DFCI Logo
DFCI Logo
Rafael A Irizarry, PhD

Rafael A Irizarry, PhD

Researcher
MAKE AN APPOINTMENT

Contact Information

Office Phone Number

+1 (617) 632-2454

Fax

617-632-2444

On This Page

Biography

Rafael A Irizarry, PhD

Rafael Irizarry received his Bachelor’s in Mathematics in 1993 from the University of Puerto Rico and went on to receive a Ph.D. in Statistics in 1998 from the University of California, Berkeley. His thesis work was on Statistical Models for Music Sound Signals. He joined the faculty of the Johns Hopkins Department of Biostatistics in 1998 and was promoted to Professor in 2007. He is now Professor and Chair of the Department of Data Science at the Dana-Farber Cancer Institute and Professor of Biostatistics at Harvard School of Public Health.

Professor Irizarry is an applied statistician generally interested in using data to help solve real-world problems. During his career he as worked and co-authored papers on a variety of topics including musical sound signals, infectious diseases, circadian patterns in health, fetal health monitoring, estimating the effects of Hurricane María in Puerto Rico, and COVID19 vaccine effectiveness. His main focus during the last two decades has been in Genomics. Specifically, he has worked on the analysis and signal processing of data generated by emerging high-throughput technologies. He has distinguished himself by disseminating statistical methodology as open source software shared through the Bioconductor Project, a leading open source and open development software project for the analysis of high-throughput genomic data. His widely downloaded software tools have helped him become one of the most highly cited scientist in his field.

Professor Irizarry’s is also dedicated to education. This is best demonstrated by the success of the numerous trainees he has mentored. He has also developed some of the most popular online courses on data analysis, which have been completed by tens of thousands of students. These courses are divided into three series: Professional Certificate in Data Science, Data Analysis for the Life Sciences and Genomics Data Analysis. He shares the material for these courses through textbooks that are freely available online and reproducible code through GitHub.

Professor Irizarry also dedicates his time providing service to the profession. Examples of this work include serving as the chair of the Genomics, Computational Biology and Technology Study Section (GCAT) National Institute of Health (NIH) study section, the search committee for the National Library of Medicine director, the National Academy of Sciences Gulf War and Health Committee, and the National Advisory Council for Human Genome Research. 

Professor Irizarry has received several awards honoring the work described above. In 2009, the Committee of Presidents of Statistical Societies (COPSS) named him the Presidents’ Award winner, arguably the most prestigious award in Statistics. That year he was also named a fellow of the American Statistical Association. In 2017 the members of Bioinformatics.org chose Professor Irizarry the laureate of the Benjamin Franklin Award in the Life Sciences. In 2020 he became an ISCB Fellows. He has also received the 2019 Research Parasite Award for outstanding contributions to the rigorous secondary analysis of data, the 2009 Mortimer Spiegelman Award which honors an outstanding public health statistician under age 40, the ASA Youden Award in Interlaboratory Testing, the 2004 American Statistical Association (ASA) Outstanding Statistical Application Award, and 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.

Researcher

Physician

Chair and Professor of Data Science, Dana-Farber Cancer Institute
Professor of Biostatistics, Harvard T.H. Chan School of Public Health
Lavine Family Chair for Preventative Cancer Therapies, Dana-Farber Cancer Institute

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

    View Dr. Irizarry’s 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.

     

    Research Departments

    Research Website

    http://rafalab.org

    Publications

      View Dr. Irizarry's Publications

      • DNA binding analysis of rare variants in homeodomains reveals homeodomain specificity-determining residues. Nat Commun. 2024 Apr 10; 15(1):3110. View in: Pubmed

      • Effects of KRAS Genetic Interactions on Outcomes in Cancers of the Lung, Pancreas, and Colorectum. Cancer Epidemiol Biomarkers Prev. 2024 01 09; 33(1):158-169. View in: Pubmed

      • Reassessing pharmacogenomic cell sensitivity with multilevel statistical models. Biostatistics. 2023 10 18; 24(4):901-921. View in: Pubmed

