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Rafael Irizarry

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Oligonucleotide Array Sequence Analysis

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TOP 3
Martin Aryee; G Steven Bova; Julia C Engelmann; David Esopi; Robert H Getzenberg; Meltem Gurel; Michael C Haffner; Rafael A Irizarry; William B Isaacs; Wennuan Liu; Jun Luo; William G Nelson; Philipp Nuhn; Jianfeng Xu; Srinivasan Yegnasubramanian
DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.
Matthew N McCall; HARRIS JAFFEE; Rafael A Irizarry
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.
Brian R Herb; Rafael A Irizarry; Benjamin Langmead; Florian Wolschin; Gro V Amdam; Martin Aryee; Kasper Daniel Hansen; Andrew P Feinberg
Reversible switching between epigenetic states in honeybee behavioral subcastes.

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All Publications

2013: Martin Aryee; G Steven Bova; Julia C Engelmann; David Esopi; Robert H Getzenberg; Meltem Gurel; Michael C Haffner; Rafael A Irizarry; William B Isaacs; Wennuan Liu; Jun Luo; William G Nelson; Philipp Nuhn; Jianfeng Xu; Srinivasan Yegnasubramanian
DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases.
Science translational medicine 2013;5(169):169ra10.
2012: Matthew N McCall; HARRIS JAFFEE; Rafael A Irizarry
fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays.
Bioinformatics (Oxford, England) 2012;28(23):3153-4.
2012: Brian R Herb; Rafael A Irizarry; Benjamin Langmead; Florian Wolschin; Gro V Amdam; Martin Aryee; Kasper Daniel Hansen; Andrew P Feinberg
Reversible switching between epigenetic states in honeybee behavioral subcastes.
Nature neuroscience 2012;15(10):1371-3.
2012: Kasper Daniel Hansen; Rafael A Irizarry; Zhijin Wu
Removing technical variability in RNA-seq data using conditional quantile normalization.
Biostatistics (Oxford, England) 2012;13(2):204-16.
2012: Yu-Yi Lin; Shang-Yun Liu; Jin-ying Lu; Yasir Suhail; Yi-hsuan Chou; Rafael A Irizarry; Chin Ni Khor; Samara Kiihl; Zheng Kuang; Chi-Long Lin; Joel S Bader; Jef Boeke
Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK.
Nature 2012;482(7384):251-5.
2012: Andrew E Jaffe; Hwajin Lee; Jeffrey T Leek; Peter Murakami; MARGARET D FALLIN; Andrew P Feinberg; Rafael A Irizarry
Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.
International journal of epidemiology 2012;41(1):200-9.
2012: Hwajin Lee; Carolina Montano; Rakel Tryggvadottir; Frank R Witter; Andrew P Feinberg; Jason I Feinberg; Lynn Rose Goldman; Julie B Herbstman; Rafael A Irizarry; Andrew E Jaffe; Martin Aryee; Shannon Brown; MARGARET D FALLIN
DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth.
International journal of epidemiology 2012;41(1):188-99.
2012: Kristof De Beuf; Wim Van Criekinge; Rafael A Irizarry; Joachim De Schrijver; Olivier Thas; Lieven Clement
Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model.
BMC bioinformatics 2012;13():303.
2012: Héctor Corrada Bravo; Rafael A Irizarry; Matthew McCall; Vasyl Pihur; Jeffrey T Leek
Gene expression anti-profiles as a basis for accurate universal cancer signatures.
BMC bioinformatics 2012;13():272.
2012: Weiliang Shi; Grace Wahba; Hector Corrada Bravo; Rafael A Irizarry; Stephen J Wright
The partitioned LASSO-patternsearch algorithm with application to gene expression data.
BMC bioinformatics 2012;13():98.
2012: Sarven Sabunciyan; Maree J Webster; Robert H Yolken; Martin Aryee; Andrew P Feinberg; Rafael A Irizarry; Walter E Kaufman; Andree Lessard; Peter Murakami; James B Potash; Michael Rongione
Genome-wide DNA methylation scan in major depressive disorder.
PloS one 2012;7(4):e34451.
2012: Lieven Clement; Kristof De Beuf; Rafael A Irizarry; Olivier Thas; Marnik Vuylsteke; Ciprian M Crainiceanu
Fast wavelet based functional models for transcriptome analysis with tiling arrays.
Statistical applications in genetics and molecular biology 2012;11(1):Article 4.
2012: Andrew E Jaffe; Rafael A Irizarry; Andrew P Feinberg; Jeffrey T Leek
Significance analysis and statistical dissection of variably methylated regions.
Biostatistics (Oxford, England) 2012;13(1):166-78.
