, and HT Bjornsson.
A ketogenic diet rescues hippocampal memory defects in a mouse model of Kabuki syndrome.
PNAS 2017, 114(1):125-130.
DOI | PMID | PMC |

A Nellore, AE Jaffe, JP Fortin, J Alquicira-Hernández, L Collado-Torres, S Wang, RA Phillips, N Karbhari, KD Hansen, B Langmead, and JT Leek.
Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.
Genome Biology 2016, 17:266.
DOI | PMID | PMC |
↳ Research highlight by Robert and Watson in Genome Biology | DOI

SV Andrews, C Ladd-Acosta, AP Feinberg, KD Hansen, MD Fallin.
‘Gap hunting’ to characterize clustered probe signals in Illumina methylation array data.
Epigenetics and Chromatin 2016, 9:56.
DOI | PMID | PMC |

X Li, Y Liu, T Salz, KD Hansen, AP Feinberg.
Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver.
Genome Research 2016, 26(12):1730-1741.
DOI | PMID | PMC |

A Nellore, C Wilks, KD Hansen, JT Leek, and B Langmead.
Rail-dbGaP: a protocol and tool for analyzing protected genomic data in a commercial cloud.
Bioinformatics 2016, 32(16):2551-2553.
DOI | PMID | PMC |

L Kannan, M Ramos, A Re, N El-Hachem, A Safikhani, DMA Gendoo, S Davis, S Gomez-Cabrero, R Castelo, KD Hansen, VJ Carey, M Morgan, AC Culhane, B Haibe-Kains, and L Waldron.
Public data and open source tools for multi-assay genomic investigation of disease.
Brief Bioinformatics 2016, 17(4):603-615.
DOI | PMID | PMC |

L Gatto, KD Hansen, MR Hoopmann, H Henning, O Kohlbacher, and A Beyer.
Testing and validation of computational methods for mass spectrometry.
Journal of Proteome Research 2016, 15(3):809-814.
DOI | PMID | PMC |

AR Vandiver, A Idrizi, L Rizzardi, AP Feinberg, and KD Hansen.
DNA methylation is stable during replication and cell cycle arrest.
Scientific Reports 2015, 5:17911.
DOI | PMID | PMC |

A Pacis, L Tailleux, AM Morin, J Lambourne, JL Maclsaac, V Yotova, A Dumaine, A Danckaert, F Luca, J Grenier, KD Hansen, B Gicquel, M Yu, A Pai, C He, J Tung, T Pastinen, MS Kobor, R Pique-Regi, Y Gilad, and LB Barreiro.
Bacterial infection remodels the DNA methylation landscape of human dendritic cells.
Genome Research 2015, 25(12):1801-1811.
DOI | PMID | PMC |

JP Fortin and KD Hansen.
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.
Genome Biology 2015, 16:180.
DOI | PMID | PMC |
↳ Research highlight by Mourad and Cuvier in Genome Biology | DOI

AR Vandiver, RA Irizarry, KD Hansen, LA Garza, A Runarsson, Arni, X Li, AL Chien, TS Wang, SG Leung, S Kang, and AP Feinberg.
Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin.
Genome Biology 2015, 16:80.
DOI | PMID | PMC |

X Hong, K Hao, C Ladd-Acosta, KD Hansen, Tsai X, HJ Liu, X Xu, TA Thornton, D Caruso, CA Keet, Y Sun, G Wang, W Luo, R Kumar, R Fuleihan, AM Singh, Kim RE, JS Story, RS Gupta, P Gao, Z Chen, SO Walker, TR Bartell, TH Beaty, MD Fallin, R Schleimer, PG Holt, Nadeau KC, RA Wood, JA Pongracic, DE Weeks, and X Wang.
Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children.
Nature Communications 2015, 6:6304.
DOI | PMID | PMC |

MJ Ziller, KD Hansen, A Meissner, MJ Aryee.
Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.
Nature Methods 2015, 12(3):230-232.
DOI | PMID | PMC |

W Huber, VJ Carey, R Gentleman, S Anders, M Carlson, BS Carvalho, H Corrada-Bravo, S Davis, L Gatto, T Girke, R Gottardo, Florian Hahne, KD Hansen, RA Irizarry, M Lawrence, MI Love, J MacDonald, V Obenchain, AK Oleś, H Pagès, A Reyes, P Shannon, GK Smyth, D Tenenbaum, L Waldron, and M Morgan.
Orchestrating high-throughput genomic analysis with Bioconductor.
Nature Methods 2015, 12(2):115-121.
DOI | PMID | PMC |

JP Fortin, A Labbe, M Lemire, BW Zanke, TJ Hudson, EJ Fertig, CMT Greenwood and KD Hansen.
Functional normalization of 450k methylation array data improves replication in large cancer studies.
Genome Biology 2014, 15:503.
DOI | PMID | PMC |