      • A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data. Epigenetics. 2023 12; 18(1):2257437. View in: Pubmed

      • UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability. Mol Cell. 2023 08 03; 83(15):2753-2767.e10. View in: Pubmed

      • Significance analysis for clustering with single-cell RNA-sequencing data. Nat Methods. 2023 08; 20(8):1196-1202. View in: Pubmed

      • Discovery of antibodies and cognate surface targets for ovarian cancer by surface profiling. Proc Natl Acad Sci U S A. 2023 01 03; 120(1):e2206751120. View in: Pubmed

      • A probabilistic gene expression barcode for annotation of cell types from single-cell RNA-seq data. Biostatistics. 2022 10 14; 23(4):1150-1164. View in: Pubmed

      • Cell type-specific inference of differential expression in spatial transcriptomics. Nat Methods. 2022 09; 19(9):1076-1087. View in: Pubmed

      • All-cause excess mortality across 90 municipalities in Gujarat, India, during the COVID-19 pandemic (March 2020-April 2021). PLOS Glob Public Health. 2022; 2(8):e0000824. View in: Pubmed

      • Differential richness inference for 16S rRNA marker gene surveys. Genome Biol. 2022 08 01; 23(1):166. View in: Pubmed

      • mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. BMC Genomics. 2022 Jun 13; 23(1):439. View in: Pubmed

      • A Flexible Statistical Framework for Estimating Excess Mortality. Epidemiology. 2022 05 01; 33(3):346-353. View in: Pubmed

      • Effectiveness estimates of three COVID-19 vaccines based on observational data from Puerto Rico. Lancet Reg Health Am. 2022 May; 9:100212. View in: Pubmed

      • Stem-like intestinal Th17 cells give rise to pathogenic effector T cells during autoimmunity. Cell. 2021 12 22; 184(26):6281-6298.e23. View in: Pubmed

      • Characterizing batch effects and binding site-specific variability in ChIP-seq data. NAR Genom Bioinform. 2021 Dec; 3(4):lqab098. View in: Pubmed

      • Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. NPJ Biofilms Microbiomes. 2021 09 10; 7(1):75. View in: Pubmed

      • Capturing discrete latent structures: choose LDs over PCs. Biostatistics. 2021 Sep 01. View in: Pubmed

      • 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. View in: Pubmed

      • Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. 2021 05 10; 39(5):632-648.e8. View in: Pubmed

      • Robust decomposition of cell type mixtures in spatial transcriptomics. Nat Biotechnol. 2022 04; 40(4):517-526. View in: Pubmed

      • 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. View in: Pubmed

      • Author Correction: Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat Med. 2020 Oct; 26(10):1663. View in: Pubmed

      • Every Body Counts: Measuring Mortality From the COVID-19 Pandemic. Ann Intern Med. 2020 12 15; 173(12):1004-1007. View in: Pubmed

      • Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23. View in: Pubmed

      • 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. View in: Pubmed

      • Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers. Genome Biol. 2020 07 03; 21(1):160. View in: Pubmed

      • Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat Med. 2020 07; 26(7):1041-1043. View in: Pubmed

      • Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model. Genome Biol. 2019 12 23; 20(1):295. View in: Pubmed

      • methylCC: technology-independent estimation of cell type composition using differentially methylated regions. Genome Biol. 2019 11 29; 20(1):261. View in: Pubmed

      • Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing. Biostatistics. 2019 07 01; 20(3):367-383. View in: Pubmed

      • A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs. Development. 2019 03 28; 146(6). View in: Pubmed

      • A Guide to Teaching Data Science. Am Stat. 2018; 72(4):382-391. View in: Pubmed

      • Selection-Corrected Statistical Inference for Region Detection With High-Throughput Assays. J Am Stat Assoc. 2019; 114(527):1351-1365. View in: Pubmed

      • Missing data and technical variability in single-cell RNA-sequencing experiments. Biostatistics. 2018 10 01; 19(4):562-578. View in: Pubmed

      • Mortality in Puerto Rico after Hurricane Maria. N Engl J Med. 2018 Jul 12; 379(2):162-170. View in: Pubmed

