Harvard Catalyst Profiles

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Rafael A. Irizarry, Ph.D.

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Overview
Rafael Irizarry is a Professor of Applied Statistics at Harvard and the Dana-Farber Cancer Institute. He was recently named Chair of the Department of Data Sciences at the Dana-Farber Cancer Institute and is a Professor of Biostatistics at Harvard T.H. Chan School of Public Health.

Rafael Irizarry received his Bachelor's in Mathematics in 1993 from the University of Puerto Rico and went on to receive a Ph.D. in Statistics in 1998 from the University of California, Berkeley. His thesis work was on Statistical Models for Music Sound Signals. He joined the faculty of the Department of Biostatistics in the Johns Hopkins Bloomberg School of Public Health in 1998 and was promoted to Professor in 2007. He is now Professor of Biostatistics and Computational Biology at the Dana-Farber Cancer Institute and a Professor of Biostatistics at Harvard School of Public Health. Since 1999, Rafael Irizarry's work has focused on Genomics and Computational Biology problems. In particular, he has worked on the analysis and signal processing of microarray, next-generation sequencing, and genomic data. He is currently interested in leveraging his knowledge in translational work, e.g. developing diagnostic tools and discovering biomarkers.

Professor Irizarry also develops open source software implementing his statistical methodology. His software tools are widely used and he is one of the leaders and founders of the Bioconductor Project, an open source and open development software project for the analysis of genomic data. Bioconductor provides one of the most widely used software tools for the analysis of microarray data.

In 2009, the Committee of Presidents of Statistical Societies (COPSS) named Professor Irizarry the Presidents' Award winner. The Presidents' Award is arguably the profession's most prestigious award honoring early career contributions. In 2017 the members of Bioinformatics.org chose Dr. Irizarry the laureate of the Benjamin Franklin Award in the Life Sciences. He also received the 2009 Mortimer Spiegelman Award which honors an outstanding public health statistician under age 40. He also won the 2001 American Statistical Association Noether Young Scholar Award for researcher, younger than 35 years of age, who has significant research accomplishments in nonparametrics statistics. Dr. Irizarry was also named a fellow of the American Statistical Association in 2009. He served as the chair of the Genomics, Computational Biology and Technology Study Section (GCAT) NIH study section from 2013-2015.

Three of Rafael Irizarry's numerous publications have been named Fast Breaking Paper, New Hot Paper, or Current Classic Paper in Mathematics by Thomson Essential Science Indicators (ESI). According to the ESI's Scientist Rankings, he is one of the most highly cited researchers in Mathematics and Computer Science. One of his publications won the 2004 American Statistical Association (ASA) Outstanding Statistical Application Award. He was awarded the ASA Youden Award in Interlaboratory Testing for another of his publications. Dr. Irizarry co-edited Bioinformatics and Computational Biology Solutions using R and Bioconductor (Springer 2005), which has been translated into Chinese and Japanese.

Professor Irizarry has developed several online courses on data analysis that are offered by HarvardX and which have been completed by thousands of students. These courses are divided into two series: Data Analysis for the Life Sciences and Genomics Data Analysis. Much of the material is included in a book with an online version available for free.

Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01HG011139 (IRIZARRY, RAFAEL ANGEL) Sep 22, 2020 - Jun 30, 2025
    NIH/NHGRI
    Next Generation Computational Tools for Functional Genomics
    Role: Principal Investigator
  2. R35GM131802 (IRIZARRY, RAFAEL ANGEL) May 1, 2019 - Apr 30, 2024
    NIH/NIGMS
    Data Analysis Tools for Emerging High-Throughput Technologies
    Role: Principal Investigator
  3. R25GM114818 (IRIZARRY, RAFAEL ANGEL) Sep 29, 2014 - Aug 31, 2017
    NIH/NIGMS
    Biomedical Data Science Online Curriculum on HarvardX
    Role: Principal Investigator
  4. U54CA151838 (POMPER, MARTIN G) Aug 25, 2010 - Jul 31, 2015
    NIH/NCI
    Center of Cancer Nanotechnology Excellence at Johns Hopkins
    Role: Co-Principal Investigator
  5. R01HG005220 (IRIZARRY, RAFAEL ANGEL) Aug 11, 2010 - May 31, 2015
    NIH/NHGRI
    Overcoming bias and unwanted variability in next generation sequencing
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Ploenzke M, Irizarry R. Reassessing pharmacogenomic cell sensitivity with multilevel statistical models. Biostatistics. 2022 Mar 12. PMID: 35277956.
    Citations:    Fields:    
  2. Robles-Fontán MM, Nieves EG, Cardona-Gerena I, Irizarry RA. Effectiveness estimates of three COVID-19 vaccines based on observational data from Puerto Rico. Lancet Reg Health Am. 2022 May; 9:100212. PMID: 35229081.
    Citations: 1     
  3. Schnell A, Huang L, Singer M, Singaraju A, Barilla RM, Regan BML, Bollhagen A, Thakore PI, Dionne D, Delorey TM, Pawlak M, Meyer Zu Horste G, Rozenblatt-Rosen O, Irizarry RA, Regev A, Kuchroo VK. Stem-like intestinal Th17 cells give rise to pathogenic effector T cells during autoimmunity. Cell. 2021 12 22; 184(26):6281-6298.e23. PMID: 34875227.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  4. Teng M, Du D, Chen D, Irizarry RA. Characterizing batch effects and binding site-specific variability in ChIP-seq data. NAR Genom Bioinform. 2021 Dec; 3(4):lqab098. PMID: 34661103.
    Citations:    
  5. Movassagh M, Bebell LM, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar SA, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga BK, Weeks AD, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts DJ, Meier FA, Irizarry RA, Broach JR, Schiff SJ, Paulson JN. Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. NPJ Biofilms Microbiomes. 2021 09 10; 7(1):75. PMID: 34508087.
