Rafael A Irizarry

发表

Salmon provides accurate, fast, and bias-aware transcript expression estimates using dual-phase inference

Geet Duggal, Carl Kingsford, Michael I. Love, 2015, bioRxiv.

Exploration, normalization, and summaries of high density oligonucleotide array probe level data.

Rafael A Irizarry, Bridget Hobbs, Francois Collin, 2003, Biostatistics.

Orchestrating high-throughput genomic analysis with Bioconductor

Raphael Gottardo, Robert Gentleman, Wolfgang Huber, 2015, Nature Methods.

On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data

Mingxiang Teng, Stephanie C. Hicks, Rafael A Irizarry, 2015 .

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro, Geet Duggal, Carl Kingsford, 2017, Nature Methods.

Frozen robust multiarray analysis (fRMA).

Rafael A Irizarry, Matthew N McCall, Benjamin M Bolstad, 2010, Biostatistics.

Processing of Agilent microRNA array data

Rafael A Irizarry, Pedro López-Romero, Manuel A González, 2010, BMC Research Notes.

Multiple-laboratory comparison of microarray platforms

John Quackenbush, Rafael A Irizarry, Michael Wilson, 2005, Nature Methods.

Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays

Zhijin Wu, Rafael A Irizarry, Richard LeBlanc, 2003 .

Using the R Package crlmm for Genotyping and Copy Number Estimation.

Matthew E Ritchie, Ingo Ruczinski, Rafael A Irizarry, 2011, Journal of statistical software.

Preprocessing of oligonucleotide array data

Zhijin Wu, Rafael A Irizarry, R. Irizarry, 2004, Nature Biotechnology.

Detection and accurate False Discovery Rate control of differentially methylated regions from Whole Genome Bisulfite Sequencing

Rafael A Irizarry, Sutirtha Chakraborty, Yuval Benjamini, 2017, bioRxiv.

Gene set enrichment analysis made simple

Rafael A Irizarry, Terence P Speed, Chi Wang, 2009, Statistical methods in medical research.

Choosing Smoothness Parameters for Smoothing Splines by Minimizing and Estimate of Risk

Rafael A Irizarry, 2004 .

Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays

Ciprian M Crainiceanu, Olivier Thas, Rafael A Irizarry, 2010, Statistical applications in genetics and molecular biology.

Model-based quality assessment and base-calling for second-generation sequencing data.

Héctor Corrada Bravo, Rafael A Irizarry, 2010, Biometrics.

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

Jeffrey T Leek, Rafael A Irizarry, Andrew P Feinberg, 2012, International journal of epidemiology.

Stacking the deck: double-tiled DNA microarrays

Rafael A Irizarry, Jef D Boeke, Francisco Martínez-Murillo, 2006, Nature Methods.

Intensity normalization improves color calling in SOLiD sequencing

Héctor Corrada Bravo, Rafael A Irizarry, H. Bravo, 2010, Nature Methods.

Correcting for cell-type heterogeneity in epigenome-wide association studies: revisiting previous analyses

Rafael A Irizarry, Kasper D Hansen, Stephan Beck, 2017, Nature Methods.

Corrigendum: Multiple-laboratory comparison of microarray platforms

John Quackenbush, Rafael A Irizarry, Hannah Lee, 2005, Nature Methods.

Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data.

Rafael A Irizarry, Terence P Speed, Henrik Bengtsson, 2006, Biostatistics.

Significance analysis and statistical dissection of variably methylated regions.

Jeffrey T Leek, Rafael A Irizarry, Andrew P Feinberg, 2012, Biostatistics.

The psychophysiology of the maternal-fetal relationship.

Rafael A Irizarry, R. Irizarry, J. DiPietro, 2004, Psychophysiology.

DNA hypomethylation arises later in prostate cancer progression than CpG island hypermethylation and contributes to metastatic tumor heterogeneity.

Zhijin Wu, Rafael A Irizarry, Toby C. Cornish, 2008, Cancer research.

Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference

Geet Duggal, Carl Kingsford, Rob Patro, 2017, Nature Methods.

Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription.

Rafael A Irizarry, Jef D Boeke, Hidekazu Takahashi, 2006, Molecular cell.

Differential expression analysis of RNA-seq data at single-base resolution

Jeffrey T Leek, Alyssa C. Frazee, Rafael A Irizarry, 2014, Biostatistics.

Oligonucleotide-microarray analysis of peripheral-blood lymphocytes in severe asthma.

Rafael A Irizarry, Sara C Hilmer, L. Cope, 2005, The Journal of laboratory and clinical medicine.

Overcoming bias and systematic errors in next generation sequencing data

Rafael A Irizarry, Margaret A Taub, R. Irizarry, 2010, Genome Medicine.

Large hypomethylated blocks as a universal defining epigenetic alteration in human solid tumors

Winston Timp, Rafael A Irizarry, Hector Corrada Bravo, 2014, Genome Medicine.

Global synthetic-lethality analysis and yeast functional profiling.

Rafael A Irizarry, Jef D Boeke, Joel S Bader, 2006, Trends in genetics : TIG.

Statistical Applications in Genetics and Molecular Biology Use of Mixture Models in a Microarray-Based Screening Procedure for Detecting Differentially Represented Yeast Mutants

Zhijin Wu, Rafael A Irizarry, Jef D Boeke, 2011 .

Accounting for GC-content bias reduces systematic errors and batch effects in ChIP-seq data.

Mingxiang Teng, Rafael A Irizarry, 2017, Genome research.

Comprehensive high-throughput arrays for relative methylation (CHARM).

Rafael A Irizarry, Andrew P Feinberg, Christine Ladd-Acosta, 2008, Genome research.

Gene expression in giant cell myocarditis: Altered expression of immune response genes.

Rafael A Irizarry, Joshua M Hare, R. Irizarry, 2005, International journal of cardiology.

DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth.

Martin J. Aryee, Martin J Aryee, Rafael A Irizarry, 2012, International journal of epidemiology.

Accurate genome-scale percentage DNA methylation estimates from microarray data.

Zhijin Wu, Martin J Aryee, Rafael A Irizarry, 2011, Biostatistics.

Feature-level exploration of a published Affymetrix GeneChip control dataset

Zhijin Wu, Rafael A Irizarry, L. Cope, 2006, Genome Biology.

Age and sun exposure-related widespread genomic blocks of hypomethylation in nonmalignant skin

Xin Li, Rafael A Irizarry, Kasper D Hansen, 2015, Genome Biology.

Analysis of Affymetrix GeneChip data using amplified RNA.

Rafael A Irizarry, Leslie Cope, L. Cope, 2006, BioTechniques.