Publications

Publication Repositories

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

Current Preprints

A Ravichandran, P Parsana, R Keener, KD Hansen, A Battle.
Aggregation of recount3 RNA-seq data improves the inference of consensus and tissue-specific gene co-expression networks.
bioRxiv 2024, 2024.01.20.576447.
DOI |

A Razi^∗, CL Lo^∗, S Wang, JT Leek^†, KD Hansen^†.
Genotype prediction of 336,463 samples from public expression data.
bioRxiv 2023, 2023.10.21.562237.
DOI |

T Kayikcioglu^∗, JS Zarb^∗, S Mohapatra, CT Lin, JA London, KD Hansen, R Fishel, T Ha.
Massively parallel single molecule tracking of sequence-dependent DNA mismatch repair in vivo.
bioRxiv 2023, 2023.01.08.523062.
DOI |

BK Johnson, JP Fortin, KD Hansen, H Shen^†, T Triche Jr^†.
Compartmap enables inference of higher-order chromatin structure in individual cells from scRNA-seq and scATAC-seq.
bioRxiv 2021, 2021.05.17.444465.
DOI |

C Ladd-Acosta^∗, SV Andrews^∗, KM Bakulski, JI Feinberg, R Tryggvadottir, R Yao, LA Croen, I Hertz-Picciotto, CJ Newschaffer, CM Salafia, AP Feinberg, KD Hansen, MD Fallin.
Placenta DNA methylation at ZNF300 is associated with fetal sex and placental morphology.
bioRxiv 2021, 2021.03.05.433992.
DOI |

L Boukas, HT Bjornsson^†, KD Hansen^†.
Purifying selection acts on germline methylation to modify the CpG mutation rate at promoters.
bioRxiv 2020, 2020.07.04.187880.
DOI | Tweetorial |

Computational Biology

2024

CW Gao, WY Lin, RC Riddle, S Chopra, L Boukas, KD Hansen, HT Bjornsson, JA Fahrner.
Growth retardation in a mouse model of Kabuki syndrome 2 bears mechanistic similarities to Kabuki syndrome 1.
PLOS Genetics 2024, 20(6):e1011310.
DOI | PMID | PMC | Preprint |

K Fletez-Brant, Y Qiu, DU Gorkin, M Hu, KD Hansen.
Removing unwanted variation between samples in Hi-C experiments.
Briefings in Bioinformatics 2024, 25(3):bbae217.
DOI | PMID | PMC | Preprint |

L Boukas^∗, TR Luperchio^∗, A Razi, KD Hansen^†, HT Bjornsson^†.
Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice.
Genome Research 2024, 34:696-710.
DOI | PMID | Preprint |

CW Gao^∗, WY Lin^∗, RC Riddle, P Kushwaha, L Boukas, HT Bjornsson, KD Hansen, JA Fahrner.
A mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition.
JCI Insight, 9(1):e173392.
DOI | PMID | PMC | Preprint |

A Kuo, KD Hansen, SC Hicks.
Quantification and statistical modeling of Chromium-based single-nucleus RNA-sequencing data.
Biostatistics 2024, in press.
DOI | PMID | Preprint |

2023

SC Zheng, G Stein-O’Brien, L Boukas, LA Goff^†, KD Hansen^†.
Pumping the brakes on RNA velocity by understanding and interpreting RNA velocity estimates.
Genome Biology 2023, 24(1):246.
DOI | PMID | PMC | Preprint |

P Wulfridge^∗, A Davidovich^∗, AC Salvador^∗, GC Manno, R Tryggvadottir, A Idrizi, MN Huda, BJ Bennett, LG Adams, KD Hansen^†, DW Threadgill^†, AP Feinberg^†.
Precision pharmacological reversal of strain-specific diet-induced metabolic syndrome in mice informed by epigenetic and transcriptional regulation.
PLOS Genetics 2023, 19(10):e1010997.
DOI | PMID | PMC | Preprint |

