Rafael A. Irizarry - Publications

Affiliations: 
Johns Hopkins University, Baltimore, MD 
Area:
Biostatistics Biology

119 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
2016 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 Biology. 17: 74. PMID 27107712 DOI: 10.1186/s13059-016-0940-1  0.92
2015 Hicks SC, Irizarry RA. quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biology. 16: 117. PMID 26040460 DOI: 10.1186/s13059-015-0679-0  0.92
2015 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, et al. Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes & Control : Ccc. 26: 959-72. PMID 25956270 DOI: 10.1007/s10552-015-0596-2  0.92
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  0.92
2014 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 Medicine. 6: 61. PMID 25191524 DOI: 10.1186/s13073-014-0061-y  0.92
2014 Liu R, Dai Z, Yeager M, Irizarry RA, Ritchie ME. KRLMM: an adaptive genotype calling method for common and low frequency variants. Bmc Bioinformatics. 15: 158. PMID 24886250 DOI: 10.1186/1471-2105-15-158  0.92
2014 Halper-Stromberg E, Steranka J, Burns KH, Sabunciyan S, Irizarry RA. Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics (Oxford, England). 30: 1514-21. PMID 24501098 DOI: 10.1093/bioinformatics/btu054  0.92
2014 Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biology. 15: R31. PMID 24495553 DOI: 10.1186/gb-2014-15-2-r31  0.92
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  0.92
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  0.92
2014 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 Research. 42: D938-43. PMID 24271388 DOI: 10.1093/nar/gkt1204  0.92
2014 Yang J, Han F, Irizarry RA, Liu H. Context aware group nearest shrunken centroids in large-scale genomic studies Journal of Machine Learning Research. 33: 1051-1059.  0.92
2013 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. Nature Methods. 10: 949-55. PMID 24076989 DOI: 10.1038/nmeth.2632  0.92
2013 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 Biology. 14: R94. PMID 24000956 DOI: 10.1186/gb-2013-14-8-r94  0.92
2013 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 (Oxford, England). 29: 1182-1189. PMID 23457041  0.92
2013 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. Science Translational Medicine. 5: 169ra10. PMID 23345608 DOI: 10.1126/scitranslmed.3005211  0.92
2012 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. 13: 303. PMID 23151247 DOI: 10.1186/1471-2105-13-303  0.92
2012 Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. Gene expression anti-profiles as a basis for accurate universal cancer signatures. Bmc Bioinformatics. 13: 272. PMID 23088656 DOI: 10.1186/1471-2105-13-272  0.92
2012 McCall MN, Jaffee HA, Irizarry RA. fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics (Oxford, England). 28: 3153-4. PMID 23044545 DOI: 10.1093/bioinformatics/bts588  0.92
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  0.92
2012 Shi W, Wahba G, Irizarry RA, Bravo HC, Wright SJ. The partitioned LASSO-patternsearch algorithm with application to gene expression data. Bmc Bioinformatics. 13: 98. PMID 22587526 DOI: 10.1186/1471-2105-13-98  0.92
2012 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. 7: e34451. PMID 22511943 DOI: 10.1371/journal.pone.0034451  0.92
2012 Clement L, De Beuf K, Thas O, Vuylsteke M, Irizarry RA, Crainiceanu CM. Fast wavelet based functional models for transcriptome analysis with tiling arrays. Statistical Applications in Genetics and Molecular Biology. 11: Article 4. PMID 22499683 DOI: 10.2202/1544-6115.1726  0.92
2012 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. International Journal of Epidemiology. 41: 200-9. PMID 22422453 DOI: 10.1093/ije/dyr238  0.92
2012 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. International Journal of Epidemiology. 41: 188-99. PMID 22422452 DOI: 10.1093/ije/dyr237  0.92
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  0.92
2012 Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylated regions. Biostatistics (Oxford, England). 13: 166-78. PMID 21685414 DOI: 10.1093/biostatistics/kxr013  0.92
