Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays MJ Aryee, AE Jaffe, H Corrada-Bravo, C Ladd-Acosta, AP Feinberg, ... Bioinformatics 30 (10), 1363-1369, 2014 | 3707 | 2014 |
Orchestrating high-throughput genomic analysis with Bioconductor W Huber, VJ Carey, R Gentleman, S Anders, M Carlson, BS Carvalho, ... Nature methods 12 (2), 115-121, 2015 | 3476 | 2015 |
Genetic effects on gene expression across human tissues GTEx Consortium Lead analysts: Aguet François 1 Brown Andrew A. 2 3 4 Castel ... Nature 550 (7675), 204-213, 2017 | 3356 | 2017 |
The GTEx Consortium atlas of genetic regulatory effects across human tissues GTEx Consortium Science 369 (6509), 1318-1330, 2020 | 2665 | 2020 |
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments JH Bullard, E Purdom, KD Hansen, S Dudoit BMC bioinformatics 11, 1-13, 2010 | 2101 | 2010 |
Increased methylation variation in epigenetic domains across cancer types KD Hansen, W Timp, HC Bravo, S Sabunciyan, B Langmead, ... Nature genetics 43 (8), 768-775, 2011 | 1197 | 2011 |
Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE modENCODE Consortium, S Roy, J Ernst, PV Kharchenko, P Kheradpour, ... Science 330 (6012), 1787-1797, 2010 | 1084 | 2010 |
Biases in Illumina transcriptome sequencing caused by random hexamer priming KD Hansen, SE Brenner, S Dudoit Nucleic acids research 38 (12), e131-e131, 2010 | 892 | 2010 |
Functional normalization of 450k methylation array data improves replication in large cancer studies JP Fortin, A Labbe, M Lemire, BW Zanke, TJ Hudson, EJ Fertig, ... Genome biology 15 (11), 503, 2014 | 822 | 2014 |
BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions KD Hansen, B Langmead, RA Irizarry Genome biology 13, 1-10, 2012 | 765 | 2012 |
The impact of sex on gene expression across human tissues M Oliva, M Muñoz-Aguirre, S Kim-Hellmuth, V Wucher, ADH Gewirtz, ... Science 369 (6509), eaba3066, 2020 | 718 | 2020 |
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi JP Fortin, TJ Triche Jr, KD Hansen Bioinformatics 33 (4), 558-560, 2017 | 681 | 2017 |
Removing technical variability in RNA-seq data using conditional quantile normalization KD Hansen, RA Irizarry, Z Wu Biostatistics 13 (2), 204-216, 2012 | 673 | 2012 |
Dynamic landscape and regulation of RNA editing in mammals MH Tan, Q Li, R Shanmugam, R Piskol, J Kohler, AN Young, KI Liu, ... Nature 550 (7675), 249-254, 2017 | 541 | 2017 |
Cloud-scale RNA-sequencing differential expression analysis with Myrna B Langmead, KD Hansen, JT Leek Genome biology 11, 1-11, 2010 | 435 | 2010 |
Reproducible RNA-seq analysis using recount2 L Collado-Torres, A Nellore, K Kammers, SE Ellis, MA Taub, KD Hansen, ... Nature biotechnology 35 (4), 319-321, 2017 | 393 | 2017 |
Common DNA methylation alterations in multiple brain regions in autism C Ladd-Acosta, KD Hansen, E Briem, MD Fallin, WE Kaufmann, ... Molecular psychiatry 19 (8), 862-871, 2014 | 364 | 2014 |
Reversible switching between epigenetic states in honeybee behavioral subcastes BR Herb, F Wolschin, KD Hansen, MJ Aryee, B Langmead, R Irizarry, ... Nature neuroscience 15 (10), 1371-1373, 2012 | 361 | 2012 |
Social environment is associated with gene regulatory variation in the rhesus macaque immune system J Tung, LB Barreiro, ZP Johnson, KD Hansen, V Michopoulos, D Toufexis, ... Proceedings of the National Academy of Sciences 109 (17), 6490-6495, 2012 | 346 | 2012 |
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data JP Fortin, KD Hansen Genome biology 16, 1-23, 2015 | 315 | 2015 |