    Citations:    Fields:    Translation:HumansCells
  6. Alexander TA, Irizarry RA, Bravo HC. Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 01. PMID: 34467372.
    Citations:    Fields:    
  7. Islam N, Shkolnikov VM, Acosta RJ, Klimkin I, Kawachi I, Irizarry RA, Alicandro G, Khunti K, Yates T, Jdanov DA, White M, Lewington S, Lacey B. Excess deaths associated with covid-19 pandemic in 2020: age and sex disaggregated time series analysis in 29 high income countries. BMJ. 2021 05 19; 373:n1137. PMID: 34011491.
    Citations: 44     Fields:    Translation:Humans
  8. Braun DA, Street K, Burke KP, Cookmeyer DL, Denize T, Pedersen CB, Gohil SH, Schindler N, Pomerance L, Hirsch L, Bakouny Z, Hou Y, Forman J, Huang T, Li S, Cui A, Keskin DB, Steinharter J, Bouchard G, Sun M, Pimenta EM, Xu W, Mahoney KM, McGregor BA, Hirsch MS, Chang SL, Livak KJ, McDermott DF, Shukla SA, Olsen LR, Signoretti S, Sharpe AH, Irizarry RA, Choueiri TK, Wu CJ. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. 2021 05 10; 39(5):632-648.e8. PMID: 33711273.
    Citations: 17     Fields:    Translation:HumansCells
  9. Cable DM, Murray E, Zou LS, Goeva A, Macosko EZ, Chen F, Irizarry RA. Robust decomposition of cell type mixtures in spatial transcriptomics. Nat Biotechnol. 2022 Apr; 40(4):517-526. PMID: 33603203.
    Citations: 19     Fields:    
  10. Acosta RJ, Kishore N, Irizarry RA, Buckee CO. Quantifying the dynamics of migration after Hurricane Maria in Puerto Rico. Proc Natl Acad Sci U S A. 2020 12 22; 117(51):32772-32778. PMID: 33293417.
    Citations: 3     Fields:    
  11. Nuzzo PV, Berchuck JE, Korthauer K, Spisak S, Nassar AH, Alaiwi SA, Chakravarthy A, Shen SY, Bakouny Z, Boccardo F, Steinharter J, Bouchard G, Curran CR, Pan W, Baca SC, Seo JH, Lee GM, Michaelson MD, Chang SL, Waikar SS, Sonpavde G, Irizarry RA, Pomerantz M, De Carvalho DD, Choueiri TK, Freedman ML. Author Correction: Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat Med. 2020 Oct; 26(10):1663. PMID: 32895574.
    Citations: 3     Fields:    
  12. Kiang MV, Irizarry RA, Buckee CO, Balsari S. Every Body Counts: Measuring Mortality From the COVID-19 Pandemic. Ann Intern Med. 2020 12 15; 173(12):1004-1007. PMID: 32915654.
    Citations: 17     Fields:    Translation:HumansCellsPHPublic Health
  13. Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23. PMID: 32841603.
    Citations: 16     Fields:    Translation:HumansCells
  14. Townes FW, Hicks SC, Aryee MJ, Irizarry RA. Author Correction: Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Genome Biol. 2020 Jul 22; 21(1):179. PMID: 32698904.
    Citations: 1     Fields:    
  15. Townes FW, Irizarry RA. Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers. Genome Biol. 2020 07 03; 21(1):160. PMID: 32620142.
    Citations: 3     Fields:    Translation:HumansAnimals
  16. Nuzzo PV, Berchuck JE, Korthauer K, Spisak S, Nassar AH, Abou Alaiwi S, Chakravarthy A, Shen SY, Bakouny Z, Boccardo F, Steinharter J, Bouchard G, Curran CR, Pan W, Baca SC, Seo JH, Lee GM, Michaelson MD, Chang SL, Waikar SS, Sonpavde G, Irizarry RA, Pomerantz M, De Carvalho DD, Choueiri TK, Freedman ML. Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat Med. 2020 07; 26(7):1041-1043. PMID: 32572266.
    Citations: 40     Fields:    Translation:HumansCells
  17. Townes FW, Hicks SC, Aryee MJ, Irizarry RA. Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Genome Biol. 2019 12 23; 20(1):295. PMID: 31870412.
    Citations: 62     Fields:    
  18. Hicks SC, Irizarry RA. methylCC: technology-independent estimation of cell type composition using differentially methylated regions. Genome Biol. 2019 11 29; 20(1):261. PMID: 31783894.
    Citations: 4     Fields:    Translation:Cells
  19. Korthauer K, Chakraborty S, Benjamini Y, Irizarry RA. Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing. Biostatistics. 2019 07 01; 20(3):367-383. PMID: 29481604.
    Citations: 38     Fields:    Translation:HumansAnimalsCells
  20. McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP. A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Development. 2019 03 28; 146(6). PMID: 30923056.
    Citations: 10     Fields:    Translation:AnimalsCells
  21. Hicks SC, Irizarry RA. A Guide to Teaching Data Science. Am Stat. 2018; 72(4):382-391. PMID: 31105314.
    Citations: 1     
  22. Hicks SC, Townes FW, Teng M, Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. 2018 10 01; 19(4):562-578. PMID: 29121214.
    Citations: 119     Fields:    Translation:HumansAnimalsCells
  23. Kishore N, Marqués D, Mahmud A, Kiang MV, Rodriguez I, Fuller A, Ebner P, Sorensen C, Racy F, Lemery J, Maas L, Leaning J, Irizarry RA, Balsari S, Buckee CO. Mortality in Puerto Rico after Hurricane Maria. N Engl J Med. 2018 Jul 12; 379(2):162-170. PMID: 29809109.
    Citations: 66     Fields:    Translation:Humans
  24. Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics. 2018 04 01; 19(2):185-198. PMID: 29036413.
    Citations: 25     Fields:    Translation:Humans
  25. Shukla CJ, McCorkindale AL, Gerhardinger C, Korthauer KD, Cabili MN, Shechner DM, Irizarry RA, Maass PG, Rinn JL. High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 2018 03 15; 37(6). PMID: 29335281.
    Citations: 35     Fields:    Translation:HumansCells
  26. Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun. 2017 12 05; 8(1):1784. PMID: 29209090.