2011 Scharpf RB, Irizarry RA, Ritchie ME, Carvalho B, Ruczinski I. Using the R Package crlmm for Genotyping and Copy Number Estimation. Journal of Statistical Software. 40: 1-32. PMID 22523482  0.92
2011 McCall MN, Irizarry RA. Thawing Frozen Robust Multi-array Analysis (fRMA). Bmc Bioinformatics. 12: 369. PMID 21923903 DOI: 10.1186/1471-2105-12-369  0.92
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  0.92
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  0.92
2011 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. 12: 313. PMID 21669002 DOI: 10.1186/1471-2164-12-313  0.92
2011 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, et al. NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva Cancer Prevention Research. 4: 1061-1072. PMID 21558411 DOI: 10.1158/1940-6207.CAPR-11-0006  0.92
2011 McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. Assessing affymetrix GeneChip microarray quality. Bmc Bioinformatics. 12: 137. PMID 21548974 DOI: 10.1186/1471-2105-12-137  0.92
2011 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, et al. Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics (Oxford, England). 27: 1052-60. PMID 21478196 DOI: 10.1093/bioinformatics/btr106  0.92
2011 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. Journal of Virology. 85: 5384-93. PMID 21430059 DOI: 10.1128/JVI.02536-10  0.92
2011 Ritchie ME, Liu R, Carvalho BS, Irizarry RA, Bahlo M, Booth DR, Broadley SA, Brown MA, Foote SJ, Griffiths LR, Kilpatrick TJ, Lechner-Scott J, Moscato P, Perreau VM, Rubio JP, et al. Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips Bmc Bioinformatics. 12. PMID 21385424 DOI: 10.1186/1471-2105-12-68  0.92
2011 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 Research. 39: D1011-5. PMID 21177656 DOI: 10.1093/nar/gkq1259  0.92
2011 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 (Oxford, England). 12: 197-210. PMID 20858772 DOI: 10.1093/biostatistics/kxq055  0.92
2011 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 (Oxford, England). 12: 33-50. PMID 20625178 DOI: 10.1093/biostatistics/kxq043  0.92
2011 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 (Science Translational Medicine (2011) 3, (65er1)) Science Translational Medicine. 3. DOI: 10.1126/scitranslmed.3002078  0.92
2010 Taub MA, Corrada Bravo H, Irizarry RA. Overcoming bias and systematic errors in next generation sequencing data. Genome Medicine. 2: 87. PMID 21144010 DOI: 10.1186/gm208  0.92
2010 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. Science Translational Medicine. 2: 49ra67. PMID 20844285 DOI: 10.1126/scitranslmed.3001262  0.92
2010 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. Nature Reviews. Genetics. 11: 733-9. PMID 20838408 DOI: 10.1038/nrg2825  0.92
2010 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, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 467: 338-42. PMID 20720541 DOI: 10.1038/nature09367  0.92
2010 Carvalho BS, Irizarry RA. A framework for oligonucleotide microarray preprocessing. Bioinformatics (Oxford, England). 26: 2363-7. PMID 20688976 DOI: 10.1093/bioinformatics/btq431  0.92
2010 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, ... ... Irizarry RA, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/nbt.1665  0.92
2010 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, ... ... Irizarry RA, et al. Epigenetic memory in induced pluripotent stem cells. Nature. 467: 285-90. PMID 20644535 DOI: 10.1038/nature09342  0.92
2010 Wu H, Irizarry RA, Bravo HC. Intensity normalization improves color calling in SOLiD sequencing. Nature Methods. 7: 336-7. PMID 20431543 DOI: 10.1038/nmeth0510-336  0.92
2010 Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA. Performance evaluation of commercial miRNA expression array platforms. Bmc Research Notes. 3: 80. PMID 20298588 DOI: 10.1186/1756-0500-3-80  0.92
2010 Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. Redefining CpG islands using hidden Markov models. Biostatistics (Oxford, England). 11: 499-514. PMID 20212320 DOI: 10.1093/biostatistics/kxq005  0.92