EKW Lo^∗, BM Mears^∗, HC Maurer, A Idrizi, KD Hansen, ED Thompson, RH Hruban, KP Olive, AP Feinberg.
Comprehensive DNA Methylation Analysis Indicates That Pancreatic Intraepithelial Neoplasia Lesions Are Acinar-Derived and Epigenetically Primed for Carcinogenesis.
Cancer Research 2023, 83(11):1905-1916.
DOI | PMID | PMC |

LM Weber, A Saha, A Datta, KD Hansen, SC Hicks.
nnSVG for the scalable identification of spatially variable genes using nearest-neighbor Gaussian processes.
Nature Communications 2023, 14:4059.
DOI | PMID | PMC | Preprint | Tweetorial (Weber) |

A Morin^∗, EE Thompson^∗, BA Helling^∗, LE Shorey-Kendrick, P Faber, Pieter, T Gebretsadik, LB Bacharier, M Kattan, GT O’Connor, K Rivera-Spoljaric, RA Wood, KC Barnes, RA Mathias, MC Altman, KD Hansen, CT McEvoy, ER Spindel, T Hartert, DJ Jackson, JE Gern, CG McKennan^†, C Ober^†, Program collaborators for Environmental Influences on Child Outcomes and Children’s Respiratory and Environmental Workgroup.
A functional genomics pipeline to identify high-value asthma and allergy CpGs in the human methylome.
The Journal of Allergy and Clinical Immunology 2023, 151(6):1609-1621.
DOI | PMID | Preprint |

SK Maden, B Walsh, K Ellrott, KD Hansen, R Thompson, A Nellore.
recountmethylation enables flexible analysis of public blood DNA methylation array data.
Bioinformatics Advances 2023, 3(1):vbad020.
DOI | PMID | PMC | Preprint |

2022

SC Zheng, G Stein-O’Brien, JJ Augustin, J Slosberg, GA Carosso, B Winer, G Shin, HT Bjornsson, LA Goff^†, KD Hansen^†.
Universal prediction of cell cycle position using transfer learning.
Genome Biology 2022, 23:41.
DOI | PMID | PMC | Preprint | Tweetorial | Tweetorial (LA Goff) |

A Arneson, A Haghani, MJ Thompson, M Pellegrini, SO Kwon, H Vu, E Maciejewski, M Yao, CZ Li, AT Lu, M Morselli, L Rubbi, B Barnes, KD Hansen, W Zhou, CE Breeze, J Ernst, S Horvath.
A mammalian methylation array for profiling methylation levels at conserved sequences.
Nature Communications 2022, 13(1):783.
DOI | PMID | PMC |

JR Hu, L Myint, AS Levery, J Coresh, LA Inker, ME Grams, E Guallar, KD Hansen, EP Rhee, T Shafi.
A metabolomics approach identified toxins associated with uremic symptoms in advanced chronic kidney disease.
Kidney International 2022, 201(2):369-378.
DOI | PMID | PMC |

2021

C Wilks, SC Zheng, FY Chen, R Charles, B Solomon, JP Ling, EL Imada, D Zhang, L Joseph, LT Leek, AE Jaffe, A Nellore, L Collado-Torres, KD Hansen^†, B Langmead^†.
recount3: summaries and queries for large-scale RNA-seq expression and splicing.
Genome Biology 2022, 22:323.
DOI | PMID | PMC | Preprint |

TR Luperchio^∗, L Boukas^∗, L Zhang, GO Pilarowski, J Jiang, A Kalinousky, KD Hansen^†, HT Bjornsson^†.
Leveraging the Mendelian disorders of the epigenetic machinery to systematically map functional epigenetic variation.
eLife 2021;10:e65884.
DOI | PMID | PMC | Tweetorial | Preprint |

LF Rizzardi, PF Hickey, A Idrizi, R Tryggvadottir, CM Callahan, KE Stephens, SD Taverna, H Zhang, S Ramazanoglu, GTEx Consortium, KD Hansen^†, AP Feinberg^†.
Human brain region-specific variably methylated regions are enriched for heritability of distinct neuropsychiatric traits.
Genome Biology 2021, 22:116.
DOI | PMID | PMC | Readcube | Preprint |

SK Maden, RF Thompson, KD Hansen, A Nellore.
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.
NAR Genomics and Bioinformatics 2021, 3(2):lqab025.
DOI | PMID | PMC | Free version | Preprint |