    Citations: 259     Fields:    Translation:HumansCells
  27. Teng M, Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res. 2017 11; 27(11):1930-1938. PMID: 29025895.
    Citations: 7     Fields:    Translation:Cells
  28. Nakayama RT, Pulice JL, Valencia AM, McBride MJ, McKenzie ZM, Gillespie MA, Ku WL, Teng M, Cui K, Williams RT, Cassel SH, Qing H, Widmer CJ, Demetri GD, Irizarry RA, Zhao K, Ranish JA, Kadoch C. SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet. 2017 Nov; 49(11):1613-1623. PMID: 28945250.
    Citations: 83     Fields:    Translation:HumansCells
  29. Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Res. 2017 Jun 02; 45(10):e77. PMID: 28126923.
    Citations: 16     Fields:    Translation:HumansCells
  30. Yuan GC, Cai L, Elowitz M, Enver T, Fan G, Guo G, Irizarry R, Kharchenko P, Kim J, Orkin S, Quackenbush J, Saadatpour A, Schroeder T, Shivdasani R, Tirosh I. Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 05 08; 18(1):84. PMID: 28482897.
    Citations: 90     Fields:    Translation:HumansAnimals
  31. Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017 Apr; 14(4):417-419. PMID: 28263959.
    Citations: 2020     Fields:    
  32. Zheng SC, Beck S, Jaffe AE, Koestler DC, Hansen KD, Houseman AE, Irizarry RA, Teschendorff AE. Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses. Nat Methods. 2017 02 28; 14(3):216-217. PMID: 28245219.
    Citations: 26     Fields:    Translation:HumansCells
  33. Campbell PT, Rebbeck TR, Nishihara R, Beck AH, Begg CB, Bogdanov AA, Cao Y, Coleman HG, Freeman GJ, Heng YJ, Huttenhower C, Irizarry RA, Kip NS, Michor F, Nevo D, Peters U, Phipps AI, Poole EM, Qian ZR, Quackenbush J, Robins H, Rogan PK, Slattery ML, Smith-Warner SA, Song M, VanderWeele TJ, Xia D, Zabor EC, Zhang X, Wang M, Ogino S. Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017 02; 28(2):167-176. PMID: 28097472.
    Citations: 11     Fields:    Translation:Humans
  34. Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 09 30; 17(1):203. PMID: 27716375.
    Citations: 4     Fields:    
  35. Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res. 2017 01 25; 45(2):e9. PMID: 27694310.
    Citations: 25     Fields:    Translation:Cells
  36. Love MI, Hogenesch JB, Irizarry RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol. 2016 Dec; 34(12):1287-1291. PMID: 27669167.
    Citations: 53     Fields:    
  37. Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 05 23; 17(1):107. PMID: 27215799.
    Citations: 2     Fields:    
  38. Teng M, Love MI, Davis CA, Djebali S, Dobin A, Graveley BR, Li S, Mason CE, Olson S, Pervouchine D, Sloan CA, Wei X, Zhan L, Irizarry RA. A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 Apr 23; 17:74. PMID: 27107712.
    Citations: 69     Fields:    Translation:HumansAnimals
  39. Mitchell CJ, Getnet D, Kim MS, Manda SS, Kumar P, Huang TC, Pinto SM, Nirujogi RS, Iwasaki M, Shaw PG, Wu X, Zhong J, Chaerkady R, Marimuthu A, Muthusamy B, Sahasrabuddhe NA, Raju R, Bowman C, Danilova L, Cutler J, Kelkar DS, Drake CG, Prasad TS, Marchionni L, Murakami PN, Scott AF, Shi L, Thierry-Mieg J, Thierry-Mieg D, Irizarry R, Cope L, Ishihama Y, Wang C, Gowda H, Pandey A. A multi-omic analysis of human naïve CD4+ T cells. BMC Syst Biol. 2015 Nov 06; 9:75. PMID: 26542228.
    Citations: 18     Fields:    Translation:HumansCells
  40. Hicks SC, Irizarry RA. quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol. 2015 Jun 04; 16:117. PMID: 26040460.
    Citations: 37     Fields:    Translation:HumansCells
  41. Ogino S, Campbell PT, Nishihara R, Phipps AI, Beck AH, Sherman ME, Chan AT, Troester MA, Bass AJ, Fitzgerald KC, Irizarry RA, Kelsey KT, Nan H, Peters U, Poole EM, Qian ZR, Tamimi RM, Tchetgen Tchetgen EJ, Tworoger SS, Zhang X, Giovannucci EL, van den Brandt PA, Rosner BA, Wang M, Chatterjee N, Begg CB. Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2015 Jul; 26(7):959-72. PMID: 25956270.
    Citations: 25     Fields:    Translation:HumansAnimals
  42. 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 Biol. 2015 Apr 16; 16:80. PMID: 25886480.
    Citations: 48     Fields:    Translation:HumansCells
  43. 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, Love MI, MacDonald J, Obenchain V, Oles AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015 Feb; 12(2):115-21. PMID: 25633503.
    Citations: 1242     Fields:    
  44. Timp W, Bravo HC, McDonald OG, Goggins M, Umbricht C, Zeiger M, Feinberg AP, Irizarry RA. Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med. 2014; 6(8):61. PMID: 25191524.
    Citations: 84     Fields:    
  45. Frazee AC, Hansen KD, Leek JT, Sabunciyan S, Irizarry RA. Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014 Jul; 15(3):584-5. PMID: 24936601.
    Citations:    
  46. Lahens NF, Kavakli IH, Zhang R, Hayer K, Black MB, Dueck H, Pizarro A, Kim J, Irizarry R, Thomas RS, Grant GR, Hogenesch JB. IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30; 15(6):R86. PMID: 24981968.
    Citations: 78     Fields:    Translation:HumansAnimalsCells
  47. Liu R, Dai Z, Yeager M, Irizarry RA, Ritchie ME. KRLMM: an adaptive genotype calling method for common and low frequency variants. BMC Bioinformatics. 2014 May 23; 15:158. PMID: 24886250.
    Citations:    Fields:    Translation:Humans
  48. Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014 Jun 01; 30(11):1514-21. PMID: 24501098.
    Citations: 1     Fields:    Translation:HumansCells
  49. Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014 Feb 04; 15(2):R31. PMID: 24495553.
    Citations: 448     Fields:    Translation:HumansCells
  50. 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. 2014 May 15; 30(10):1363-9. PMID: 24478339.