2010 López-Romero P, González MA, Callejas S, Dopazo A, Irizarry RA. Processing of Agilent microRNA array data. Bmc Research Notes. 3: 18. PMID 20205787 DOI: 10.1186/1756-0500-3-18  0.92
2010 McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics (Oxford, England). 11: 242-53. PMID 20097884 DOI: 10.1093/biostatistics/kxp059  0.92
2010 Feinberg AP, Irizarry RA. Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences of the United States of America. 107: 1757-64. PMID 20080672 DOI: 10.1073/pnas.0906183107  0.92
2010 Bravo HC, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics. 66: 665-74. PMID 19912177 DOI: 10.1111/j.1541-0420.2009.01353.x  0.92
2010 Carvalho BS, Louis TA, Irizarry RA. Quantifying uncertainty in genotype calls. Bioinformatics (Oxford, England). 26: 242-9. PMID 19906825 DOI: 10.1093/bioinformatics/btp624  0.92
2010 Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Evolutionary flux of canonical micrornAs and mirtrons in Drosophila Nature Genetics. 42: 5-6. DOI: 10.1038/ng0110-5  0.92
2009 Irizarry RA, Wang C, Zhou Y, Speed TP. Gene set enrichment analysis made simple. Statistical Methods in Medical Research. 18: 565-75. PMID 20048385 DOI: 10.1177/0962280209351908  0.92
2009 Irizarry RA, Wu H, Feinberg AP. A species-generalized probabilistic model-based definition of CpG islands. Mammalian Genome : Official Journal of the International Mammalian Genome Society. 20: 674-80. PMID 19777308 DOI: 10.1007/s00335-009-9222-5  0.92
2009 Ritchie ME, Carvalho BS, Hetrick KN, Tavaré S, Irizarry RA. R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics (Oxford, England). 25: 2621-3. PMID 19661241 DOI: 10.1093/bioinformatics/btp470  0.92
2009 Wen B, Wu H, Shinkai Y, Irizarry RA, Feinberg AP. Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nature Genetics. 41: 246-50. PMID 19151716 DOI: 10.1038/ng.297  0.92
2009 Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P, Cui H, Gabo K, Rongione M, Webster M, Ji H, Potash JB, Sabunciyan S, Feinberg AP. The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nature Genetics. 41: 178-86. PMID 19151715 DOI: 10.1038/ng.298  0.92
2009 Carvalho B, Irizarry RA, Scharpf RB, Carey VJ. Processing and analyzing Affymetrix SNP chips with Bioconductor Statistics in Biosciences. 1: 160-180. DOI: 10.1007/s12561-009-9015-0  0.92
2008 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 Research. 68: 8954-67. PMID 18974140 DOI: 10.1158/0008-5472.CAN-07-6088  0.92
2008 Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA. Estimating genome-wide copy number using allele-specific mixture models. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 15: 857-66. PMID 18707534 DOI: 10.1089/cmb.2007.0148  0.92
2008 McCall MN, Irizarry RA. Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Research. 36: e108. PMID 18676452 DOI: 10.1093/nar/gkn430  0.92
2008 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, et al. Intra-individual change over time in DNA methylation with familial clustering. Jama. 299: 2877-83. PMID 18577732 DOI: 10.1001/jama.299.24.2877  0.92
2008 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 Biology. 9: R63. PMID 18387188 DOI: 10.1186/gb-2008-9-4-r63  0.92
2008 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 Research. 18: 771-9. PMID 18369178 DOI: 10.1101/gr.073254.107  0.92
2008 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 Research. 18: 780-90. PMID 18316654 DOI: 10.1101/gr.7301508  0.92
2008 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. 9: 34. PMID 18215314 DOI: 10.1186/1471-2164-9-34  0.92
2007 Zilliox MJ, Irizarry RA. A gene expression bar code for microarray data. Nature Methods. 4: 911-3. PMID 17906632 DOI: 10.1038/nmeth1102  0.92
2007 Carvalho B, Bengtsson H, Speed TP, Irizarry RA. Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (Oxford, England). 8: 485-99. PMID 17189563 DOI: 10.1093/biostatistics/kxl042  0.92