      • Smooth quantile normalization. Biostatistics. 2018 04 01; 19(2):185-198. View in: Pubmed

      • High-throughput identification of RNA nuclear enrichment sequences. EMBO J. 2018 03 15; 37(6). View in: Pubmed

      • Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun. 2017 12 05; 8(1):1784. View in: Pubmed

      • Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data. Genome Res. 2017 11; 27(11):1930-1938. View in: Pubmed

      • SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters. Nat Genet. 2017 Nov; 49(11):1613-1623. View in: Pubmed

      • Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Res. 2017 Jun 02; 45(10):e77. View in: Pubmed

      • Challenges and emerging directions in single-cell analysis. Genome Biol. 2017 05 08; 18(1):84. View in: Pubmed

      • Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017 Apr; 14(4):417-419. View in: Pubmed

      • Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses. Nat Methods. 2017 02 28; 14(3):216-217. View in: Pubmed

      • Proceedings of the third international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2017 02; 28(2):167-176. View in: Pubmed

      • Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 09 30; 17(1):203. View in: Pubmed

      • Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Res. 2017 01 25; 45(2):e9. View in: Pubmed

      • Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation. Nat Biotechnol. 2016 Dec; 34(12):1287-1291. View in: Pubmed

      • Erratum to: A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 05 23; 17(1):107. View in: Pubmed

      • A benchmark for RNA-seq quantification pipelines. Genome Biol. 2016 Apr 23; 17:74. View in: Pubmed

      • A multi-omic analysis of human naïve CD4+ T cells. BMC Syst Biol. 2015 Nov 06; 9:75. View in: Pubmed

      • quantro: a data-driven approach to guide the choice of an appropriate normalization method. Genome Biol. 2015 Jun 04; 16:117. View in: Pubmed

      • Proceedings of the second international molecular pathological epidemiology (MPE) meeting. Cancer Causes Control. 2015 Jul; 26(7):959-72. View in: Pubmed

      • Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin. Genome Biol. 2015 Apr 16; 16:80. View in: Pubmed

      • Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015 Feb; 12(2):115-21. View in: Pubmed

      • Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors. Genome Med. 2014; 6(8):61. View in: Pubmed

      • Corrigendum: Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014 Jul; 15(3):584-5. View in: Pubmed

      • IVT-seq reveals extreme bias in RNA sequencing. Genome Biol. 2014 Jun 30; 15(6):R86. View in: Pubmed

      • KRLMM: an adaptive genotype calling method for common and low frequency variants. BMC Bioinformatics. 2014 May 23; 15:158. View in: Pubmed

      • Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol. 2014 Feb 04; 15(2):R31. View in: Pubmed

      • Visualization and probability-based scoring of structural variants within repetitive sequences. Bioinformatics. 2014 Jun 01; 30(11):1514-21. View in: Pubmed

      • Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014 May 15; 30(10):1363-9. View in: Pubmed

      • Differential expression analysis of RNA-seq data at single-base resolution. Biostatistics. 2014 Jul; 15(3):413-26. View in: Pubmed

      • MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014; 15(12):554. View in: Pubmed

      • The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Res. 2014 Jan; 42(Database issue):D938-43. View in: Pubmed

      • 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. View in: Pubmed

      • Retraction: Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2013 Nov 07; 503(7474):146. View in: Pubmed

      • Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods. 2013 Oct; 10(10):949-55. View in: Pubmed

      • Measuring cell-type specific differential methylation in human brain tissue. Genome Biol. 2013 Aug 30; 14(8):R94. View in: Pubmed

      • ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics. 2013 May 01; 29(9):1182-9. View in: Pubmed

      • DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases. Sci Transl Med. 2013 Jan 23; 5(169):169ra10. View in: Pubmed

      • Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model. BMC Bioinformatics. 2012 Nov 15; 13:303. View in: Pubmed

      • Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics. 2012 Oct 22; 13:272. View in: Pubmed

      • fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics. 2012 Dec 01; 28(23):3153-4. View in: Pubmed

      • BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012 Oct 03; 13(10):R83. View in: Pubmed