    Citations: 1374     Fields:    Translation:HumansCells
  51. Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT. Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014 Jul; 15(3):413-26. PMID: 24398039.
    Citations: 24     Fields:    Translation:Humans
  52. Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014; 15(12):554. PMID: 25476604.
    Citations: 533     Fields:    Translation:HumansCells
  53. McCall MN, Jaffee HA, Zelisko SJ, Sinha N, Hooiveld G, Irizarry RA, Zilliox MJ. The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D938-43. PMID: 24271388.
    Citations: 38     Fields:    Translation:HumansAnimalsCells
  54. Brebi P, Maldonado L, Noordhuis MG, Ili C, Leal P, Garcia P, Brait M, Ribas J, Michailidi C, Perez J, Soudry E, Tapia O, Guzman P, Muñoz S, Van Neste L, Van Criekinge W, Irizarry R, Sidransky D, Roa JC, Guerrero-Preston R. Genome-wide methylation profiling reveals Zinc finger protein 516 (ZNF516) and FK-506-binding protein 6 (FKBP6) promoters frequently methylated in cervical neoplasia, associated with HPV status and ethnicity in a Chilean population. Epigenetics. 2014 Feb; 9(2):308-17. PMID: 24241165.
    Citations: 9     Fields:    Translation:HumansCells
  55. Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2013 Nov 07; 503(7474):146. PMID: 24201285.
    Citations: 1     Fields:    
  56. Michels KB, Binder AM, Dedeurwaerder S, Epstein CB, Greally JM, Gut I, Houseman EA, Izzi B, Kelsey KT, Meissner A, Milosavljevic A, Siegmund KD, Bock C, Irizarry RA. Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. PMID: 24076989.
    Citations: 173     Fields:    Translation:HumansAnimalsCells
  57. Montaño CM, Irizarry RA, Kaufmann WE, Talbot K, Gur RE, Feinberg AP, Taub MA. Measuring cell-type specific differential methylation in human brain tissue. Genome Biol. 2013 Aug 30; 14(8):R94. PMID: 24000956.
    Citations: 47     Fields:    Translation:HumansCells
  58. Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H. ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics. 2013 May 01; 29(9):1182-9. PMID: 23457041.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  59. Aryee MJ, Liu W, Engelmann JC, Nuhn P, Gurel M, Haffner MC, Esopi D, Irizarry RA, Getzenberg RH, Nelson WG, Luo J, Xu J, Isaacs WB, Bova GS, Yegnasubramanian S. DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med. 2013 Jan 23; 5(169):169ra10. PMID: 23345608.
    Citations: 132     Fields:    Translation:HumansCells
  60. Beuf KD, Schrijver JD, Thas O, Criekinge WV, Irizarry RA, Clement L. Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics. 2012 Nov 15; 13:303. PMID: 23151247.
    Citations: 7     Fields:    Translation:Cells
  61. Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics. 2012 Oct 22; 13:272. PMID: 23088656.
    Citations: 25     Fields:    Translation:HumansCells
  62. McCall MN, Jaffee HA, Irizarry RA. fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics. 2012 Dec 01; 28(23):3153-4. PMID: 23044545.
    Citations: 22     Fields:    Translation:HumansCells
  63. Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012 Oct 03; 13(10):R83. PMID: 23034175.
    Citations: 270     Fields:    Translation:HumansCells
  64. Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP. Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci. 2012 Oct; 15(10):1371-3. PMID: 22983211.
    Citations: 125     Fields:    Translation:AnimalsCells
  65. Shi W, Wahba G, Irizarry RA, Bravo HC, Wright SJ. The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC Bioinformatics. 2012 May 15; 13:98. PMID: 22587526.
    Citations:    Fields:    Translation:Humans
  66. Sabunciyan S, Aryee MJ, Irizarry RA, Rongione M, Webster MJ, Kaufman WE, Murakami P, Lessard A, Yolken RH, Feinberg AP, Potash JB. Genome-wide DNA methylation scan in major depressive disorder. PLoS One. 2012; 7(4):e34451. PMID: 22511943.
    Citations: 62     Fields:    Translation:HumansCells
  67. Lin YY, Kiihl S, Suhail Y, Liu SY, Chou YH, Kuang Z, Lu JY, Khor CN, Lin CL, Bader JS, Irizarry R, Boeke JD. Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2012 Feb 08; 482(7384):251-5. PMID: 22318606.
    Citations: 45     Fields:    Translation:HumansCells
  68. Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C, Aryee MJ, Irizarry RA, Herbstman J, Witter FR, Goldman LR, Feinberg AP, Fallin MD. DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. Int J Epidemiol. 2012 Feb; 41(1):188-99. PMID: 22422452.
    Citations: 40     Fields:    Translation:HumansCells
  69. Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol. 2012 Feb; 41(1):200-9. PMID: 22422453.
    Citations: 289     Fields:    Translation:HumansCells
  70. Hansen KD, Irizarry RA, Wu Z. Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics. 2012 Apr; 13(2):204-16. PMID: 22285995.
    Citations: 259     Fields:    Translation:Humans
  71. Clement L, De Beuf K, Thas O, Vuylsteke M, Irizarry RA, Crainiceanu CM. Fast wavelet based functional models for transcriptome analysis with tiling arrays. Stat Appl Genet Mol Biol. 2012 Jan 06; 11(1):Article 4. PMID: 22499683.
    Citations: 2     Fields:    Translation:Animals
  72. Niranjan TS, Adamczyk A, Bravo HC, Taub MA, Wheelan SJ, Irizarry R, Wang T. Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biol. 2011 Sep 28; 12(9):R93. PMID: 21955804.
    Citations: 10     Fields:    Translation:Humans
  73. McCall MN, Irizarry RA. Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinformatics. 2011 Sep 16; 12:369. PMID: 21923903.
    Citations: 24     Fields:    Translation:HumansAnimalsCells
  74. Hansen KD, Wu Z, Irizarry RA, Leek JT. Sequencing technology does not eliminate biological variability. Nat Biotechnol. 2011 Jul 11; 29(7):572-3. PMID: 21747377.
