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Rafael A Irizarry, PhD


Researcher

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Researcher

  • Professor of Biostatistics and Computational Biology, Dana-Farber Cancer Institute

Contact Information

  • Office Phone Number617-632-3012
  • Fax617-632-2444

Bio

Dr. 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 Bloomberg School of Public Health in 1998 and was promoted to Professor in 2007. For the past ten years, Dr. Irizarry's work has focused on Genomics and Computational Biology problems. In particular, he has worked on the analysis and pre-processing of microarray, second-generation sequencing, and genomic data. He is currently interested in leveraging his knowledge in translational work, e.g. developing diagnostic tools and discovering biomarkers.Dr. 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 the most widely used software tool for the analysis of microarray data and garnered a 2003 Insightful Innovation Award.In 2009, the Committee of Presidents of Statistical Societies (COPSS) named Dr. Irizarry the Presidents' Award winner. The Presidents' Award is arguably the profession's most prestigious award honoring early career contributions. Dr. Irizarry 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.Three of Dr. 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 to Chinese and Japanese.

Recent Awards:

  • The Benjamin Franklin Award for Open Access in the Life Sciences
  • Myrto Lefkopoulou Distinguished Lecturer Award
  • Ranked second-most cited mathematical scientist in the world by Essential Science Indicators.
  • COPSS President’s Award presented to a young member of the statistical community in recognition of an outstanding contribution to the profession.
  • Mortimer Spiegelman Award which recognizes a statistician age 40 years or younger who has made outstanding contributions to public health statistics.
  • American Statistical Association Fellow
  • Distinguished Alumni. College of Natural Sciences, University of Puerto Rico, Río Piedras.
  • Main author of Fast Breaking Paper in Mathematics awarded by Thomson Essential Science Indicators (ESI).
  • ASA Youden Award in Interlaboratory Testing
  • ASA Outstanding Statistical Application Award which recognizes a paper that is an outstanding application of statistics in any substantive field.
  • Dean’s Lecture: Bloomberg School of Public Health
  • Main author of Fast Breaking Paper and New Hot Paper in Mathematics awarded by Thomson Essential Science Indicators (ESI).
  • American Statistical Association Noether Young Scholar Award for researcher, younger than 35 years of age, who has significant research accomplishments in nonparametrics statistics
  • Outstanding Graduate Student Instructor Award, University of California, Berkeley
  • Chancellor's Predoctoral Opportunity Fellowship, University of California, Berkeley
  • National Science Foundation Graduate Fellow
  • Facundo Bueso Medal, School of Natural Science, University of Puerto Rico
  • Mathematics Medal, University of Puerto Rico
  • First Prize Inter-collegiate Advanced Programming Competition, University of Puerto Rico, Río Piedras
  • First Prize University Mathematics Olympics, University of Puerto Rico, Cayey

Research

The unprecedented advancements in digital technology during the second half of the 20th century has produced a measurement revolution that is transforming science. In biomedical research, the Genomics revolution is being driven by new technologies that permit us to observe molecular entities analogous to identifying microorganisms and other breakthroughs permitted by the invention of the microscope. Choice examples of these technologies are next generation sequencing (NGS) and microarrays.
Scientific fields that have traditionally relied upon simple data analysis techniques have been turned on their heads by these technologies. Interpreting information extracted from these massive and complex datasets requires sophisticated statistical methodology as one can easily be fooled by patterns arising by chance or systematic errors that are hard to detect.
Rafael Irizarry’s lab is interested in the development of statistical tools that help researchers better interpret their data. The lab disseminates these tools through open source that is available for free online. This software has tens of thousands of users and the scientific publications in which these methods are highly cited.

 

Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. NPJ Biofilms Microbiomes. 2021 09 10; 7(1):75.
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Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 01.
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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.
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Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. 2021 May 10; 39(5):632-648.e8.
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Robust decomposition of cell type mixtures in spatial transcriptomics. Nat Biotechnol. 2021 Feb 18.
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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.
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Author Correction: Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat Med. 2020 Oct; 26(10):1663.
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Every Body Counts: Measuring Mortality From the COVID-19 Pandemic. Ann Intern Med. 2020 12 15; 173(12):1004-1007.
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Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23.
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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.
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Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers. Genome Biol. 2020 07 03; 21(1):160.
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Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat Med. 2020 07; 26(7):1041-1043.
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Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Genome Biol. 2019 12 23; 20(1):295.
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methylCC: technology-independent estimation of cell type composition using differentially methylated regions. Genome Biol. 2019 11 29; 20(1):261.
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Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing. Biostatistics. 2019 07 01; 20(3):367-383.
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A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Development. 2019 03 28; 146(6).
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A Guide to Teaching Data Science. Am Stat. 2018; 72(4):382-391.
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Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. 2018 10 01; 19(4):562-578.
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Mortality in Puerto Rico after Hurricane Maria. N Engl J Med. 2018 Jul 12; 379(2):162-170.
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Smooth quantile normalization. Biostatistics. 2018 04 01; 19(2):185-198.
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High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 2018 03 15; 37(6).
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Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun. 2017 12 05; 8(1):1784.
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Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res. 2017 11; 27(11):1930-1938.
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SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet. 2017 Nov; 49(11):1613-1623.
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Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Res. 2017 Jun 02; 45(10):e77.
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Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 05 08; 18(1):84.
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Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017 Apr; 14(4):417-419.
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Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses. Nat Methods. 2017 02 28; 14(3):216-217.
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Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017 02; 28(2):167-176.
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Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 09 30; 17(1):203.
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Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res. 2017 01 25; 45(2):e9.
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Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol. 2016 Dec; 34(12):1287-1291.
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Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 05 23; 17(1):107.
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A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 Apr 23; 17:74.
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A multi-omic analysis of human naïve CD4+ T cells. BMC Syst Biol. 2015 Nov 06; 9:75.
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quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol. 2015 Jun 04; 16:117.
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Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2015 Jul; 26(7):959-72.
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Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol. 2015 Apr 16; 16:80.
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Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015 Feb; 12(2):115-21.
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Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med. 2014; 6(8):61.
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Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014 Jul; 15(3):584-5.
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IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30; 15(6):R86.
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KRLMM: an adaptive genotype calling method for common and low frequency variants. BMC Bioinformatics. 2014 May 23; 15:158.
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Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014 Feb 04; 15(2):R31.
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Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014 Jun 01; 30(11):1514-21.
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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014 May 15; 30(10):1363-9.
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Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014 Jul; 15(3):413-26.
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MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014; 15(12):554.
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The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D938-43.
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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.
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Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2013 Nov 07; 503(7474):146.
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Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55.
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Measuring cell-type specific differential methylation in human brain tissue. Genome Biol. 2013 Aug 30; 14(8):R94.
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ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics. 2013 May 01; 29(9):1182-9.
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DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med. 2013 Jan 23; 5(169):169ra10.
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Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics. 2012 Nov 15; 13:303.
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Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics. 2012 Oct 22; 13:272.
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fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics. 2012 Dec 01; 28(23):3153-4.
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BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012 Oct 03; 13(10):R83.
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Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci. 2012 Oct; 15(10):1371-3.
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The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC Bioinformatics. 2012 May 15; 13:98.
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Genome-wide DNA methylation scan in major depressive disorder. PLoS One. 2012; 7(4):e34451.
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Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2012 Feb 08; 482(7384):251-5.
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Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol. 2012 Feb; 41(1):200-9.
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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.
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Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics. 2012 Apr; 13(2):204-16.
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Fast wavelet based functional models for transcriptome analysis with tiling arrays. Stat Appl Genet Mol Biol. 2012 Jan 06; 11(1):Article 4.
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Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biol. 2011 Sep 28; 12(9):R93.
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Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinformatics. 2011 Sep 16; 12:369.
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Sequencing technology does not eliminate biological variability. Nat Biotechnol. 2011 Jul 11; 29(7):572-3.
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Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011 Jun 26; 43(8):768-75.
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Significance analysis and statistical dissection of variably methylated regions. Biostatistics. 2012 Jan; 13(1):166-78.
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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.
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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.
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Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics. 2011 May 07; 12:137.
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Using the R Package crlmm for Genotyping and Copy Number Estimation. J Stat Softw. 2011 May 01; 40(12):1-32.
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Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics. 2011 Apr 15; 27(8):1052-60.
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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.
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Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. BMC Bioinformatics. 2011 Mar 08; 12:68.
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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.
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Overcoming bias and systematic errors in next generation sequencing data. Genome Med. 2010 Dec 10; 2(12):87.
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Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics. 2011 Apr; 12(2):197-210.
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Epigenetic memory in induced pluripotent stem cells. Nature. 2010 Sep 16; 467(7313):285-90.
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Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med. 2010 Sep 15; 2(49):49ra67.
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Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010 10; 11(10):733-9.
