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Kasper D. Hansen - Publications

Affiliations: 
2009 University of California, Berkeley, Berkeley, CA, United States 
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44 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2023 Kuo A, Hansen KD, Hicks SC. Quantification and statistical modeling of droplet-based single-nucleus RNA-sequencing data. Biostatistics (Oxford, England). PMID 37257175 DOI: 10.1093/biostatistics/kxad010  0.378
2020 Boukas L, Bjornsson HT, Hansen KD. Promoter CpG Density Predicts Downstream Gene Loss-of-Function Intolerance. American Journal of Human Genetics. PMID 32800095 DOI: 10.1016/J.Ajhg.2020.07.014  0.371
2019 Myint L, Wang R, Boukas L, Hansen KD, Goff LA, Avramopoulos D. A screen of 1,049 schizophrenia and 30 Alzheimer's-associated variants for regulatory potential. American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics : the Official Publication of the International Society of Psychiatric Genetics. PMID 31503409 DOI: 10.1002/Ajmg.B.32761  0.335
2019 Carosso GA, Boukas L, Augustin JJ, Nguyen HN, Winer BL, Cannon GH, Robertson JD, Zhang L, Hansen KD, Goff LA, Bjornsson HT. Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome. Jci Insight. PMID 31465303 DOI: 10.1172/Jci.Insight.129375  0.324
2019 Wulfridge P, Langmead B, Feinberg AP, Hansen KD. Analyzing whole genome bisulfite sequencing data from highly divergent genotypes. Nucleic Acids Research. PMID 31392989 DOI: 10.1093/Nar/Gkz674  0.381
2019 Myint L, Avramopoulos DG, Goff LA, Hansen KD. Linear models enable powerful differential activity analysis in massively parallel reporter assays. Bmc Genomics. 20: 209. PMID 30866806 DOI: 10.1186/S12864-019-5556-X  0.302
2019 Boukas L, Havrilla JM, Hickey PF, Quinlan AR, Bjornsson HT, Hansen KD. Coexpression patterns define epigenetic regulators associated with neurological dysfunction. Genome Research. PMID 30858344 DOI: 10.1101/Gr.239442.118  0.364
2019 Rizzardi LF, Hickey PF, Rodriguez DiBlasi V, Tryggvadóttir R, Callahan CM, Idrizi A, Hansen KD, Feinberg AP. Neuronal brain-region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability. Nature Neuroscience. PMID 30643296 DOI: 10.1038/S41593-018-0297-8  0.315
2017 Ramos M, Schiffer L, Re A, Azhar R, Basunia A, Rodriguez C, Chan T, Chapman P, Davis SR, Gomez-Cabrero D, Culhane AC, Haibe-Kains B, Hansen KD, Kodali H, Louis MS, et al. Software for the Integration of Multiomics Experiments in Bioconductor. Cancer Research. 77: e39-e42. PMID 29092936 DOI: 10.1158/0008-5472.Can-17-0344  0.326
2017 Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Reproducible RNA-seq analysis using recount2. Nature Biotechnology. 35: 319-321. PMID 28398307 DOI: 10.1038/Nbt.3838  0.337
2017 Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD. Joint bounding of peaks across samples improves differential analysis in mass spectrometry-based metabolomics. Analytical Chemistry. PMID 28221771 DOI: 10.1021/Acs.Analchem.6B04719  0.309
2017 Torres LC, Nellore A, Kammers K, Ellis S, Taub M, Hansen K, Jaffe A, Leek J. 694. RNA-Seq Samples Beyond the Known Transcriptome with Derfinder Available via Recount Biological Psychiatry. 81. DOI: 10.1016/J.Biopsych.2017.02.761  0.338
2016 Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips Iii RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biology. 17: 266. PMID 28038678 DOI: 10.1186/S13059-016-1118-6  0.436
2016 Fortin JP, Triche TJ, Hansen KD. Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics (Oxford, England). PMID 28035024 DOI: 10.1093/Bioinformatics/Btw691  0.319
2016 Li X, Liu Y, Salz T, Hansen KD, Feinberg AP. Whole genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver. Genome Research. PMID 27737935 DOI: 10.1101/Gr.211854.116  0.402
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  0.331
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  0.334
2015 Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A. Testing and validation of computational methods for mass spectrometry. Journal of Proteome Research. PMID 26549429 DOI: 10.1021/Acs.Jproteome.5B00852  0.311
2015 Kannan L, Ramos M, Re A, El-Hachem N, Safikhani Z, Gendoo DM, Davis S, Gomez-Cabrero D, Castelo R, Hansen KD, Carey VJ, Morgan M, Culhane AC, Haibe-Kains B, Waldron L. Public data and open source tools for multi-assay genomic investigation of disease. Briefings in Bioinformatics. PMID 26463000 DOI: 10.1093/Bib/Bbv080  0.401
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  0.343
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  0.384
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  0.324
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  0.312
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  0.32
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  0.417
2015 Huber W, Carey V, Davis S, Hansen KD, Morgan M. The Bioconductor channel in F1000Research F1000research. 4. DOI: 10.12688/F1000Research.6758.1  0.307
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  0.33
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  0.353
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  0.463
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  0.322
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  0.349
2014 Frazee AC, Hansen KD, Leek JT, Sabunciyan S, Irizarry RA. Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution Biostatistics. 15: 584-585. DOI: 10.1093/Biostatistics/Kxu022  0.373
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  0.325
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  0.443
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  0.316
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  0.432
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  0.393
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  0.327
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  0.649
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  0.45
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  0.622
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  0.687
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  0.65
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  0.688
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