Rafael A. Irizarry

发表

FROZEN ROBUST MULTI-ARRAY ANALYSIS (fRMA)

Matthew N. McCall, Benjamin M. Bolstad, Rafael A. Irizarry, 2009 .

High-resolution spatial normalization for microarrays containing embedded technical replicates

Rafael A. Irizarry, Daniel S. Yuan, R. Irizarry, 2006, Bioinform..

The Gene Expression Barcode 3.0: improved data processing and mining tools

Matthew N. McCall, Rafael A. Irizarry, Harris A. Jaffee, 2013, Nucleic Acids Res..

derfinder : Software for annotation-agnostic RNA-seq differential expression analysis

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2015 .

Discovery with Data: Leveraging Statistics with Computer Science to Transform Science and Society

Cynthia Rudin, Rafael A. Irizarry, Eric B. Laber, 2014 .

Robust decomposition of cell type mixtures in spatial transcriptomics

Rafael A. Irizarry, Aleksandrina Goeva, Evan Z. Macosko, 2020, Nature Biotechnology.

Comparison of Affymetrix GeneChip expression measures

Rafael A. Irizarry, Zhijin Wu, Harris A. Jaffee, 2006, Bioinform..

The partitioned LASSO-patternsearch algorithm with application to gene expression data

Stephen J. Wright, Rafael A. Irizarry, Grace Wahba, 2012, BMC Bioinformatics.

Multiple Lab Comparison of Microarray Platforms

Rafael A. Irizarry, R. Irizarry, 2004 .

Some wavelet-based analyses of Markov chain data

David R. Brillinger, Rafael A. Irizarry, Pedro Alberto Morettin, 2000, Signal Processing.

affy - analysis of Affymetrix GeneChip data at the probe level

Benjamin M. Bolstad, Rafael A. Irizarry, Laurent Gautier, 2004, Bioinform..

A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database

Rafael A. Irizarry, Xue Lin, Simon Katz, 2006, BMC Bioinformatics.

The Analysis of Gene Expression Data: Methods and Software

Scott L. Zeger, Rafael A. Irizarry, Giovanni Parmigiani, 2013 .

The analysis of tiling array data using wavelet based functional mixed models

Rafael A. Irizarry, Ciprian M. Crainiceanu, Olivier Thas, 2009 .

Empirical Bayes Analysis of a Microarray Experiment

Rafael A. Irizarry, R. Irizarry, 2008 .

Interpretable Convolution Methods for Learning Genomic Sequence Motifs

Rafael A. Irizarry, Matthew Ploenzke, R. Irizarry, 2018, bioRxiv.

Statistical Analysis of Sound Signals Using a Local Harmonic Model

Rafael A. Irizarry, R. Irizarry, 1998 .

An investigation of the second- and higher-order spectra of music

David R. Brillinger, Rafael A. Irizarry, D. Brillinger, 1998, Signal Process..

Stochastic models inspired by hybridization theory for short oligonucleotide arrays

Rafael A. Irizarry, Zhijin Wu, R. Irizarry, 2004, J. Comput. Biol..

Varying-Censoring Aware Matrix Factorization for Single Cell RNA-Sequencing

Rafael A. Irizarry, Stephanie C. Hicks, Martin J. Aryee, 2017, bioRxiv.

A statistical framework for the analysis of microarray probe-level data

Rafael A. Irizarry, Zhijin Wu, R. Irizarry, 2007, 0712.2115.

Parameters with Musical Interpretations

Rafael A. Irizarry, 2004 .

fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays

Matthew N. McCall, Rafael A. Irizarry, Harris A. Jaffee, 2012, Bioinform..

Quality Assessment of Affymetrix GeneChip Data

Terence P. Speed, Benjamin M. Bolstad, Rafael A. Irizarry, 2005 .

Assessments of Affymetrix GeneChip Microarray Quality for Laboratories and Single Samples

Matthew N. McCall, Rafael A. Irizarry, Wolfgang Huber, 2011, BMC Bioinform..

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

Rafael A. Irizarry, Andrew P. Feinberg, Martin J. Aryee, 2014, Bioinform..

Correcting for cell-type heterogeneity in epigenome-wide association studies: premature analyses and conclusions

Devin C. Koestler, Rafael A. Irizarry, Andrew E. Teschendorff, 2017, bioRxiv.