2011: Kasper Daniel Hansen; Rafael A Irizarry; Benjamin Langmead; Yun Liu; Oliver G McDonald; Sarven Sabunciyan; Winston Timp; Bo Wen; Hao Wu; Kun Zhang; Héctor Corrada Bravo; Eirikur Briem; Dinh Diep; Andrew P Feinberg
Increased methylation variation in epigenetic domains across cancer types.
Nature genetics 2011;43(8):768-75.
2011: Kasper Daniel Hansen; Rafael A Irizarry; Zhijin Wu; Jeffrey T Leek
Sequencing technology does not eliminate biological variability.
Nature biotechnology 2011;29(7):572-3.
2011: RAFAEL GUERRERO-PRESTON; C Ili-Gangas; Rafael A Irizarry; A Jaffe; Wayne M Koch; G Macía-Colón; L Moreno-López; M Orera; J Acero; M Berdasco; P Brebi-Mieville; Joseph A Califano; C Engstrom; Manel Esteller; Y Fu; E Soudry; William H Westra; David Sidransky
NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva.
Cancer prevention research (Philadelphia, Pa.) 2011;4(7):1061-72.
2011: Liang Shan; Hung-Chih Yang; S Alireza Rabi; Hector C Bravo; Neeta S Shroff; Rafael A Irizarry; Hao Zhang; Joseph B Margolick; Janet D Siliciano; Robert Siliciano
Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model.
Journal of virology 2011;85(11):5384-93.
2011: Eitan Halper-Stromberg; Laurence Frelin; Ingo Ruczinski; Robert B Scharpf; Chunfa Jie; Benilton Carvalho; Haiping Hao; Kurt Hetrick; Anne E Jedlicka; Amanda Dziedzic; Kim Doheny; Alan F Scott; Stephen B Baylin; Jonathan Pevsner; Forrest Spencer; Rafael A Irizarry
Performance assessment of copy number microarray platforms using a spike-in experiment.
Bioinformatics (Oxford, England) 2011;27(8):1052-60.
2011: Martin J Aryee; Zhijin Wu; Christine Ladd-Acosta; Brian Herb; Andrew P Feinberg; Srinivasan Yegnasubramanian; Rafael A Irizarry
Accurate genome-scale percentage DNA methylation estimates from microarray data.
Biostatistics (Oxford, England) 2011;12(2):197-210.
2011: Tejasvi S Niranjan; Margaret A Taub; Abby Adamczyk; Héctor Corrada Bravo; Rafael A Irizarry; Sarah J Wheelan; Tao Wang
Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis.
Genome biology 2011;12(9):R93.
2011: Matthew N McCall; Rafael A Irizarry
Thawing Frozen Robust Multi-array Analysis (fRMA).
BMC bioinformatics 2011;12():369.
2011: Srinivasan Yegnasubramanian; Qizhi Zheng; Zhijin Wu; Martin Aryee; Raghav Badrinath; Benilton Carvalho; Angelo M DeMarzo; David Esopi; Michael C Haffner; Tony L He; Rafael A Irizarry; James D Morgan; William G Nelson
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;12():313.
2011: Matthew N McCall; Peter N Murakami; Margus Lukk; Wolfgang Huber; Rafael A Irizarry
Assessing affymetrix GeneChip microarray quality.
BMC bioinformatics 2011;12():137.
2011: Matthew Ritchie; Ruijie Liu; Benilton S Carvalho; Rafael A Irizarry
Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips.
BMC bioinformatics 2011;12():68.
2011: Matthew N McCall; Karan Uppal; HARRIS JAFFEE; Michael J Zilliox; Rafael A Irizarry
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes.
Nucleic acids research 2011;39(Database issue):D1011-5.
2011: Robert B Scharpf; Ingo Ruczinski; Benilton Carvalho; Betty Doan; Aravinda Chakravarti; Rafael A Irizarry
A multilevel model to address batch effects in copy number estimation using SNP arrays.
Biostatistics (Oxford, England) 2011;12(1):33-50.
2010: Jeffrey T Leek; Robert B Scharpf; Héctor Corrada Bravo; David Simcha; Benjamin Langmead; W Evan Johnson; Donald Geman; Keith Baggerly; Rafael A Irizarry
Tackling the widespread and critical impact of batch effects in high-throughput data.
Nature reviews. Genetics 2010;11(10):733-9.
2010: Benilton S Carvalho; Rafael A Irizarry
A framework for oligonucleotide microarray preprocessing.
Bioinformatics (Oxford, England) 2010;26(19):2363-7.