JJ Credle, ML Robinson, J Gunn, D Monaco, B Sie, A Tchir, J Hardick, X Zheng, K Shaw-Saliba, RE Rothman, SH Eshleman, A Pekosz, KD Hansen, H Mostafa, M Steinegger, HB Larman.
Highly multiplexed oligonucleotide probe-ligation testing enables efficient extraction-free SARS-CoV-2 detection and viral genotyping.
Modern Pathology 2021, In press.
DOI | PMID | PMC | Preprint |

2020

I Lee, R Razaghi, T Gilpatrick, M Molnar, A Gershman, N Sadowski, FJ Sedlazeck, KD Hansen, JT Simpson, W Timp.
Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing.
Nature Methods 2020, 17(12):1191-1199.
DOI | PMID | PMC | Readcube |

S Rajagopalan^∗†, B Park^∗, R Palanivel, V Vinayachandran, JA Deiuliis, RS Gangwar, LM Das, J Yin, Y Choi, S Al-Kindi, MK Jain, KD Hansen, Shyam Biswal^†.
Metabolic effects of air pollution exposure and reversibility.
JCI 2020, 130(11):6034-6040.
DOI | PMID | PMC |

L Myint, R Wang, L Boukas, KD Hansen, LA Goff, DG Avramopoulos.
A screen of 1,049 schizophrenia and 30 Alzheimer’s-associated variants for regulatory potential
American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 2030, 183(1):61-73.
DOI | PMID | PMC | Preprint |

2019

DU Gorkin^∗, Y Qiu^∗, M Hu^∗,†, K Fletez-Brant, T Liu, AD Schmitt, A Noor, J Chiou, KJ Gaulton, J Sebat, Y Li, KD Hansen, B Ren^†.
Common DNA sequence variation influences 3-dimensional conformation of the human genome.
Genome Biology 2019, 20:255
DOI | PMID | PMC | Preprint |

JA Fahrner^†, and W-Y Lin, RC Riddle, L Boukas, VB DeLeon, S Chopra, SE Lad, TR Luperchio, KD Hansen, HT Bjornsson^†.
Precocious chondrocyte differentiation disrupts skeletal growth in Kabuki syndrome mice.
JCI Insight 2019, 4(20):129380.
DOI | PMID | PMC | Preprint |

GA Carosso, L Boukas , JJ Augustin, HN Nguyen, BL Winer, GH Cannon, JD Robertson, L Zhang, KD Hansen, Johanna D, LA Goff, HT Bjornsson.
Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome.
JCI Insight 2019, 4(20):129375.
DOI | PMID | PMC | Preprint |

P Wulfridge, B Langmead, AP Feinberg, KD Hansen^†.
Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.
Nucleic Acids Research 2019, 47(19):e117.
DOI | PMID | PMC | Preprint |

L Myint, DG Avramopoulos, LA Goff, KD Hansen.
Linear models enable powerful differential activity analysis in massively parallel reporter assays.
BMC Genomics 2019, 20:209.
DOI | PMID | PMC | Preprint |

L Boukas, JM Havrilla, PF Hickey, AR Quinlan, HT Bjornsson^†, KD Hansen^†.
Co-expression patterns define epigenetic regulators associated with neurological dysfunction.
Genome Research 2019, 29(4):532-542.
DOI | PMID | PMC | Preprint |

LF Rizzardi^∗, PF Hickey^∗, VR DiBlasi, R Tryggvadottir, CM Callahan, A Idrizi, KD Hansen^†, AP Feinberg^†.
Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability.
Nature Neuroscience 2019, 22(2):307-316.
UCSC Genome Browser Hub
DOI | PMID | PMC | Preprint |

2018

V Gaysinskaya, BF Miller, GW van der Heijden, KD Hansen, A Bortvin.
Transient reduction of DNA methylation at the onset of meiosis in male mice.
Epigenetics & Chromatin 2018, 11(1):15.
DOI | PMID | PMC | Preprint |

