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Exploration, normalization, and summaries of high density oligonucleotide array probe level data RA Irizarry, B Hobbs, F Collin, YD Beazer‐Barclay, KJ Antonellis, U Scherf, ... Biostatistics 4 (2), 249-264, 2003 | 12530 | 2003 |
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias BM Bolstad, RA Irizarry, M Åstrand, TP Speed Bioinformatics 19 (2), 185-193, 2003 | 10024 | 2003 |
Salmon provides fast and bias-aware quantification of transcript expression R Patro, G Duggal, MI Love, RA Irizarry, C Kingsford Nature methods 14 (4), 417-419, 2017 | 9616 | 2017 |
Summaries of Affymetrix GeneChip probe level data RA Irizarry, BM Bolstad, F Collin, LM Cope, B Hobbs, TP Speed Nucleic acids research 31 (4), e15-e15, 2003 | 5975 | 2003 |
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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 | 3920 | 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 | 3637 | 2015 |
Bioinformatics and computational biology solutions using R and Bioconductor R Gentleman, V Carey, W Huber, R Irizarry, S Dudoit Springer Verlag, 2005 | 3602 | 2005 |
Epigenetic memory in induced pluripotent stem cells K Kim, A Doi, B Wen, K Ng, R Zhao, P Cahan, J Kim, MJ Aryee, H Ji, ... Nature 467 (7313), 285-290, 2010 | 2691 | 2010 |
The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores RA Irizarry, C Ladd-Acosta, B Wen, Z Wu, C Montano, P Onyango, H Cui, ... Nature genetics 41 (2), 178-186, 2009 | 2588 | 2009 |
Tackling the widespread and critical impact of batch effects in high-throughput data JT Leek, RB Scharpf, HC Bravo, D Simcha, B Langmead, WE Johnson, ... Nature Reviews Genetics 11 (10), 733-739, 2010 | 2213 | 2010 |
A model-based background adjustment for oligonucleotide expression arrays Z Wu, RA Irizarry, R Gentleman, F Martinez-Murillo, F Spencer Journal of the American statistical Association 99 (468), 909-917, 2004 | 2176 | 2004 |
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens W Li, H Xu, T Xiao, L Cong, MI Love, F Zhang, RA Irizarry, JS Liu, ... Genome biology 15, 1-12, 2014 | 2150 | 2014 |
A framework for oligonucleotide microarray preprocessing BS Carvalho, RA Irizarry Bioinformatics 26 (19), 2363-2367, 2010 | 1588 | 2010 |
Differential methylation of tissue-and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts A Doi, IH Park, B Wen, P Murakami, MJ Aryee, R Irizarry, B Herb, ... Nature genetics 41 (12), 1350-1353, 2009 | 1415 | 2009 |
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 | 1221 | 2011 |
Accounting for cellular heterogeneity is critical in epigenome-wide association studies AE Jaffe, RA Irizarry Genome biology 15, 1-9, 2014 | 1086 | 2014 |
Multiple-laboratory comparison of microarray platforms RA Irizarry, D Warren, F Spencer, IF Kim, S Biswal, BC Frank, ... Nature methods 2 (5), 345-350, 2005 | 1075 | 2005 |
Meta-analysis of gut microbiome studies identifies disease-specific and shared responses C Duvallet, SM Gibbons, T Gurry, RA Irizarry, EJ Alm Nature communications 8 (1), 1784, 2017 | 951 | 2017 |