      • Reversible switching between epigenetic states in honeybee behavioral subcastes. Nat Neurosci. 2012 Oct; 15(10):1371-3. View in: Pubmed

      • The partitioned LASSO-patternsearch algorithm with application to gene expression data. BMC Bioinformatics. 2012 May 15; 13:98. View in: Pubmed

      • Genome-wide DNA methylation scan in major depressive disorder. PLoS One. 2012; 7(4):e34451. View in: Pubmed

      • Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature. 2012 Feb 08; 482(7384):251-5. View in: Pubmed

      • Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. Int J Epidemiol. 2012 Feb; 41(1):200-9. View in: Pubmed

      • 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. View in: Pubmed

      • Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics. 2012 Apr; 13(2):204-16. View in: Pubmed

      • Fast wavelet based functional models for transcriptome analysis with tiling arrays. Stat Appl Genet Mol Biol. 2012 Jan 06; 11(1):Article 4. View in: Pubmed

      • Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis. Genome Biol. 2011 Sep 28; 12(9):R93. View in: Pubmed

      • Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinformatics. 2011 Sep 16; 12:369. View in: Pubmed

      • Sequencing technology does not eliminate biological variability. Nat Biotechnol. 2011 Jul 11; 29(7):572-3. View in: Pubmed

      • Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011 Jun 26; 43(8):768-75. View in: Pubmed

      • Significance analysis and statistical dissection of variably methylated regions. Biostatistics. 2012 Jan; 13(1):166-78. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • Assessing affymetrix GeneChip microarray quality. BMC Bioinformatics. 2011 May 07; 12:137. View in: Pubmed

      • Using the R Package crlmm for Genotyping and Copy Number Estimation. J Stat Softw. 2011 May 01; 40(12):1-32. View in: Pubmed

      • Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics. 2011 Apr 15; 27(8):1052-60. View in: Pubmed

      • 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. View in: Pubmed

      • Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. BMC Bioinformatics. 2011 Mar 08; 12:68. View in: Pubmed

      • 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. View in: Pubmed

      • Overcoming bias and systematic errors in next generation sequencing data. Genome Med. 2010 Dec 10; 2(12):87. View in: Pubmed

      • Accurate genome-scale percentage DNA methylation estimates from microarray data. Biostatistics. 2011 Apr; 12(2):197-210. View in: Pubmed

      • Epigenetic memory in induced pluripotent stem cells. Nature. 2010 Sep 16; 467(7313):285-90. View in: Pubmed

      • Personalized epigenomic signatures that are stable over time and covary with body mass index. Sci Transl Med. 2010 Sep 15; 2(49):49ra67. View in: Pubmed

      • Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010 10; 11(10):733-9. View in: Pubmed

      • Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics. 2010 Sep; 66(3):665-74. View in: Pubmed

      • Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature. 2010 Sep 16; 467(7313):338-42. View in: Pubmed

      • A framework for oligonucleotide microarray preprocessing. Bioinformatics. 2010 Oct 01; 26(19):2363-7. View in: Pubmed

      • 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. View in: Pubmed

      • A multilevel model to address batch effects in copy number estimation using SNP arrays. Biostatistics. 2011 Jan; 12(1):33-50. View in: Pubmed

      • Intensity normalization improves color calling in SOLiD sequencing. Nat Methods. 2010 May; 7(5):336-7. View in: Pubmed

      • Performance evaluation of commercial miRNA expression array platforms. BMC Res Notes. 2010 Mar 18; 3:80. View in: Pubmed

      • Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting. Blood. 2010 Jun 10; 115(23):4798-809. View in: Pubmed

      • Redefining CpG islands using hidden Markov models. Biostatistics. 2010 Jul; 11(3):499-514. View in: Pubmed

      • Processing of Agilent microRNA array data. BMC Res Notes. 2010 Jan 22; 3:18. View in: Pubmed

      • Frozen robust multiarray analysis (fRMA). Biostatistics. 2010 Apr; 11(2):242-53. View in: Pubmed