The Additive Sinusoidal Plus Residual Model: A Statistical Analysis

Rafael A. Irizarry, 1998, ICMC.

Context Aware Group Nearest Shrunken Centroids in Large-Scale Genomic Studies

Rafael A. Irizarry, Fang Han, Han Liu, 2014, AISTATS.

A MULTILEVEL MODEL TO ADDRESS BATCH EFFECTS IN COPY NUMBER USING SNP ARRAYS

Ingo Ruczinski, Rafael A. Irizarry, Robert B. Scharpf, 2009 .

A multi-omic analysis of human naïve CD4+ T cells

Min Sik Kim, Rafael A. Irizarry, Jean Thierry-Mieg, 2015, BMC Systems Biology.

A benchmark for Affymetrix GeneChip expression measures

Terence P. Speed, Rafael A. Irizarry, Zhijin Wu, 2004, Bioinform..

R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips

Rafael A. Irizarry, Simon Tavaré, Matthew E. Ritchie, 2009, Bioinform..

Estimating Genome-Wide Copy Number Using Allele-Specific Mixture Models

Wenyi Wang, Jonathan Pevsner, Rafael A. Irizarry, 2008, J. Comput. Biol..

Gene expression anti-profiles as a basis for accurate universal cancer signatures

Vasyl Pihur, Matthew N. McCall, Rafael A. Irizarry, 2012, BMC Bioinformatics.

Wavelet-based functional mixed models for transcriptome analysis

Rafael A. Irizarry, Ciprian M. Crainiceanu, Olivier Thas, 2009 .

An R Package for Analyses of Affymetrix Oligonucleotide Arrays

Rafael A. Irizarry, Laurent Gautier, Leslie Cope, 2003 .

ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data

Matthew N. McCall, Rafael A. Irizarry, Michael J. Zilliox, 2013, Bioinform..

Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips

Ruijie Liu, Rafael A. Irizarry, Matthew E. Ritchie, 2011, BMC Bioinformatics.

The Role of Academia in Data Science Education

Rafael A. Irizarry, R. Irizarry, 2020, 2.1.

The Analysis of Gene Expression Data: An Overview of Methods and Software

Scott L. Zeger, Rafael A. Irizarry, Giovanni Parmigiani, 2003 .

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes

Matthew N. McCall, Rafael A. Irizarry, Harris A. Jaffee, 2010, Nucleic Acids Res..

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Paul T. Spellman, Rafael A. Irizarry, John Quackenbush, 2006, BMC Bioinformatics.

Improved base-calling and quality scores for 454 sequencing based on a Hurdle Poisson model

Rafael A. Irizarry, Olivier Thas, Lieven Clement, 2012, BMC Bioinformatics.

Introduction to Data Science

Rafael A. Irizarry, R. Irizarry, 2019 .

Thawing Frozen Robust Multi-array Analysis (fRMA)

Matthew N. McCall, Rafael A. Irizarry, R. Irizarry, 2011, BMC Bioinformatics.

Erratum: Gene set enrichment analysis made simple (Statistical Methods in Medical Research (2009) 18:6 (565-575))

Yun Zhou, Terence P. Speed, Rafael A. Irizarry, 2011 .

KRLMM: an adaptive genotype calling method for common and low frequency variants

Ruijie Liu, Rafael A. Irizarry, Matthew E. Ritchie, 2014, BMC Bioinformatics.

Selection Corrected Statistical Inference for Region Detection with High-throughput Assays

Rafael A. Irizarry, Jonathan Taylor, Yuval Benjamini, 2016 .

Inference for High Dimensional Data

Rafael A. Irizarry, Michael I. Love, R. Irizarry, 2016 .

When to use Quantile Normalization?

Rafael A. Irizarry, Stephanie C. Hicks, R. Irizarry, 2014, bioRxiv.

Performance assessment of copy number microarray platforms using a spike-in experiment

Ingo Ruczinski, Jonathan Pevsner, Rafael A. Irizarry, 2011, Bioinform..

A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

Rafael A. Irizarry, Zhijin Wu, Robert Gentleman, 2004 .

A Guide to Teaching Data Science

Rafael A. Irizarry, Stephanie C. Hicks, R. Irizarry, 2016, The American statistician.

Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays

Rafael A. Irizarry, Zhijin Wu, 2005, J. Comput. Biol..