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Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics. 2010 Sep; 66(3):665-74.
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Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010 Sep 16; 467(7313):338-42.
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A framework for oligonucleotide microarray preprocessing. Bioinformatics. 2010 Oct 01; 26(19):2363-7.
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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.
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A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics. 2011 Jan; 12(1):33-50.
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Intensity normalization improves color calling in SOLiD sequencing. Nat Methods. 2010 May; 7(5):336-7.
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Performance evaluation of commercial miRNA expression array platforms. BMC Res Notes. 2010 Mar 18; 3:80.
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Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting. Blood. 2010 Jun 10; 115(23):4798-809.
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Redefining CpG islands using hidden Markov models. Biostatistics. 2010 Jul; 11(3):499-514.
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Processing of Agilent microRNA array data. BMC Res Notes. 2010 Jan 22; 3:18.
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Frozen robust multiarray analysis (fRMA). Biostatistics. 2010 Apr; 11(2):242-53.
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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.
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Gene set enrichment analysis made simple. Stat Methods Med Res. 2009 Dec; 18(6):565-75.
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Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15; 26(2):242-9.
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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.
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A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome. 2009 Sep-Oct; 20(9-10):674-80.
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R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics. 2009 Oct 01; 25(19):2621-3.
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Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet. 2009 Feb; 41(2):246-50.
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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.
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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.
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Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Res. 2008 Nov; 18(11):1806-13.
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Estimating genome-wide copy number using allele-specific mixture models. J Comput Biol. 2008 Sep; 15(7):857-66.
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Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Res. 2008 Oct; 36(17):e108.
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Intra-individual change over time in DNA methylation with familial clustering. JAMA. 2008 Jun 25; 299(24):2877-83.
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Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol. 2008 Apr 03; 9(4):R63.
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SNP-specific array-based allele-specific expression analysis. Genome Res. 2008 May; 18(5):771-9.
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Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008 May; 18(5):780-90.
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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.
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Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics. 2008 Mar 15; 24(6):759-67.
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Statistical analysis of fitness data determined by TAG hybridization on microarrays. Methods Mol Biol. 2008; 416:369-81.
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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.
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A gene expression bar code for microarray data. Nat Methods. 2007 Nov; 4(11):911-3.
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Air pollution sources and childhood asthma attacks in Catano, Puerto Rico. Am J Epidemiol. 2007 Apr 15; 165(8):927-35.
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Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr; 8(2):485-99.
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Transposon insertion site profiling chip (TIP-chip). Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17632-7.
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A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489.
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Stacking the deck: double-tiled DNA microarrays. Nat Methods. 2006 Nov; 3(11):903-7.
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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.
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High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics. 2006 Dec 15; 22(24):3054-60.
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Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell. 2006 Jul 21; 23(2):207-17.
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Response to Shields: 'MIAME, we have a problem'. Trends Genet. 2006 Sep; 22(9):471-2.
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Prenatal development of intrafetal and maternal-fetal synchrony. Behav Neurosci. 2006 Jun; 120(3):687-701.
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Top-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24.
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Analysis of Affymetrix GeneChip data using amplified RNA. Biotechniques. 2006 Feb; 40(2):165-6, 168, 170.
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Comparison of Affymetrix GeneChip expression measures. Bioinformatics. 2006 Apr 01; 22(7):789-94.
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Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol. 2006; 7(8):404.
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On time series analysis of public health and biomedical data. Annu Rev Public Health. 2006; 27:57-79.
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Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 2006 Jan; 22(1):56-63.
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The External RNA Controls Consortium: a progress report. Nat Methods. 2005 Oct; 2(10):731-4.
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Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res. 2005 Sep 15; 33(16):e140.
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Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa. Respiration. 2006; 73(1):27-33.
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Gene expression in giant cell myocarditis: Altered expression of immune response genes. Int J Cardiol. 2005 Jul 10; 102(2):333-40.
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Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol. 2005 Jul-Aug; 12(6):882-93.
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Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res. 2005 Jul 01; 33(12):e103.
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In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology. BMC Genomics. 2005 May 04; 6:62.
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Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma. J Lab Clin Med. 2005 May; 145(5):263-74.
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Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005 May; 2(5):345-50.
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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.
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On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci U S A. 2005 Mar 22; 102(12):4252-7.
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Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation. 2004 Nov 30; 110(22):3444-51.
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Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80.
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The psychophysiology of the maternal-fetal relationship. Psychophysiology. 2004 Jul; 41(4):510-20.
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Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun; 22(6):656-8; author reply 658.
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Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol. 2004; 5(5):R34.
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A benchmark for Affymetrix GeneChip expression measures. Bioinformatics. 2004 Feb 12; 20(3):323-31.
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affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004 Feb 12; 20(3):307-15.
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S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion. Mol Biol Cell. 2004 Apr; 15(4):1724-35.
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Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand. Nature. 2004 Jan 22; 427(6972):344-7.
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Leydig cell gene expression: effects of age and caloric restriction. Exp Gerontol. 2004 Jan; 39(1):31-43.
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Experimental design and low-level analysis of microarray data. Int Rev Neurobiol. 2004; 60:25-58.
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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.
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Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data. Biometrics. 2003 Sep; 59(3):601-13.
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Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol Genomics. 2003 Jun 24; 14(1):25-34.
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Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr; 4(2):249-64.
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Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Stat Appl Genet Mol Biol. 2003; 2:Article1.
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Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003 Feb 15; 31(4):e15.
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A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22; 19(2):185-93.
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Unstable heart rate and temperature regulation predict mortality in AKR/J mice. . 2003 Mar; 284(3):R742-50.
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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.
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Electrocorticographic gamma activity during word production in spoken and sign language. Neurology. 2001 Dec 11; 57(11):2045-53.
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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.
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Assessing homeostasis through circadian patterns. Biometrics. 2001 Dec; 57(4):1228-37.
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