      • 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. View in: Pubmed

      • Gene set enrichment analysis made simple. Stat Methods Med Res. 2009 Dec; 18(6):565-75. View in: Pubmed

      • Quantifying uncertainty in genotype calls. Bioinformatics. 2010 Jan 15; 26(2):242-9. View in: Pubmed

      • 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. View in: Pubmed

      • A species-generalized probabilistic model-based definition of CpG islands. Mamm Genome. 2009 Sep-Oct; 20(9-10):674-80. View in: Pubmed

      • R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips. Bioinformatics. 2009 Oct 01; 25(19):2621-3. View in: Pubmed

      • Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells. Nat Genet. 2009 Feb; 41(2):246-50. View in: Pubmed

      • 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. View in: Pubmed

      • 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. View in: Pubmed

      • Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification. Genome Res. 2008 Nov; 18(11):1806-13. View in: Pubmed

      • Estimating genome-wide copy number using allele-specific mixture models. J Comput Biol. 2008 Sep; 15(7):857-66. View in: Pubmed

      • Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Res. 2008 Oct; 36(17):e108. View in: Pubmed

      • Intra-individual change over time in DNA methylation with familial clustering. JAMA. 2008 Jun 25; 299(24):2877-83. View in: Pubmed

      • Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays. Genome Biol. 2008 Apr 03; 9(4):R63. View in: Pubmed

      • SNP-specific array-based allele-specific expression analysis. Genome Res. 2008 May; 18(5):771-9. View in: Pubmed

      • Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 2008 May; 18(5):780-90. View in: Pubmed

      • 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. View in: Pubmed

      • Estimation and assessment of raw copy numbers at the single locus level. Bioinformatics. 2008 Mar 15; 24(6):759-67. View in: Pubmed

      • Statistical analysis of fitness data determined by TAG hybridization on microarrays. Methods Mol Biol. 2008; 416:369-81. View in: Pubmed

      • 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. View in: Pubmed

      • A gene expression bar code for microarray data. Nat Methods. 2007 Nov; 4(11):911-3. View in: Pubmed

      • Air pollution sources and childhood asthma attacks in Catano, Puerto Rico. Am J Epidemiol. 2007 Apr 15; 165(8):927-35. View in: Pubmed

      • Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics. 2007 Apr; 8(2):485-99. View in: Pubmed

      • Transposon insertion site profiling chip (TIP-chip). Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17632-7. View in: Pubmed

      • A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. BMC Bioinformatics. 2006 Nov 06; 7:489. View in: Pubmed

      • Stacking the deck: double-tiled DNA microarrays. Nat Methods. 2006 Nov; 3(11):903-7. View in: Pubmed

      • 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. View in: Pubmed

      • High-resolution spatial normalization for microarrays containing embedded technical replicates. Bioinformatics. 2006 Dec 15; 22(24):3054-60. View in: Pubmed

      • Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription. Mol Cell. 2006 Jul 21; 23(2):207-17. View in: Pubmed

      • Response to Shields: 'MIAME, we have a problem'. Trends Genet. 2006 Sep; 22(9):471-2. View in: Pubmed

      • Prenatal development of intrafetal and maternal-fetal synchrony. Behav Neurosci. 2006 Jun; 120(3):687-701. View in: Pubmed

      • Top-down standards will not serve systems biology. Nature. 2006 Mar 02; 440(7080):24. View in: Pubmed

      • Analysis of Affymetrix GeneChip data using amplified RNA. Biotechniques. 2006 Feb; 40(2):165-6, 168, 170. View in: Pubmed

      • Comparison of Affymetrix GeneChip expression measures. Bioinformatics. 2006 Apr 01; 22(7):789-94. View in: Pubmed

      • Feature-level exploration of a published Affymetrix GeneChip control dataset. Genome Biol. 2006; 7(8):404. View in: Pubmed

      • On time series analysis of public health and biomedical data. Annu Rev Public Health. 2006; 27:57-79. View in: Pubmed

      • Global synthetic-lethality analysis and yeast functional profiling. Trends Genet. 2006 Jan; 22(1):56-63. View in: Pubmed