2010: Hong Ji; Lauren I R Ehrlich; Jun Seita; Peter Murakami; Akiko Doi; Paul Lindau; Hwajin Lee; Martin Aryee; Rafael A Irizarry; Kitai Kim; Derrick J Rossi; Matthew A Inlay; Thomas Serwold; Holger Karsunky; Lena Ho; George Q Daley; Irving L Weissman; Andrew P Feinberg
Comprehensive methylome map of lineage commitment from haematopoietic progenitors.
Nature 2010;467(7313):338-42.
2010: K Kim; A Doi; Bo Wen; K Ng; R Zhao; Patrick Cahan; Jonghwan Kim; Martin Aryee; Hongxiu Ji; L I R Ehrlich; A Yabuuchi; A Takeuchi; K C Cunniff; H Hongguang; S McKinney-Freeman; O Naveiras; T J Yoon; Rafael A Irizarry; N Jung; J Seita; J Hanna; P Murakami; Rudolf Jaenisch; R Weissleder; S H Orkin; I L Weissman; Andrew P Feinberg; George Q Daley
Epigenetic memory in induced pluripotent stem cells.
Nature 2010;467(7313):285-90.
2010: Andrew P Feinberg; Rafael A Irizarry; Delphine Fradin; Martin Aryee; Peter Murakami; Thor Aspelund; Gudny Eiriksdottir; Tamara B Harris; Lenore Launer; Vilmundur Gudnason; MARGARET D FALLIN
Personalized epigenomic signatures that are stable over time and covary with body mass index.
Science translational medicine 2010;2(49):49ra67.
2010: Héctor Corrada Bravo; Rafael A Irizarry
Model-based quality assessment and base-calling for second-generation sequencing data.
Biometrics 2010;66(3):665-74.
2010: Leming Shi; Gregory Campbell; Wendell D Jones; Fabien Campagne; Zhining Wen; Stephen J Walker; Zhenqiang Su; Tzu-Ming Chu; Federico M Goodsaid; Lajos Pusztai; John D Shaughnessy; André Oberthuer; Russell S Thomas; Richard S Paules; Mark Fielden; Bart Barlogie; Weijie Chen; Pan Du; Matthias Fischer; Cesare Furlanello; Brandon D Gallas; Xijin Ge; Dalila B Megherbi; W Fraser Symmans; May D Wang; John Zhang; Hans Bitter; Benedikt Brors; Pierre R Bushel; Max Bylesjo; Minjun Chen; Jie Cheng; Jing Cheng; Jeff Chou; Timothy S Davison; Mauro Delorenzi; Youping Deng; Viswanath Devanarayan; David J Dix; Joaquin Dopazo; Kevin C Dorff; Fathi Elloumi; Jianqing Fan; Shicai Fan; Xiaohui Fan; Hong Fang; Nina Gonzaludo; Kenneth R Hess; Huixiao Hong; Jun Huan; Rafael A Irizarry; Richard Judson; Dilafruz Juraeva; Samir Lababidi; Christophe G Lambert; Li Li; Yanen Li; Zhen Li; Simon M Lin; Guozhen Liu; Edward K Lobenhofer; Jun Luo; Wen Luo; Matthew N McCall; Yuri Nikolsky; Gene A Pennello; Roger G Perkins; Reena Philip; Vlad Popovici; Nathan D Price; Feng Qian; Andreas Scherer; Tieliu Shi; Weiwei Shi; Jaeyun Sung; Danielle Thierry-Mieg; Jean Thierry-Mieg; Venkata Thodima; Johan Trygg; Lakshmi Vishnuvajjala; Sue Jane Wang; Jianping Wu; Yichao Wu; Qian Xie; Waleed A Yousef; Liang Zhang; Xuegong Zhang; Sheng Zhong; Yiming Zhou; Sheng Zhu; Dhivya Arasappan; Wenjun Bao; Anne Bergstrom Lucas; Frank Berthold; Richard Brennan; Andreas Buness; Jennifer G Catalano; Chang Chang; Rong Chen; Yiyu Cheng; Jian Cui; Wendy Czika; Francesca Demichelis; Xutao Deng; Damir Dosymbekov; Roland Eils; Yang Feng; Jennifer Fostel; Stephanie Fulmer-Smentek; James C Fuscoe; Laurent Gatto; Weigong Ge; Darlene R Goldstein; Li Guo; Donald N Halbert; Jing Han; Stephen C Harris; Christos Hatzis; Damir Herman; Jianping Huang; Roderick V Jensen; Rui Jiang; Charles D Johnson; Giuseppe Jurman; Yvonne Kahlert; Sadik A Khuder; Matthias Kohl; Jianying Li; Li Li; Menglong Li; Quan-Zhen Li; Shao Li; Zhiguang Li; Jie Liu; Ying Liu; Zhichao Liu; Lu Meng; Manuel Madera; Francisco Martinez-Murillo; Ignacio Medina; Joseph Meehan; Kelci Miclaus; Richard A Moffitt; David Montaner; Piali Mukherjee; George