    Citations: 91     Fields:    
  75. 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. Nat Genet. 2011 Jun 26; 43(8):768-75. PMID: 21706001.
    Citations: 515     Fields:    Translation:HumansCells
  76. Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylated regions. Biostatistics. 2012 Jan; 13(1):166-78. PMID: 21685414.
    Citations: 50     Fields:    Translation:HumansCells
  77. Yegnasubramanian S, Wu Z, Haffner MC, Esopi D, Aryee MJ, Badrinath R, He TL, Morgan JD, Carvalho B, Zheng Q, De Marzo AM, Irizarry RA, Nelson WG. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences. BMC Genomics. 2011 Jun 13; 12:313. PMID: 21669002.
    Citations: 35     Fields:    Translation:HumansCells
  78. Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, Koch W, Califano J, Sidransky D. NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva. Cancer Prev Res (Phila). 2011 Jul; 4(7):1061-72. PMID: 21558411.
    Citations: 55     Fields:    Translation:HumansCells
  79. McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics. 2011 May 07; 12:137. PMID: 21548974.
    Citations: 36     Fields:    Translation:Humans
  80. Scharpf RB, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I. Using the R Package crlmm for Genotyping and Copy Number Estimation. J Stat Softw. 2011 May 01; 40(12):1-32. PMID: 22523482.
    Citations: 43     
  81. Halper-Stromberg E, Frelin L, Ruczinski I, Scharpf R, Jie C, Carvalho B, Hao H, Hetrick K, Jedlicka A, Dziedzic A, Doheny K, Scott AF, Baylin S, Pevsner J, Spencer F, Irizarry RA. Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics. 2011 Apr 15; 27(8):1052-60. PMID: 21478196.
    Citations: 10     Fields:    Translation:Humans
  82. Shan L, Yang HC, Rabi SA, Bravo HC, Shroff NS, Irizarry RA, Zhang H, Margolick JB, Siliciano JD, Siliciano RF. Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model. J Virol. 2011 Jun; 85(11):5384-93. PMID: 21430059.
    Citations: 76     Fields:    Translation:HumansCells
  83. Ritchie ME, Liu R, Carvalho BS, Irizarry RA. Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. BMC Bioinformatics. 2011 Mar 08; 12:68. PMID: 21385424.
    Citations: 22     Fields:    Translation:Humans
  84. McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res. 2011 Jan; 39(Database issue):D1011-5. PMID: 21177656.
    Citations: 100     Fields:    Translation:HumansAnimals
  85. Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Med. 2010 Dec 10; 2(12):87. PMID: 21144010.
    Citations: 35     Fields:    
  86. Aryee MJ, Wu Z, Ladd-Acosta C, Herb B, Feinberg AP, Yegnasubramanian S, Irizarry RA. Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics. 2011 Apr; 12(2):197-210. PMID: 20858772.
    Citations: 46     Fields:    Translation:HumansCells
  87. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich LI, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, McKinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. Epigenetic memory in induced pluripotent stem cells. Nature. 2010 Sep 16; 467(7313):285-90. PMID: 20644535.
    Citations: 1029     Fields:    Translation:AnimalsCells
  88. Feinberg AP, Irizarry RA, Fradin D, Aryee MJ, Murakami P, Aspelund T, Eiriksdottir G, Harris TB, Launer L, Gudnason V, Fallin MD. Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med. 2010 Sep 15; 2(49):49ra67. PMID: 20844285.
    Citations: 153     Fields:    Translation:HumansCells
  89. Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010 10; 11(10):733-9. PMID: 20838408.
    Citations: 765     Fields:    
  90. Bravo HC, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics. 2010 Sep; 66(3):665-74. PMID: 19912177.
    Citations: 32     Fields:    Translation:HumansCells
  91. Ji H, Ehrlich LI, Seita J, Murakami P, Doi A, Lindau P, Lee H, Aryee MJ, Irizarry RA, Kim K, Rossi DJ, Inlay MA, Serwold T, Karsunky H, Ho L, Daley GQ, Weissman IL, Feinberg AP. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010 Sep 16; 467(7313):338-42. PMID: 20720541.
    Citations: 316     Fields:    Translation:AnimalsCells
  92. Carvalho BS, Irizarry RA. A framework for oligonucleotide microarray preprocessing. Bioinformatics. 2010 Oct 01; 26(19):2363-7. PMID: 20688976.
    Citations: 684     Fields:    
  93. Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nat Biotechnol. 2010 Aug; 28(8):827-38. PMID: 20676074.
    Citations: 343     Fields:    Translation:HumansAnimals
  94. Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA. A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics. 2011 Jan; 12(1):33-50. PMID: 20625178.
    Citations: 27     Fields:    Translation:Humans
  95. Wu H, Irizarry RA, Bravo HC. Intensity normalization improves color calling in SOLiD sequencing. Nat Methods. 2010 May; 7(5):336-7. PMID: 20431543.
    Citations: 8     Fields:    Translation:HumansCells
  96. Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA. Performance evaluation of commercial miRNA expression array platforms. BMC Res Notes. 2010 Mar 18; 3:80. PMID: 20298588.
    Citations: 17     Fields:    
  97. Schafer E, Irizarry R, Negi S, McIntyre E, Small D, Figueroa ME, Melnick A, Brown P. Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting. Blood. 2010 Jun 10; 115(23):4798-809. PMID: 20215641.
    Citations: 41     Fields:    Translation:HumansCells
  98. Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. Redefining CpG islands using hidden Markov models. Biostatistics. 2010 Jul; 11(3):499-514. PMID: 20212320.
    Citations: 85     Fields:    Translation:HumansCells
  99. McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics. 2010 Apr; 11(2):242-53. PMID: 20097884.
    Citations: 298     Fields:    Translation:Humans
  100. López-Romero P, González MA, Callejas S, Dopazo A, Irizarry RA. Processing of Agilent microRNA array data. BMC Res Notes. 2010 Jan 22; 3:18. PMID: 20205787.
    Citations: 40     Fields:    
  101. Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proc Natl Acad Sci U S A. 2010 Jan 26; 107 Suppl 1:1757-64. PMID: 20080672.