HT Bjornsson∗,†, JS Benjamin, L Zhang, J Weissman, EE Gerber, YC Chen, RG Vaurio, MC Potter, KD Hansen, HC Dietz.
Histone deacetylase inhibition rescues structural and functional brain deficits in a mouse model of Kabuki syndrome.
Science Translational Medicine 2014, 6(256):256ra135.
DOI | PMID | PMC |

JP Fortin, EJ Fertig, KD Hansen.
shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.
F1000Research 2014, 3:175.
DOI | PMID | PMC |

MJ Aryee, AE Jaffe, H Corrada-Bravo, C Ladd-Acosta, AP Feinberg, KD Hansen, RA Irizarry.
Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays.
Bioinformatics 2014, 30(10):1363-1369.
DOI | PMID | PMC |

AC Frazee, S Sabunciyan, KD Hansen, RA Irizarry, JT Leek.
Differential expression analysis of RNA-seq data at single-base resolution.
Biostatistics 2014, 15(3):413-426.
DOI | PMID | PMC |

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 2014, 19(8):862-871.
DOI | PMID | PMC |
↳ Faculty of 1000 review URL

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 2014, 24(2):177-184.
DOI | PMID | PMC |

ML Smith, KA Baggerly, H Bengtsson, ME Ritchie, KD Hansen.
illuminaio: An open source IDAT parsing tool for Illumina microarrays.
F1000Research 2013, 2:264.
DOI | PMID | PMC |

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

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 | PMC |
↳ Coverage by Nature News URL
↳ Press coverage: LA Time | The New Republic | The Guardian UK | Discover Magazine | The Scientist

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 | PMC |
↳ Faculty of 1000 review URL
↳ Press Coverage: NY Times | Genomeweb | Videnskab.dk

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 | PMC |

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 | PMC |

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 | PMC |
↳ Comment by JP Issa in Nat Genet, Epigenetic variation and cellular Darwinism. DOI | PMID
↳ Faculty of 1000 review URL
↳ Described in Cell DOI
↳ Press Coverage: Genomeweb

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

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 | PMC |

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

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

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 | PMC |

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 | PMC |

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 | PMC |

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 | PMC |

Editorials (not peer-reviewed)

W Huber, V Carey, S Davis, KD Hansen and M Morgan.
The Bioconductor channel in F1000Research.
F1000Research 2015, 4.
DOI

Books

KD Hansen.
Bioconductor, Introduction to Core Technologies.
Leanpub, 2016.
URL

Published Preprints

A Nellore, AE Jaffe, JP Fortin, J Alquicira-Hernández, L Collado-Torres, S Wang, RA Phillips, N Karbhari, KD Hansen, B Langmead, and JT Leek.
Human splicing diversity across the Sequence Read Archive.
bioRxiv 2016.
DOI | | Published in Genome Biology 2016.

JP Fortin, T Triche Jr, KD Hansen.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array.
bioRxiv, 2016.
DOI | | Published in Bioinformatics 2017.

SV Andrews, C Ladd-Acosta, AP Feinberg, KD Hansen, MD Fallin.
‘Gap hunting’ to identify multimodal distributions of DNA methylation.
bioRxiv 2016.
DOI | | Published in Epigenetics and Chromatin 2016.

X Li, Y Liu, T Salz, KD Hansen, AP Feinberg.
Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver.
bioRxiv 2016.
DOI | | Published in Genome Research 2016.

A Nellore, C Wilks, KD Hansen, JT Leek, and B Langmead.
Rail-dbGaP: a protocol and tool for analyzing protected genomic data in a commercial cloud.
bioRxiv 2015.
DOI | | Published in Bioinformatics 2016.

A Pacis, L Tailleux, J Lambourne, V Yotova, A Dumaine, A Danckaert, F Luca, JC Grenier, KD Hansen, B Gicquel, M Yu, A Pai, J Tung, C He, T Pastinen, R Pique-Regi, Y Gilad and L Barreiro.
Bacterial Infection Remodels the DNA Methylation Landscape of Human Dendritic Cells.
bioRxiv 2015.
DOI | | Published in Genome Research 2015.

JP Fortin and KD Hansen.
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data.
bioRxiv, 2015.
DOI | | Published in Genome Biology 2015.

JP Fortin, A Labbe, M Lemire, BW Zanke, TJ Hudson, EJ Fertig, CMT Greenwood and KD Hansen.
Functional normalization of 450k methylation array data improves replication in large cancer studies.
bioRxiv, 2014.
DOI | | Published in Genome Biology 2014.

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.
URL | Published in Biostatistics 2012.

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 | Published in BMC Bioinformatics 2010.

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 | Abandoned.

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