J Mulligan; Padraic Neville; Tatiana Nikolskaya; Baitang Ning; Grier P Page; Joel Parker; R Mitchell Parry; Xuejun Peng; Ron L Peterson; John H Phan; Brian Quanz; Yi Ren; Samantha Riccadonna; Alan H Roter; Frank W Samuelson; Martin M Schumacher; Joseph D Shambaugh; Qiang Shi; Richard Shippy; Shengzhu Si; Aaron Smalter; C Sotiriou; Mat Soukup; Staedtler Frank; Guido Steiner; Todd H Stokes; Qinglan Sun; Pei-Yi Tan; Rong Tang; Zivana Tezak; Brett Thorn; Marina Tsyganova; Yaron Turpaz; Silvia C Vega; Roberto Visintainer; Juergen von Frese; Charles Wang; Eric Wang; Junwei Wang; Wei Wang; Frank Westermann; James C Willey; Matthew Woods; Shujian Wu; Nianqing Xiao; Joshua Xu; Lei Xu; Lun Yang; Xiao Zeng; Jialu Zhang; Li Zhang; Min Zhang; Chen Zhao; Raj K Puri; Uwe Scherf; Weida Tong; Russell D Wolfinger
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models.
Nature biotechnology 2010;28(8):827-38.
2010: Hao Wu; BRIAN CAFFO; HARRIS JAFFEE; Rafael A Irizarry; Andrew P Feinberg
Redefining CpG islands using hidden Markov models.
Biostatistics (Oxford, England) 2010;11(3):499-514.
2010: Eric Schafer; Rafael A Irizarry; Sandeep Negi; Emily McIntyre; Donald Small; MARIA FIGUEROA; Ari Melnick; Patrick Brown
Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting.
Blood 2010;115(23):4798-809.
2010: Hao Wu; Rafael A Irizarry; Héctor Corrada Bravo
Intensity normalization improves color calling in SOLiD sequencing.
Nature methods 2010;7(5):336-7.
2010: Matthew N McCall; Benjamin M Bolstad; Rafael A Irizarry
Frozen robust multiarray analysis (fRMA).
Biostatistics (Oxford, England) 2010;11(2):242-53.
2010: Andrew P Feinberg; Rafael A Irizarry
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 2010;107 Suppl 1():1757-64.
2010: Benilton S Carvalho; Thomas A Louis; Rafael A Irizarry
Quantifying uncertainty in genotype calls.
Bioinformatics (Oxford, England) 2010;26(2):242-9.
2010: Margaret A Taub; Hector Corrada Bravo; Rafael A Irizarry
Overcoming bias and systematic errors in next generation sequencing data.
Genome medicine 2010;2(12):87.
2010: Sachin Sah; Matthew N McCall; Deepa Eveleigh; Michael Wilson; Rafael A Irizarry
Performance evaluation of commercial miRNA expression array platforms.
BMC research notes 2010;3():80.
2010: Pedro López-Romero; Manuel A González; Sergio Callejas; Ana Dopazo; Rafael A Irizarry
Processing of Agilent microRNA array data.
BMC research notes 2010;3():18.
2009: Rafael A Irizarry; Chi Wang; Yun Zhou; Terence P Speed
Gene set enrichment analysis made simple.
Statistical methods in medical research 2009;18(6):565-75.
2009: Akiko Doi; In-Hyun Park; Bo Wen; Peter Murakami; Martin Aryee; Rafael A Irizarry; Brian Herb; Christine Ladd-Acosta; Junsung Rho; Sabine Loewer; Justine Miller; Thorsten Schlaeger; George Q Daley; Andrew P Feinberg
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts.
Nature genetics 2009;41(12):1350-3.
2009: Matthew Ritchie; Benilton S Carvalho; Kurt N Hetrick; Simon Tavaré; Rafael A Irizarry
R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.
Bioinformatics (Oxford, England) 2009;25(19):2621-3.
2009: Rafael A Irizarry; Hao Wu; Andrew P Feinberg
A species-generalized probabilistic model-based definition of CpG islands.
Mammalian genome : official journal of the International Mammalian Genome Society 2009;20(9-10):674-80.
2009: Bo Wen; Hao Wu; Yoichi Shinkai; Rafael A Irizarry; Andrew P Feinberg
Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells.
Nature genetics 2009;41(2):246-50.