    Citations: 215     Fields:    Translation:HumansAnimalsCells
  102. Irizarry RA, Wang C, Zhou Y, Speed TP. Gene set enrichment analysis made simple. Stat Methods Med Res. 2009 Dec; 18(6):565-75. PMID: 20048385.
    Citations: 94     Fields:    Translation:Humans
  103. Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15; 26(2):242-9. PMID: 19906825.
    Citations: 26     Fields:    
  104. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J, Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP. Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet. 2009 Dec; 41(12):1350-3. PMID: 19881528.
    Citations: 565     Fields:    Translation:HumansCells
  105. Irizarry RA, Wu H, Feinberg AP. A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome. 2009 Sep-Oct; 20(9-10):674-80. PMID: 19777308.
    Citations: 29     Fields:    Translation:HumansAnimalsCells
  106. Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics. 2009 Oct 01; 25(19):2621-3. PMID: 19661241.
    Citations: 28     Fields:    
  107. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash J, Sabunciyan S, Feinberg AP. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet. 2009 Feb; 41(2):178-186. PMID: 19151715.
    Citations: 1052     Fields:    Translation:HumansCells
  108. Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet. 2009 Feb; 41(2):246-50. PMID: 19151716.
    Citations: 293     Fields:    Translation:HumansAnimalsCells
  109. Yegnasubramanian S, Haffner MC, Zhang Y, Gurel B, Cornish TC, Wu Z, Irizarry RA, Morgan J, Hicks J, DeWeese TL, Isaacs WB, Bova GS, De Marzo AM, Nelson WG. DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity. Cancer Res. 2008 Nov 01; 68(21):8954-67. PMID: 18974140.
    Citations: 103     Fields:    Translation:HumansCells
  110. Wen B, Wu H, Bjornsson H, Green RD, Irizarry R, Feinberg AP. Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Res. 2008 Nov; 18(11):1806-13. PMID: 18849526.
    Citations: 19     Fields:    Translation:HumansCells
  111. Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA. Estimating genome-wide copy number using allele-specific mixture models. J Comput Biol. 2008 Sep; 15(7):857-66. PMID: 18707534.
    Citations: 14     Fields:    Translation:Humans
  112. McCall MN, Irizarry RA. Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Res. 2008 Oct; 36(17):e108. PMID: 18676452.
    Citations: 25     Fields:    Translation:Humans
  113. Bjornsson HT, Sigurdsson MI, Fallin MD, Irizarry RA, Aspelund T, Cui H, Yu W, Rongione MA, Ekström TJ, Harris TB, Launer LJ, Eiriksdottir G, Leppert MF, Sapienza C, Gudnason V, Feinberg AP. Intra-individual change over time in DNA methylation with familial clustering. JAMA. 2008 Jun 25; 299(24):2877-83. PMID: 18577732.
    Citations: 314     Fields:    Translation:HumansCells
  114. Lin S, Carvalho B, Cutler DJ, Arking DE, Chakravarti A, Irizarry RA. Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol. 2008 Apr 03; 9(4):R63. PMID: 18387188.
    Citations: 17     Fields:    
  115. Bjornsson HT, Albert TJ, Ladd-Acosta CM, Green RD, Rongione MA, Middle CM, Irizarry RA, Broman KW, Feinberg AP. SNP-specific array-based allele-specific expression analysis. Genome Res. 2008 May; 18(5):771-9. PMID: 18369178.
    Citations: 34     Fields:    Translation:HumansCells
  116. Irizarry RA, Ladd-Acosta C, Carvalho B, Wu H, Brandenburg SA, Jeddeloh JA, Wen B, Feinberg AP. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008 May; 18(5):780-90. PMID: 18316654.
    Citations: 228     Fields:    Translation:HumansCells
  117. Rodríguez-Quiñones JF, Irizarry RA, Díaz-Blanco NL, Rivera-Molina FE, Gómez-Garzón D, Rodríguez-Medina JR. Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions. BMC Genomics. 2008 Jan 23; 9:34. PMID: 18215314.
    Citations: 10     Fields:    Translation:AnimalsCells
  118. Bengtsson H, Irizarry R, Carvalho B, Speed TP. Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics. 2008 Mar 15; 24(6):759-67. PMID: 18204055.
    Citations: 77     Fields:    Translation:Cells
  119. Peyser BD, Irizarry R, Spencer FA. Statistical analysis of fitness data determined by TAG hybridization on microarrays. Methods Mol Biol. 2008; 416:369-81. PMID: 18392981.
    Citations: 1     Fields:    Translation:Animals
  120. Meluh PB, Pan X, Yuan DS, Tiffany C, Chen O, Sookhai-Mahadeo S, Wang X, Peyser BD, Irizarry R, Spencer FA, Boeke JD. Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray. Methods Mol Biol. 2008; 416:221-47. PMID: 18392971.
    Citations: 7     Fields:    Translation:Animals
  121. Zilliox MJ, Irizarry RA. A gene expression bar code for microarray data. Nat Methods. 2007 Nov; 4(11):911-3. PMID: 17906632.
    Citations: 81     Fields:    Translation:HumansAnimals
  122. Loyo-Berríos NI, Irizarry R, Hennessey JG, Tao XG, Matanoski G. Air pollution sources and childhood asthma attacks in Catano, Puerto Rico. Am J Epidemiol. 2007 Apr 15; 165(8):927-35. PMID: 17308332.
    Citations: 18     Fields:    Translation:HumansPHPublic Health
  123. Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr; 8(2):485-99. PMID: 17189563.
    Citations: 123     Fields:    Translation:Humans
  124. Wheelan SJ, Scheifele LZ, Martínez-Murillo F, Irizarry RA, Boeke JD. Transposon insertion site profiling chip (TIP-chip). Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17632-7. PMID: 17101968.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  125. Rayner TF, Rocca-Serra P, Spellman PT, Causton HC, Farne A, Holloway E, Irizarry RA, Liu J, Maier DS, Miller M, Petersen K, Quackenbush J, Sherlock G, Stoeckert CJ, White J, Whetzel PL, Wymore F, Parkinson H, Sarkans U, Ball CA, Brazma A. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489. PMID: 17087822.
