
Rafael Irizarry, PhD
Dana-Farber Cancer Institute
Dana-Farber Cancer Institute
Phone: (617) 632-3012
Rafael Irizarry, PhD
Dana-Farber Cancer Institute
EDUCATIONAL TITLES
DF/HCC PROGRAM AFFILIATION
- Teng M, Du D, Chen D, Irizarry RA. Characterizing batch effects and binding site-specific variability in ChIP-seq data. NAR Genom Bioinform 2021; 3:lqab098. PubMed
- 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; 39:632-648.e8. PubMed
- 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 2021. PubMed
- 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; 182:1474-1489.e23. PubMed
- Townes FW, Irizarry RA. Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers. Genome Biol 2020; 21:160. PubMed
- 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. PubMed
- 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; 20:295. PubMed
- 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 reveals complex spatiotemporal regulation of lncRNAs. Development 2019. PubMed
- Hicks SC, Irizarry RA. methylCC: technology-independent estimation of cell type composition using differentially methylated regions. Genome Biol 2019; 20:261. PubMed
- 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. PubMed
- 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 2018. PubMed
- Hicks SC, Irizarry RA. A Guide to Teaching Data Science. Am Stat 2018; 72:382-391. PubMed
- 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; 8:1784. PubMed
- Hicks SC, Townes FW, Teng M, Irizarry RA. Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics 2017. PubMed
- Teng M, Irizarry RA. Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res 2017; 27:1930-1938. PubMed
- 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. PubMed
- Hicks SC, Okrah K, Paulson JN, Quackenbush J, Irizarry RA, Bravo HC. Smooth quantile normalization. Biostatistics 2017. PubMed
- 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; 18:84. PubMed
- 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; 14:216-217. PubMed
- 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. PubMed
- 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 2016. PubMed
- Love MI, Hogenesch JB, Irizarry RA. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol 2016. PubMed
- 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; 17:74. PubMed
- 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; 26:959-72. PubMed
- 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; 9:75. PubMed
- Hicks SC, Irizarry RA. quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol 2015; 16:117. PubMed
- Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT. Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics 2014. PubMed
- Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics 2014. PubMed
- 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. PubMed
- 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; 9:308-17. PubMed
- 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; 6:61. PubMed
- 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; 15:158. PubMed
- 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; 42:D938-43. PubMed
- Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol 2014; 15:R31. PubMed
- 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; 14:R94. PubMed
- Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol 2012; 13:R83. PubMed
- 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; 13:272. PubMed
- 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; 13:303. PubMed
- 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; 40:1-32. PubMed