2009: Rafael A Irizarry; Christine Ladd-Acosta; Bo Wen; Zhijin Wu; Carolina Montano; Patrick Onyango; Hengmi Cui; Kevin Gabo; Michael Rongione; Maree Webster; Hong Ji; James B Potash; Sarven Sabunciyan; Andrew P Feinberg
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores.
Nature genetics 2009;41(2):178-86.
2008: Srinivasan Yegnasubramanian; Michael C Haffner; YONGGANG ZHANG; Bora Gurel; Toby C Cornish; Zhijin Wu; Rafael A Irizarry; James Morgan; Jessica Hicks; Theodore L DeWeese; William B Isaacs; G Steven Bova; Angelo M DeMarzo; William G Nelson
DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity.
Cancer research 2008;68(21):8954-67.
2008: Bo Wen; Hao Wu; Hans Bjornsson; Roland D Green; Rafael A Irizarry; Andrew P Feinberg
Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification.
Genome research 2008;18(11):1806-13.
2008: Matthew N McCall; Rafael A Irizarry
Consolidated strategy for the analysis of microarray spike-in data.
Nucleic acids research 2008;36(17):e108.
2008: Wenyi Wang; Benilton Carvalho; Neil R Miller; Jonathan Pevsner; Aravinda Chakravarti; Rafael A Irizarry
Estimating genome-wide copy number using allele-specific mixture models.
Journal of computational biology : a journal of computational molecular cell biology 2008;15(7):857-66.
2008: Hans T Bjornsson; Martin Sigurdsson; MARGARET D FALLIN; Rafael A Irizarry; Thor Aspelund; Hengmi Cui; Wenqiang Yu; Michael A Rongione; Tomas J Ekström; Tamara B Harris; Lenore J Launer; Gudny Eiriksdottir; Mark F Leppert; Carmen Sapienza; Vilmundur Gudnason; Andrew P Feinberg
Intra-individual change over time in DNA methylation with familial clustering.
JAMA : the journal of the American Medical Association 2008;299(24):2877-83.
2008: Hans T Bjornsson; Thomas J Albert; Christine M Ladd-Acosta; Roland D Green; Michael A Rongione; Christina M Middle; Rafael A Irizarry; Karl W Broman; Andrew P Feinberg
SNP-specific array-based allele-specific expression analysis.
Genome research 2008;18(5):771-9.
2008: Rafael A Irizarry; Christine Ladd-Acosta; Benilton Carvalho; Hao Wu; Sheri A Brandenburg; Jeffrey A Jeddeloh; Bo Wen; Andrew P Feinberg
Comprehensive high-throughput arrays for relative methylation (CHARM).
Genome research 2008;18(5):780-90.
2008: Henrik Bengtsson; Rafael A Irizarry; B Carvalho; Terence P Speed
Estimation and assessment of raw copy numbers at the single locus level.
Bioinformatics (Oxford, England) 2008;24(6):759-67.
2008: Brian D Peyser; Rafael A Irizarry; Forrest Spencer
Statistical analysis of fitness data determined by TAG hybridization on microarrays.
Methods in molecular biology (Clifton, N.J.) 2008;416():369-81.
2008: Pamela B Meluh; Xuewen Pan; Daniel S Yuan; CAROL TIFFANY; Ou Chen; Sharon Sookhai-Mahadeo; Xiaoling Wang; Brian D Peyser; Rafael A Irizarry; Forrest Spencer; Jef Boeke
Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray.
Methods in molecular biology (Clifton, N.J.) 2008;416():221-47.
2008: Shin Lin; Benilton Carvalho; David J Cutler; Dan E Arking; Aravinda Chakravarti; Rafael A Irizarry
Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays.
Genome biology 2008;9(4):R63.
2008: José F Rodríguez-Quiñones; Rafael A Irizarry; Nitza L Díaz-Blanco; Félix E Rivera-Molina; Diana Gómez-Garzón; José R Rodríguez-Medina
Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions.
BMC genomics 2008;9():34.
2007: Michael J Zilliox; Rafael A Irizarry
A gene expression bar code for microarray data.
Nature methods 2007;4(11):911-3.
2007: Nilsa I Loyo-Berríos; Rafael A Irizarry; Joseph G Hennessey; XU GUANG TAO; Genevieve M Matanoski
Air pollution sources and childhood asthma attacks in Catano, Puerto Rico.
American journal of epidemiology 2007;165(8):927-35.
2007: Benilton Carvalho; Henrik Bengtsson; Terence P Speed; Rafael A Irizarry
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.
Biostatistics (Oxford, England) 2007;8(2):485-99.
2006: Daniel S Yuan; Rafael A Irizarry
High-resolution spatial normalization for microarrays containing embedded technical replicates.