    Citations: 103     Fields:    Translation:Humans
  126. Wheelan SJ, Martínez-Murillo F, Irizarry RA, Boeke JD. Stacking the deck: double-tiled DNA microarrays. Nat Methods. 2006 Nov; 3(11):903-7. PMID: 17060914.
    Citations: 2     Fields:    Translation:AnimalsCells
  127. Yuan DS, Irizarry RA. High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics. 2006 Dec 15; 22(24):3054-60. PMID: 17060357.
    Citations: 7     Fields:    
  128. Katz S, Irizarry RA, Lin X, Tripputi M, Porter MW. A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. BMC Bioinformatics. 2006 Oct 23; 7:464. PMID: 17059591.
    Citations: 34     Fields:    
  129. Takahashi H, McCaffery JM, Irizarry RA, Boeke JD. Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell. 2006 Jul 21; 23(2):207-17. PMID: 16857587.
    Citations: 226     Fields:    Translation:Cells
  130. Quackenbush J, Irizarry RA. Response to Shields: 'MIAME, we have a problem'. Trends Genet. 2006 Sep; 22(9):471-2. PMID: 16859802.
    Citations: 3     Fields:    
  131. DiPietro JA, Caulfield LE, Irizarry RA, Chen P, Merialdi M, Zavaleta N. Prenatal development of intrafetal and maternal-fetal synchrony. Behav Neurosci. 2006 Jun; 120(3):687-701. PMID: 16768620.
    Citations: 16     Fields:    Translation:Humans
  132. Quackenbush J, Stoeckert C, Ball C, Brazma A, Gentleman R, Huber W, Irizarry R, Salit M, Sherlock G, Spellman P, Winegarden N. Top-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24. PMID: 16511469.
    Citations: 6     Fields:    
  133. Cope L, Hartman SM, Göhlmann HW, Tiesman JP, Irizarry RA. Analysis of Affymetrix GeneChip data using amplified RNA. Biotechniques. 2006 Feb; 40(2):165-6, 168, 170. PMID: 16526405.
    Citations: 14     Fields:    Translation:Cells
  134. Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics. 2006 Apr 01; 22(7):789-94. PMID: 16410320.
    Citations: 149     Fields:    
  135. Irizarry RA, Cope LM, Wu Z. Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol. 2006; 7(8):404. PMID: 16953902.
    Citations: 29     Fields:    Translation:Animals
  136. Zeger SL, Irizarry R, Peng RD. On time series analysis of public health and biomedical data. Annu Rev Public Health. 2006; 27:57-79. PMID: 16533109.
    Citations: 51     Fields:    Translation:HumansPHPublic Health
  137. Ooi SL, Pan X, Peyser BD, Ye P, Meluh PB, Yuan DS, Irizarry RA, Bader JS, Spencer FA, Boeke JD. Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 2006 Jan; 22(1):56-63. PMID: 16309778.
    Citations: 60     Fields:    Translation:Animals
  138. Baker SC, Bauer SR, Beyer RP, Brenton JD, Bromley B, Burrill J, Causton H, Conley MP, Elespuru R, Fero M, Foy C, Fuscoe J, Gao X, Gerhold DL, Gilles P, Goodsaid F, Guo X, Hackett J, Hockett RD, Ikonomi P, Irizarry RA, Kawasaki ES, Kaysser-Kranich T, Kerr K, Kiser G, Koch WH, Lee KY, Liu C, Liu ZL, Lucas A, Manohar CF, Miyada G, Modrusan Z, Parkes H, Puri RK, Reid L, Ryder TB, Salit M, Samaha RR, Scherf U, Sendera TJ, Setterquist RA, Shi L, Shippy R, Soriano JV, Wagar EA, Warrington JA, Williams M, Wilmer F, Wilson M, Wolber PK, Wu X, Zadro R. The External RNA Controls Consortium: a progress report. Nat Methods. 2005 Oct; 2(10):731-4. PMID: 16179916.
    Citations: 144     Fields:    Translation:HumansAnimals
  139. Peyser BD, Irizarry RA, Tiffany CW, Chen O, Yuan DS, Boeke JD, Spencer FA. Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res. 2005 Sep 15; 33(16):e140. PMID: 16166654.
    Citations: 3     Fields:    Translation:Animals
  140. Lechtzin N, John M, Irizarry R, Merlo C, Diette GB, Boyle MP. Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa. Respiration. 2006; 73(1):27-33. PMID: 16113513.
    Citations: 37     Fields:    Translation:Humans
  141. Kittleson MM, Minhas KM, Irizarry RA, Ye SQ, Edness G, Breton E, Conte JV, Tomaselli G, Garcia JG, Hare JM. Gene expression in giant cell myocarditis: Altered expression of immune response genes. Int J Cardiol. 2005 Jul 10; 102(2):333-40. PMID: 15982506.
    Citations: 20     Fields:    Translation:HumansCells
  142. Yuan DS, Pan X, Ooi SL, Peyser BD, Spencer FA, Irizarry RA, Boeke JD. Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res. 2005 Jul 01; 33(12):e103. PMID: 15994458.
    Citations: 20     Fields:    Translation:Animals
  143. Wu Z, Irizarry RA. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol. 2005 Jul-Aug; 12(6):882-93. PMID: 16108723.
    Citations: 139     Fields:    Translation:Cells
  144. Grigoryev DN, Ma SF, Simon BA, Irizarry RA, Ye SQ, Garcia JG. In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology. BMC Genomics. 2005 May 04; 6:62. PMID: 15871745.
    Citations: 22     Fields:    Translation:HumansAnimalsCells
  145. Hansel NN, Hilmer SC, Georas SN, Cope LM, Guo J, Irizarry RA, Diette GB. Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma. J Lab Clin Med. 2005 May; 145(5):263-74. PMID: 15902098.
    Citations: 16     Fields:    Translation:HumansCells
  146. Irizarry RA, Warren D, Spencer F, Kim IF, Biswal S, Frank BC, Gabrielson E, Garcia JG, Geoghegan J, Germino G, Griffin C, Hilmer SC, Hoffman E, Jedlicka AE, Kawasaki E, Martínez-Murillo F, Morsberger L, Lee H, Petersen D, Quackenbush J, Scott A, Wilson M, Yang Y, Ye SQ, Yu W. Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005 May; 2(5):345-50. PMID: 15846361.