2007 Wang W, Carvalho B, Miller N, Pevsner J, Chakravarti A, Irizarry RA. Estimating genome-wide copy number using allele specific mixture models Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4453: 137-150.  0.92
2006 Wheelan SJ, Scheifele LZ, Martínez-Murillo F, Irizarry RA, Boeke JD. Transposon insertion site profiling chip (TIP-chip). Proceedings of the National Academy of Sciences of the United States of America. 103: 17632-7. PMID 17101968 DOI: 10.1073/pnas.0605450103  0.92
2006 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, et al. A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. Bmc Bioinformatics. 7: 489. PMID 17087822 DOI: 10.1186/1471-2105-7-489  0.92
2006 Wheelan SJ, Martínez-Murillo F, Irizarry RA, Boeke JD. Stacking the deck: double-tiled DNA microarrays. Nature Methods. 3: 903-7. PMID 17060914 DOI: 10.1038/nmeth951  0.92
2006 Yuan DS, Irizarry RA. High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics (Oxford, England). 22: 3054-60. PMID 17060357 DOI: 10.1093/bioinformatics/btl542  0.92
2006 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. 7: 464. PMID 17059591 DOI: 10.1186/1471-2105-7-464  0.92
2006 Quackenbush J, Irizarry RA. Response to Shields: 'MIAME, we have a problem'. Trends in Genetics : Tig. 22: 471-2. PMID 16859802 DOI: 10.1016/j.tig.2006.07.007  0.92
2006 Takahashi H, McCaffery JM, Irizarry RA, Boeke JD. Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Molecular Cell. 23: 207-17. PMID 16857587 DOI: 10.1016/j.molcel.2006.05.040  0.92
2006 DiPietro JA, Caulfield LE, Irizarry RA, Chen P, Merialdi M, Zavaleta N. Prenatal development of intrafetal and maternal-fetal synchrony. Behavioral Neuroscience. 120: 687-701. PMID 16768620 DOI: 10.1037/0735-7044.120.3.687  0.92
2006 Cope L, Hartman SM, Göhlmann HW, Tiesman JP, Irizarry RA. Analysis of Affymetrix GeneChip data using amplified RNA. Biotechniques. 40: 165-6, 168, 170. PMID 16526405 DOI: 10.2144/000112057  0.92
2006 Irizarry RA, Wu Z, Jaffee HA. Comparison of Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England). 22: 789-94. PMID 16410320 DOI: 10.1093/bioinformatics/btk046  0.92
2006 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 in Genetics : Tig. 22: 56-63. PMID 16309778 DOI: 10.1016/j.tig.2005.11.003  0.92
2005 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, ... ... Irizarry RA, et al. The External RNA Controls Consortium: a progress report. Nature Methods. 2: 731-4. PMID 16179916 DOI: 10.1038/nmeth1005-731  0.92
2005 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 Research. 33: e140. PMID 16166654 DOI: 10.1093/nar/gni138  0.92
2005 Wu Z, Irizarry RA. Stochastic models inspired by hybridization theory for short oligonucleotide arrays. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 882-93. PMID 16108723 DOI: 10.1089/cmb.2005.12.882  0.92
2005 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 Research. 33: e103. PMID 15994458 DOI: 10.1093/nar/gni105  0.92
2005 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. International Journal of Cardiology. 102: 333-40. PMID 15982506 DOI: 10.1016/j.ijcard.2005.03.075  0.92
2005 Hansel NN, Hilmer SC, Georas SN, Cope LM, Guo J, Irizarry RA, Diette GB. Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma. The Journal of Laboratory and Clinical Medicine. 145: 263-74. PMID 15902098 DOI: 10.1016/j.lab.2005.02.010  0.92
2005 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. 6: 62. PMID 15871745 DOI: 10.1186/1471-2164-6-62  0.92
2005 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, et al. Multiple-laboratory comparison of microarray platforms. Nature Methods. 2: 345-50. PMID 15846361 DOI: 10.1038/nmeth756  0.92
2005 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. Physiological Genomics. 21: 299-307. PMID 15769906 DOI: 10.1152/physiolgenomics.00255.2004  0.92
2005 Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN. On the utility of pooling biological samples in microarray experiments. Proceedings of the National Academy of Sciences of the United States of America. 102: 4252-7. PMID 15755808 DOI: 10.1073/pnas.0500607102  0.92