Bioinformatics (Oxford, England) 2006;22(24):3054-60.
2006: Sarah J Wheelan; Lisa Z Scheifele; Francisco Martínez-Murillo; Rafael A Irizarry; Jef Boeke
Transposon insertion site profiling chip (TIP-chip).
Proceedings of the National Academy of Sciences of the United States of America 2006;103(47):17632-7.
2006: Sarah J Wheelan; Francisco Martínez-Murillo; Rafael A Irizarry; Jef Boeke
Stacking the deck: double-tiled DNA microarrays.
Nature methods 2006;3(11):903-7.
2006: John Quackenbush; Rafael A Irizarry
Response to Shields: 'MIAME, we have a problem'.
Trends in genetics : TIG 2006;22(9):471-2.
2006: Hidekazu Takahashi; J Michael McCaffery; Rafael A Irizarry; Jef Boeke
Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription.
Molecular cell 2006;23(2):207-17.
2006: Janet A DiPietro; Laura E Caulfield; Rafael A Irizarry; Ping Chen; Mario Merialdi; Nelly Zavaleta
Prenatal development of intrafetal and maternal-fetal synchrony.
Behavioral neuroscience 2006;120(3):687-701.
2006: Rafael A Irizarry; Zhijin Wu; HARRIS JAFFEE
Comparison of Affymetrix GeneChip expression measures.
Bioinformatics (Oxford, England) 2006;22(7):789-94.
2006: John Quackenbush; Christian J Stoeckert; Catherine Ball; Alvis Brazma; Robert Gentleman; Wolfgang Huber; Rafael A Irizarry; Marc Salit; Gavin Sherlock; Paul Spellman; Neil Winegarden
Top-down standards will not serve systems biology.
Nature 2006;440(7080):24.
2006: Leslie Cope; Scott M Hartman; Hinrich Göhlmann; Jay P Tiesman; Rafael A Irizarry
Analysis of Affymetrix GeneChip data using amplified RNA.
BioTechniques 2006;40(2):165-6, 168, 170.
2006: Tim Rayner; Philippe Rocca-Serra; Paul Spellman; Helen C Causton; Anna Farne; Ele Holloway; Rafael A Irizarry; Junmin Liu; Donald S Maier; Michael Miller; Kjell Petersen; John Quackenbush; Gavin Sherlock; Christian J Stoeckert; Joseph White; Patricia L Whetzel; Farrell Wymore; Helen Parkinson; Ugis Sarkans; Catherine A Ball; Alvis Brazma
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB.
BMC bioinformatics 2006;7():489.
2006: Simon Katz; Rafael A Irizarry; Xue Lin; Mark Tripputi; Mark Porter
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database.
BMC bioinformatics 2006;7():464.
2006: Rafael A Irizarry; Leslie Cope; Zhijin Wu
Feature-level exploration of a published Affymetrix GeneChip control dataset.
Genome biology 2006;7(8):404.
2006: Scott Zeger; Rafael A Irizarry; Roger D Peng
On time series analysis of public health and biomedical data.
Annual review of public health 2006;27():57-79.
2006: Siew Loon Ooi; Xuewen Pan; Brian D Peyser; Ping Ye; Pamela B Meluh; Daniel S Yuan; Rafael A Irizarry; Joel S Bader; Forrest Spencer; Jef Boeke
Global synthetic-lethality analysis and yeast functional profiling.
Trends in genetics : TIG 2006;22(1):56-63.
2006: Noah Lechtzin; Majnu John; Rafael A Irizarry; Christian A Merlo; Gregory B Diette; Michael P Boyle
Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa.
Respiration; international review of thoracic diseases 2006;73(1):27-33.
2005: Shawn C Baker; Steven R Bauer; Richard P Beyer; James D Brenton; Bud Bromley; John Burrill; Helen Causton; Michael P Conley; Rosalie Elespuru; Michael Fero; Carole Foy; James Fuscoe; Xiaolian Gao; David Lee Gerhold; Patrick Gilles; Federico Goodsaid; Xu Guo; Joe Hackett; Richard D Hockett; Pranvera Ikonomi; Rafael A Irizarry; Ernest S Kawasaki; Tamma Kaysser-Kranich; Kathleen Kerr; Gretchen Kiser; Walter H Koch; Kathy Y Lee; Chunmei Liu; Z Lewis Liu; Anne Lucas; Chitra F Manohar; Garry Miyada; Zora Modrusan; Helen Parkes; Raj K Puri; Laura Reid; Thomas B Ryder; Marc Salit; Raymond R Samaha; Uwe Scherf; Timothy J Sendera; Robert A Setterquist; Leming Shi; Richard Shippy; Jesus V Soriano; Elizabeth A Wagar; Janet A Warrington; Mickey Williams; Frederike Wilmer; Mike Wilson; Paul K Wolber; Xiaoning Wu; Renata Zadro
The External RNA Controls Consortium: a progress report.