    Citations: 344     Fields:    Translation:Humans
  147. Kittleson MM, Minhas KM, Irizarry RA, Ye SQ, Edness G, Breton E, Conte JV, Tomaselli G, Garcia JG, Hare JM. Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure. Physiol Genomics. 2005 May 11; 21(3):299-307. PMID: 15769906.
    Citations: 82     Fields:    Translation:Humans
  148. Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN. On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci U S A. 2005 Mar 22; 102(12):4252-7. PMID: 15755808.
    Citations: 197     Fields:    Translation:Animals
  149. Kittleson MM, Ye SQ, Irizarry RA, Minhas KM, Edness G, Conte JV, Parmigiani G, Miller LW, Chen Y, Hall JL, Garcia JG, Hare JM. Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation. 2004 Nov 30; 110(22):3444-51. PMID: 15557369.
    Citations: 51     Fields:    Translation:HumansCells
  150. Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. PMID: 15461798.
    Citations: 6217     Fields:    
  151. Dipietro JA, Irizarry RA, Costigan KA, Gurewitsch ED. The psychophysiology of the maternal-fetal relationship. Psychophysiology. 2004 Jul; 41(4):510-20. PMID: 15189474.
    Citations: 12     Fields:    Translation:Humans
  152. Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun; 22(6):656-8; author reply 658. PMID: 15175677.
    Citations: 187     Fields:    Translation:Cells
  153. Grigoryev DN, Ma SF, Irizarry RA, Ye SQ, Quackenbush J, Garcia JG. Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol. 2004; 5(5):R34. PMID: 15128448.
    Citations: 64     Fields:    Translation:HumansAnimalsCells
  154. Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics. 2004 Feb 12; 20(3):323-31. PMID: 14960458.
    Citations: 109     Fields:    
  155. Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004 Feb 12; 20(3):307-15. PMID: 14960456.
    Citations: 2514     Fields:    
  156. Warren CD, Eckley DM, Lee MS, Hanna JS, Hughes A, Peyser B, Jie C, Irizarry R, Spencer FA. S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion. Mol Biol Cell. 2004 Apr; 15(4):1724-35. PMID: 14742710.
    Citations: 72     Fields:    Translation:AnimalsCells
  157. Cummings DA, Irizarry RA, Huang NE, Endy TP, Nisalak A, Ungchusak K, Burke DS. Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand. Nature. 2004 Jan 22; 427(6972):344-7. PMID: 14737166.
    Citations: 168     Fields:    Translation:Humans
  158. Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Experimental design and low-level analysis of microarray data. Int Rev Neurobiol. 2004; 60:25-58. PMID: 15474586.
    Citations: 52     Fields:    Translation:HumansAnimals
  159. Chen H, Irizarry RA, Luo L, Zirkin BR. Leydig cell gene expression: effects of age and caloric restriction. Exp Gerontol. 2004 Jan; 39(1):31-43. PMID: 14724062.
    Citations: 9     Fields:    Translation:AnimalsCells
  160. Sidransky D, Irizarry R, Califano JA, Li X, Ren H, Benoit N, Mao L. Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer patients from control subjects. J Natl Cancer Inst. 2003 Nov 19; 95(22):1711-7. PMID: 14625262.
    Citations: 19     Fields:    Translation:Humans
  161. Scharfstein DO, Irizarry RA. Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data. Biometrics. 2003 Sep; 59(3):601-13. PMID: 14601761.
    Citations: 5     Fields:    Translation:Humans
  162. Cappola TP, Cope L, Cernetich A, Barouch LA, Minhas K, Irizarry RA, Parmigiani G, Durrani S, Lavoie T, Hoffman EP, Ye SQ, Garcia JG, Hare JM. Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol Genomics. 2003 Jun 24; 14(1):25-34. PMID: 12709511.
    Citations: 13     Fields:    Translation:AnimalsCells
  163. Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, Scherf U, Speed TP. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr; 4(2):249-64. PMID: 12925520.
    Citations: 5382     Fields:    Translation:HumansAnimals
  164. Irizarry RA, Ooi SL, Wu Z, Boeke JD. Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Stat Appl Genet Mol Biol. 2003; 2:Article1. PMID: 16646779.
    Citations: 41     Fields:    
  165. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003 Feb 15; 31(4):e15. PMID: 12582260.
    Citations: 2478     Fields:    Translation:Humans
  166. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22; 19(2):185-93. PMID: 12538238.
    Citations: 3909     Fields:    
  167. Tankersley CG, Irizarry R, Flanders SE, Rabold R, Frank R. Unstable heart rate and temperature regulation predict mortality in AKR/J mice. Am J Physiol Regul Integr Comp Physiol. 2003 Mar; 284(3):R742-50. PMID: 12388436.
    Citations: 6     Fields:    Translation:Animals
  168. Tankersley CG, Irizarry R, Flanders S, Rabold R. Circadian rhythm variation in activity, body temperature, and heart rate between C3H/HeJ and C57BL/6J inbred strains. J Appl Physiol (1985). 2002 Feb; 92(2):870-7. PMID: 11796704.
    Citations: 22     Fields:    Translation:Animals
  169. Crone NE, Hao L, Hart J, Boatman D, Lesser RP, Irizarry R, Gordon B. Electrocorticographic gamma activity during word production in spoken and sign language. Neurology. 2001 Dec 11; 57(11):2045-53. PMID: 11739824.
    Citations: 119     Fields:    Translation:Humans
  170. Dipietro JA, Irizarry RA, Hawkins M, Costigan KA, Pressman EK. Cross-correlation of fetal cardiac and somatic activity as an indicator of antenatal neural development. Am J Obstet Gynecol. 2001 Dec; 185(6):1421-8. PMID: 11744919.
    Citations: 22     Fields:    Translation:Humans
  171. Irizarry RA, Tankersley C, Frank R, Flanders S. Assessing homeostasis through circadian patterns. Biometrics. 2001 Dec; 57(4):1228-37. PMID: 11764264.
    Citations: 5     Fields:    Translation:Animals
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.