WT Barrington, P Wulfridge, AE Wells, CM Rojas, SYF Howe, A Perry, K Hua, MA Pellizzon, KD Hansen, BH Voy, BJ Bennett, D Pomp, AP Feinberg, DW Threadgill.
Improving metabolic health through precision dietetics in mice.
Genetics 2018, 208(1):399-417.
DOI | PMID | PMC |

2017

R Marcel, LSchiffer, A Re, RA Azhar, A Basunia, C Rodriguez, T Chan, P Chapman, SR Davis, D Gomez-Cabrero, AC Culhane, B Haibe-Kains, KD Hansen, H Kodali, MS Louis, AS Mer, M Riester, M Morgan, VJ Carey, Vince, L Waldron.
Software for the Integration of Multiomics Experiments in Bioconductor.
Cancer Research 2017, 77(21):e39-e42.
DOI | PMID | PMC | Preprint |

L Collado-Torres, A Nellore, K Kammers, SE Ellis, MA Taub, KD Hansen, AE Jaffe, B Langmead, JT Leek.
Reproducible RNA-seq analysis using recount2.
Nature Biotechnology 2017, 35(4):319-321.
DOI | PMID | PMC | Preprint |

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 | PMC |

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, 89(6):3517-3523.
DOI | PMID | PMC |

JP Fortin, T Triche Jr, KD Hansen^†.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
Bioinformatics 2017, 33(4):558-560.
DOI | PMID | PMC | Preprint |

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 |

2016

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 | Preprint |
↳ 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 | Preprint |

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 | Preprint |

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 | Preprint |

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 |

2015

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 | Preprint |

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 | Preprint |
↳ 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 |

2014

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 | Preprint |

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 |

2013

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 |

2012

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 | Preprint |

2011

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 |

2010

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 | Preprint |

2009 and earlier

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

SC Zheng, S Beck, AE Jaffe, DC Koestler, KD Hansen, AE Houseman, RA Irizarry, M Widschwendter, AE Teschendorff.
Correcting For Cell-Type Heterogeneity In Epigenome-Wide Association Studies: Premature Analyses And Conclusions.
bioRxiv 2017, 121533.
DOI |

Books

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

Published Preprints

K Fletez-Brant, Y Qiu, DU Gorkin, M Hu, KD Hansen.
Removing unwanted variation between samples in Hi-C experiments.
bioRxiv 2020, 214361.
DOI |

CW Gao^∗, WY Lin^∗, RC Riddle, P Kushwaha, L Boukas, HT Bjornsson, KD Hansen, JA Fahrner.
Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition.
bioRxiv 2023, 2023.06.23.546270.
DOI |

P Wulfridge^∗, A Davidovich^∗, AC Salvador^∗, GC Manno, R Tryggvadottir, A Idrizi, MN Huda, BJ Bennett, LG Adams, KD Hansen^†, DW Threadgill^†, AP Feinberg^†.
Precision pharmacological reversal of genotype-specific diet-induced metabolic syndrome in mice informed by transcriptional regulation.
bioRxiv 2023, 2023.04.25.538156.
DOI |

SC Zheng, G Stein-O’Brien, L Boukas, LA Goff^†, KD Hansen^†.
Pumping the brakes on RNA velocity - understanding and interpreting RNA velocity estimates.
bioRxiv 2022, 2022.06.19.494717.
DOI |

LM Weber, A Saha, A Datta, KD Hansen, SC Hicks.
nnSVG: scalable identification of spatially variable genes using nearest-neighbor Gaussian processes.
bioRxiv 2022, 2022.05.16.492124.
DOI | Tweetorial (Weber) |

A Kuo, KD Hansen, SC Hicks.
Quantification and statistical modeling of Chromium-based single-nucleus RNA-sequencing data.
bioRxiv 2022, 2022.05.20.492835.
DOI |

SK Maden, B Walsh, K Ellrott, KD Hansen, R Thompson, A Nellore.
recountmethylation enables flexible analysis of public blood DNA methylation array data.
bioRxiv 2022, 2022.05.19.492680.
DOI |

Y Wang, SC Hicks, KD Hansen.
Co-expression analysis is biased by a mean-correlation relationship.
bioRxiv 2020, 2020.02.13.944777.
DOI | Tweetorial |