      • The External RNA Controls Consortium: a progress report. Nat Methods. 2005 Oct; 2(10):731-4. View in: Pubmed

      • Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools. Nucleic Acids Res. 2005 Sep 15; 33(16):e140. View in: Pubmed

      • Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa. Respiration. 2006; 73(1):27-33. View in: Pubmed

      • Gene expression in giant cell myocarditis: Altered expression of immune response genes. Int J Cardiol. 2005 Jul 10; 102(2):333-40. View in: Pubmed

      • Stochastic models inspired by hybridization theory for short oligonucleotide arrays. J Comput Biol. 2005 Jul-Aug; 12(6):882-93. View in: Pubmed

      • Improved microarray methods for profiling the Yeast Knockout strain collection. Nucleic Acids Res. 2005 Jul 01; 33(12):e103. View in: Pubmed

      • In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology. BMC Genomics. 2005 May 04; 6:62. View in: Pubmed

      • Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma. J Lab Clin Med. 2005 May; 145(5):263-74. View in: Pubmed

      • Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005 May; 2(5):345-50. View in: Pubmed

      • 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. View in: Pubmed

      • On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci U S A. 2005 Mar 22; 102(12):4252-7. View in: Pubmed

      • Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy. Circulation. 2004 Nov 30; 110(22):3444-51. View in: Pubmed

      • Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5(10):R80. View in: Pubmed

      • The psychophysiology of the maternal-fetal relationship. Psychophysiology. 2004 Jul; 41(4):510-20. View in: Pubmed

      • Preprocessing of oligonucleotide array data. Nat Biotechnol. 2004 Jun; 22(6):656-8; author reply 658. View in: Pubmed

      • Orthologous gene-expression profiling in multi-species models: search for candidate genes. Genome Biol. 2004; 5(5):R34. View in: Pubmed

      • A benchmark for Affymetrix GeneChip expression measures. Bioinformatics. 2004 Feb 12; 20(3):323-31. View in: Pubmed

      • affy--analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 2004 Feb 12; 20(3):307-15. View in: Pubmed

      • S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion. Mol Biol Cell. 2004 Apr; 15(4):1724-35. View in: Pubmed

      • Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand. Nature. 2004 Jan 22; 427(6972):344-7. View in: Pubmed

      • Leydig cell gene expression: effects of age and caloric restriction. Exp Gerontol. 2004 Jan; 39(1):31-43. View in: Pubmed

      • Experimental design and low-level analysis of microarray data. Int Rev Neurobiol. 2004; 60:25-58. View in: Pubmed

      • 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. View in: Pubmed

      • Generalized additive selection models for the analysis of studies with potentially nonignorable missing outcome data. Biometrics. 2003 Sep; 59(3):601-13. View in: Pubmed

      • Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy. Physiol Genomics. 2003 Jun 24; 14(1):25-34. View in: Pubmed

      • Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr; 4(2):249-64. View in: Pubmed

      • Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants. Stat Appl Genet Mol Biol. 2003; 2:Article1. View in: Pubmed

      • Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003 Feb 15; 31(4):e15. View in: Pubmed

      • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics. 2003 Jan 22; 19(2):185-93. View in: Pubmed

      • Unstable heart rate and temperature regulation predict mortality in AKR/J mice. Am J Physiol Regul Integr Comp Physiol. 2003 Mar; 284(3):R742-50. View in: Pubmed

      • 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. View in: Pubmed

      • Electrocorticographic gamma activity during word production in spoken and sign language. Neurology. 2001 Dec 11; 57(11):2045-53. View in: Pubmed

      • 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. View in: Pubmed

      • Assessing homeostasis through circadian patterns. Biometrics. 2001 Dec; 57(4):1228-37. View in: Pubmed

      Locations

      Location Avtar

      55130

      3 Blackfan Circle Center for Life Science Building 10048 Boston, MA 02215
      Get Directions

      55130

      Location Avtar

      55130

      3 Blackfan Circle Center for Life Science Building 10048 Boston, MA 02215
      Get Direction
      42.3394, -71.1042

      Discovery and Insights

      Back to Top