Nature methods 2005;2(10):731-4.
2005: Michelle M Kittleson; Khalid M Minhas; Rafael A Irizarry; Shui Q Ye; Gina Edness; Elayne Breton; John V Conte; Gordon F Tomaselli; Joe G. N. Garcia; Joshua M Hare
Gene expression in giant cell myocarditis: Altered expression of immune response genes.
International journal of cardiology 2005;102(2):333-40.
2005: Zhijin Wu; Rafael A Irizarry
Stochastic models inspired by hybridization theory for short oligonucleotide arrays.
Journal of computational biology : a journal of computational molecular cell biology 2005;12(6):882-93.
2005: Michelle M Kittleson; Khalid M Minhas; Rafael A Irizarry; Shui Q Ye; Gina Edness; Elayne Breton; John V Conte; Gordon F Tomaselli; Joe G. N. Garcia; Joshua M Hare
Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure.
Physiological genomics 2005;21(3):299-307.
2005: Nadia N Hansel; Sara C Hilmer; Steve N Georas; Leslie Cope; Jia Guo; Rafael A Irizarry; Gregory B Diette
Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma.
The Journal of laboratory and clinical medicine 2005;145(5):263-74.
2005: Rafael A Irizarry; Daniel S Warren; Forrest Spencer; Irene F Kim; Shyam Biswal; Bryan C Frank; Edward Gabrielson; Joe G. N. Garcia; Joel Geoghegan; Gregory G Germino; Constance A Griffin; Sara C Hilmer; Eric Hoffman; Anne E Jedlicka; Ernest Kawasaki; Francisco Martínez-Murillo; Laura Morsberger; Hannah Lee; David Petersen; John Quackenbush; Alan L Scott; Michael Wilson; Yanqin Yang; Shui Q Ye; Wayne Yu
Multiple-laboratory comparison of microarray platforms.
Nature methods 2005;2(5):345-50.
2005: Christina Kendziorski; Rafael A Irizarry; K-S Chen; Jill D Haag; Michael N Gould
On the utility of pooling biological samples in microarray experiments.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(12):4252-7.
2005: Brian D Peyser; Rafael A Irizarry; CAROL TIFFANY; Ou Chen; Daniel S Yuan; Jef Boeke; Forrest Spencer
Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools.
Nucleic acids research 2005;33(16):e140.
2005: Daniel S Yuan; Xuewen Pan; Siew Loon Ooi; Brian D Peyser; Forrest Spencer; Rafael A Irizarry; Jef Boeke
Improved microarray methods for profiling the Yeast Knockout strain collection.
Nucleic acids research 2005;33(12):e103.
2005: Dmitry N Grigoryev; Shwu-Fan Ma; Bret Simon; Rafael A Irizarry; Shui Q Ye; Joe G. N. Garcia
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.
BMC genomics 2005;6():62.
2004: Michelle M Kittleson; Shui Q Ye; Rafael A Irizarry; Khalid M Minhas; Gina Edness; John V Conte; Giovanni Parmigiani; Leslie W Miller; Yingjie Chen; Jennifer L Hall; Joe G. N. Garcia; Joshua M Hare
Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy.
Circulation 2004;110(22):3444-51.
2004: Janet A DiPietro; Rafael A Irizarry; Kathleen A Costigan; Edith D Gurewitsch
The psychophysiology of the maternal-fetal relationship.
Psychophysiology 2004;41(4):510-20.
2004: Zhijin Wu; Rafael A Irizarry
Preprocessing of oligonucleotide array data.
Nature biotechnology 2004;22(6):656-8; author reply 658.
2004: Cheryl D Warren; D Mark Eckley; Marina S Lee; Joseph S Hanna; Adam Hughes; Brian D Peyser; Chunfa Jie; Rafael A Irizarry; Forrest Spencer
S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion.
Molecular biology of the cell 2004;15(4):1724-35.
2004: Leslie Cope; Rafael A Irizarry; HARRIS JAFFEE; Zhijin Wu; Terence P Speed
A benchmark for Affymetrix GeneChip expression measures.
Bioinformatics (Oxford, England) 2004;20(3):323-31.
2004: Laurent Gautier; Leslie Cope; Benjamin M Bolstad; Rafael A Irizarry
affy--analysis of Affymetrix GeneChip data at the probe level.
Bioinformatics (Oxford, England) 2004;20(3):307-15.