SC Zheng, G Stein-O’Brien, JJ Augustin, J Slosberg, GA Carosso, B Winer, G Shin, HT Bjornsson, LA Goff^†, KD Hansen^†.
Universal prediction of cell cycle position using transfer learning.
bioRxiv 2021, 2021.04.06.438463.
DOI | Tweetorial | Tweetorial (LA Goff) |

TR Luperchio^∗, L Boukas^∗, L Zhang, GO Pilarowski, J Jiang, A Kalinousky, KD Hansen^†, HT Bjornsson^†.
Leveraging the Mendelian Disorders of the Epigenetic Machinery to Systematically Map Functional Epigenetic Variation.
bioRxiv 2020, 2020.11.08.373456.
DOI | Tweetorial |

SK Maden, RF Thompson, KD Hansen, A Nellore.
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.
bioRxiv 2020, 2020.11.17.387548.
DOI |

LF Rizzardi, PF Hickey, A Idrizi, R Tryggvadottir, CM Callahan, KE Stephens, SD Taverna, H Zhang, S Ramazanoglu, GTEx Consortium, KD Hansen^†, AP Feinberg^†.
Human brain region-specific variably methylated regions (VMRs) are enriched for heritability of distinct neuropsychiatric traits.
bioRxiv 2021, 2021.01.02.425010.
DOI |

L Boukas, HT Bjornsson, KD Hansen.
Promoter CpG density predicts downstream gene loss-of-function intolerance.
bioRxiv 2020, 10.1101/2020.02.15.936351.
DOI | Tweetorial |

DU Gorkin, Y Qiu, M Hu^†, K Fletez-Brant, T Liu, AD Schmitt, A Noor, J Chiou, KJ Gaulton, J Sebat, Y Li, KD Hansen, B Ren^†.
Common DNA sequence variation influences 3-dimensional conformation of the human genome.
bioRxiv 2019, 592741
DOI |

L Myint, R Wang, L Boukas, KD Hansen, LA Goff, DG Avramopoulos.
Testing the Regulatory Consequences of 1,049 Schizophrenia Associated Variants With a Massively Parallel Reporter Assay.
bioRxiv 2018, 447557
DOI |

P Wulfridge, B Langmead, AP Feinberg, KD Hansen^†.
Analyzing whole genome bisulfite sequencing data from highly divergent genotypes.
bioRxiv 2018, 076844__ DOI |

L Myint, DG Avramopoulos, LA Goff, KD Hansen.
Linear models enable powerful differential activity analysis in massively parallel reporter assays.
bioRxiv 2017, 196394.
DOI | | Publish in BMC Genomics 2019

L Boukas, JM Havrilla, AR Quinlan, HT Bjornsson, KD Hansen.
Co-expression patterns define epigenetic regulators associated with neurological dysfunction.
bioRxiv 2018, 219097
DOI | | Published in Genome Research 2019

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, 120386.
UCSC Genome Browser Hub
DOI | | Published in Nature Neuroscience 2019

V Gaysinskaya, BF Miller, GW van der Heijden, KD Hansen, A Bortvin.
Transient Reduction Of DNA Methylation At The Onset Of Meiosis In Male Mice.
bioRxiv 2017, 177535.
DOI | | Published in Epigenetics & Chromatin 2018

M Ramos, L Schiffer, A Re, A Azhar, A Basunia, CR Cabrera, T Chan, P Chapman, S Davis, D Gomez-Cabrero, AC Culhane, B Haibe-Kains, KD Hansen, H Kodali, MS Louis, AS Mer, M Riester, M Morgan, V Carey, L Waldron.
Software for the integration of multi-omics experiments in Bioconductor.
bioRxiv 2017, 144774.
DOI | | Published in Cancer Research 2017

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, 068478.
DOI | | Published in Nature Biotechnology 2017.

JP Fortin, T Triche Jr, KD Hansen^†.
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array.
bioRxiv 2016, 065490.
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, 059659.
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, 062588.
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, 035287.
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, 016022.
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, 019000.
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, 002956.
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