2004 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. 110: 3444-51. PMID 15557369 DOI: 10.1161/01.CIR.0000148178.19465.11  0.92
2004 Bolstad BM, Collin F, Simpson KM, Irizarry RA, Speed TP. Experimental Design and Low-Level Analysis of Microarray Data International Review of Neurobiology. 60: 25-58. PMID 15474586 DOI: 10.1016/S0074-7742(04)60002-X  0.92
2004 Dipietro JA, Irizarry RA, Costigan KA, Gurewitsch ED. The psychophysiology of the maternal-fetal relationship. Psychophysiology. 41: 510-20. PMID 15189474 DOI: 10.1111/j.1469-8986.2004.00187.x  0.92
2004 Wu Z, Irizarry RA. Preprocessing of oligonucleotide array data. Nature Biotechnology. 22: 656-8; author reply . PMID 15175677 DOI: 10.1038/nbt0604-656b  0.92
2004 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 Biology. 5: R34. PMID 15128448 DOI: 10.1186/gb-2004-5-5-r34  0.92
2004 Cope LM, Irizarry RA, Jaffee HA, Wu Z, Speed TP. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (Oxford, England). 20: 323-31. PMID 14960458 DOI: 10.1093/bioinformatics/btg410  0.92
2004 Gautier L, Cope L, Bolstad BM, Irizarry RA. affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics (Oxford, England). 20: 307-15. PMID 14960456 DOI: 10.1093/bioinformatics/btg405  0.92
2004 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. 427: 344-7. PMID 14737166 DOI: 10.1038/nature02225  0.92
2004 Chen H, Irizarry RA, Luo L, Zirkin BR. Leydig cell gene expression: effects of age and caloric restriction. Experimental Gerontology. 39: 31-43. PMID 14724062 DOI: 10.1016/j.exger.2003.09.021  0.92
2004 Wu Z, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer F. A model-based background adjustment for oligonucleotide expression arrays Journal of the American Statistical Association. 99: 909-917. DOI: 10.1198/016214504000000683  0.92
2003 Scharfstein DO, Irizarry RA. Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data. Biometrics. 59: 601-13. PMID 14601761 DOI: 10.1111/1541-0420.00070  0.92
2003 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 (Oxford, England). 4: 249-64. PMID 12925520 DOI: 10.1093/biostatistics/4.2.249  0.92
2003 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. Physiological Genomics. 14: 25-34. PMID 12709511 DOI: 10.1152/physiolgenomics.00156.2002  0.92
2003 Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Research. 31: e15. PMID 12582260 DOI: 10.1093/nar/gng015  0.92
2003 Bolstad BM, Irizarry RA, Åstrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias Bioinformatics. 19: 185-193. PMID 12538238 DOI: 10.1093/bioinformatics/19.2.185  0.92
2002 Irizarry RA. Weighted estimation of harmonic components in a musical sound signal Journal of Time Series Analysis. 23: 29-48. DOI: 10.1111/1467-9892.01515  0.92
2001 Irizarry RA, Tankersley C, Frank R, Flanders S. Consultant's forum: Assessing homeostasis through circadian patterns Biometrics. 57: 1228-1237. PMID 11764264  0.92
2001 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. American Journal of Obstetrics and Gynecology. 185: 1421-8. PMID 11744919 DOI: 10.1067/mob.2001.119108  0.92
2001 Irizarry RA. Local regression with meaningful parameters American Statistician. 55: 72-79. DOI: 10.1198/000313001300339969  0.92
2001 Irizarry RA. Local Harmonic Estimation in Musical Sound Signals Journal of the American Statistical Association. 96: 357-367.  0.92
2001 Irizarry RA. Information and Posterior Probability Criteria for Model Selection in Local Likelihood Estimation Journal of the American Statistical Association. 96: 303-315.  0.92
2000 Brillinger DR, Morettin PA, Irizarry RA, Chiann C. Some wavelet-based analyses of Markov chain data Signal Processing. 80: 1607-1627. DOI: 10.1016/S0165-1684(00)00097-9  0.92
2000 Irizarry RA. Asymptotic distribution of estimates for a time-varying parameter in a harmonic model with multiple fundamentals Statistica Sinica. 10: 1041-1067.  0.92
1998 Brillinger DR, Irizarry RA. An investigation of the second- and higher-order spectra of music Signal Processing. 65: 161-179.  0.92
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