2004: Derek A T Cummings; Rafael A Irizarry; Norden E Huang; Timothy Endy; Ananda Nisalak; Kumnuan Ungchusak; Donald S. Burke
Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand.
Nature 2004;427(6972):344-7.
2004: Benjamin M Bolstad; F Collin; Ken M Simpson; Rafael A Irizarry; Terence P Speed
Experimental design and low-level analysis of microarray data.
International review of neurobiology 2004;60():25-58.
2004: Robert Gentleman; Vincent J Carey; Douglas M Bates; Ben Bolstad; Michael Dettling; Sandrine Dudoit; Byron Ellis; Laurent Gautier; Yongchao Ge; Jeff Gentry; Kurt Hornik; Torsten Hothorn; Wolfgang Huber; Stefano Iacus; Rafael A Irizarry; Franz Leisch; Cheng Li; Martin Maechler; Anthony J Rossini; Gunther Sawitzki; Colin Smith; Gordon Smyth; Luke Tierney; Jean Y H Yang; Jianhua Zhang
Bioconductor: open software development for computational biology and bioinformatics.
Genome biology 2004;5(10):R80.
2004: Dmitry N Grigoryev; Shwu-Fan Ma; Rafael A Irizarry; Shui Q Ye; John Quackenbush; Joe G. N. Garcia
Orthologous gene-expression profiling in multi-species models: search for candidate genes.
Genome biology 2004;5(5):R34.
2004: Haolin Chen; Rafael A Irizarry; LIN-DI LUO; Barry R Zirkin
Leydig cell gene expression: effects of age and caloric restriction.
Experimental gerontology 2004;39(1):31-43.
2003: David Sidransky; Rafael A Irizarry; Joseph A Califano; Xianbin Li; Hening Ren; Nicole Benoit; Li Mao
Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer patients from control subjects.
Journal of the National Cancer Institute 2003;95(22):1711-7.
2003: Daniel O Scharfstein; Rafael A Irizarry
Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data.
Biometrics 2003;59(3):601-13.
2003: Thomas P Cappola; Leslie Cope; Amy Cernetich; Lili A Barouch; Khalid M Minhas; Rafael A Irizarry; Giovanni Parmigiani; Sarfraz Durrani; Tera Lavoie; Eric Hoffman; Shui Q Ye; Joe G. N. Garcia; Joshua M Hare
Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy.
Physiological genomics 2003;14(1):25-34.
2003: Rafael A Irizarry; Bridget Hobbs; Francois Collin; Yasmin D Beazer-Barclay; Kristen J Antonellis; Uwe Scherf; Terence P Speed
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
Biostatistics (Oxford, England) 2003;4(2):249-64.
2003: Clarke G Tankersley; Rafael A Irizarry; Susan E Flanders; Richard Rabold; Robert Frank
Unstable heart rate and temperature regulation predict mortality in AKR/J mice.
American journal of physiology. Regulatory, integrative and comparative physiology 2003;284(3):R742-50.
2003: Rafael A Irizarry; Benjamin M Bolstad; Francois Collin; Leslie Cope; Bridget Hobbs; Terence P Speed
Summaries of Affymetrix GeneChip probe level data.
Nucleic acids research 2003;31(4):e15.
2003: Benjamin M Bolstad; Rafael A Irizarry; M Astrand; Terence P Speed
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.
Bioinformatics (Oxford, England) 2003;19(2):185-93.
2003: Rafael A Irizarry; Siew Loon Ooi; Zhijin Wu; Jef Boeke
Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants.
Statistical applications in genetics and molecular biology 2003;2():Article1.
2002: Clarke G Tankersley; Rafael A Irizarry; Susan E Flanders; Richard Rabold
Circadian rhythm variation in activity, body temperature, and heart rate between C3H/HeJ and C57BL/6J inbred strains.
Journal of applied physiology (Bethesda, Md. : 1985) 2002;92(2):870-7.
2001: Nathan E Crone; L Hao; John Hart; Dana F Boatman; Ronald P Lesser; Rafael A Irizarry; Barry Gordon
Electrocorticographic gamma activity during word production in spoken and sign language.
Neurology 2001;57(11):2045-53.
2001: Rafael A Irizarry; Clarke G Tankersley; R Frank; S Flanders
Assessing homeostasis through circadian patterns.
Biometrics 2001;57(4):1228-37.
2001: Janet A DiPietro; Rafael A Irizarry; MELISSA HAWKINS; Kathleen A Costigan; Eva K Pressman
Cross-correlation of fetal cardiac and somatic activity as an indicator of antenatal neural development.
American journal of obstetrics and gynecology 2001;185(6):1421-8.