Selection-Corrected Statistical Inference for Region Detection With High-Throughput Assays

Rafael A. Irizarry, Jonathan Taylor, Yuval Benjamini, 2019 .

Quantifying uncertainty in genotype calls

Thomas A. Louis, Rafael A. Irizarry, Benilton Carvalho, 2010, Bioinform..

Preprocessing High-density Oligonucleotide Arrays

Benjamin M. Bolstad, Rafael A. Irizarry, Laurent Gautier, 2005 .

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

Mingxiang Teng, Rafael A. Irizarry, 2016 .

Estimation and assessment of raw copy numbers at the single locus level

Terence P. Speed, Rafael A. Irizarry, Henrik Bengtsson, 2008, Bioinform..

Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models

Wenyi Wang, Jonathan Pevsner, Rafael A. Irizarry, 2007, RECOMB.

Local Harmonic Estimation in Musical Sound Signals

Rafael A. Irizarry, R. Irizarry, 2001 .

Additional file 19: Figure S10. of A multi-omic analysis of human naĂŻve CD4+ T cells

Rafael A. Irizarry, Jean Thierry-Mieg, Xinyan Wu, 2015 .

Bioinformatics and Computational Biology Solutions using R and Bioconductor

Rafael A. Irizarry, Sandrine Dudoit, Robert Gentleman, 2005 .

Visualization and probability-based scoring of structural variants within repetitive sequences

Rafael A. Irizarry, Sarven Sabunciyan, Kathleen H. Burns, 2014, Bioinform..

Basic Machine Learning

Rafael A. Irizarry, Michael I. Love, R. Irizarry, 2016 .

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2016, bioRxiv.

A framework for oligonucleotide microarray preprocessing

Rafael A. Irizarry, Benilton S. Carvalho, R. Irizarry, 2010, Bioinform..

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

Terence P. Speed, Benjamin M. Bolstad, Rafael A. Irizarry, 2003, Bioinform..

Evolutionary flux of canonical micrornAs and mirtrons in Drosophila

Rafael A. Irizarry, Andrew P. Feinberg, Yoichi Shinkai, 2010 .

ASYMPTOTIC DISTRIBUTION OF ESTIMATES FOR A TIME- VARYING PARAMETER IN A HARMONIC MODEL WITH MULTIPLE FUNDAMENTALS

Rafael A. Irizarry, R. Irizarry, 2000 .

A comprehensive methylome map of lineage commitment from hematopoietic progenitors

Irving L. Weissman, Rafael A. Irizarry, Andrew P. Feinberg, 2010, Nature.

Information and Posterior Probability Criteria for Model Selection in Local Likelihood Estimation

Rafael A. Irizarry, R. Irizarry, 2001 .

Erratum: A benchmark for RNA-seq quantification pipelines [Genome Biol. (2016), 17, 74], DOI: 10.1186/s13059-016-0940-1

Xintao Wei, Mingxiang Teng, Rafael A. Irizarry, 2016 .

Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools

Rafael A. Irizarry, Daniel S. Yuan, Jef D. Boeke, 2005, Nucleic acids research.

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

Rafael A. Irizarry, Yuval Benjamini, Keegan D. Korthauer, 2017 .

Transcriptomics: Translation of Global Expression Analysis to Genomic Medicine

Rafael A. Irizarry, Joshua M. Hare, R. Irizarry, 2009 .

Personalized Epigenomic Signatures That Are Stable Over Time and Covary with Body Mass Index

Rafael A. Irizarry, Andrew P. Feinberg, Martin J. Aryee, 2010, Science Translational Medicine.

Measures of gene expression for affymetrix high density oligonucleotide arrays

Rafael A. Irizarry, 2003 .

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2015, bioRxiv.

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

Rafael A. Irizarry, Claire Duvallet, Eric J. Alm, 2017, Nature Communications.

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

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

Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model

Rafael A. Irizarry, Stephanie C. Hicks, Martin J. Aryee, 2019, Genome Biology.

Local Regression With Meaningful Parameters

Rafael A. Irizarry, 2001 .

Genome-wide methylation analysis of human colon cancer reveals similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

Rafael A. Irizarry, Zhijin Wu, Andrew P. Feinberg, 2008, Nature Genetics.

quantro: a data-driven approach to guide the choice of an appropriate normalization method

Rafael A. Irizarry, Stephanie C. Hicks, R. Irizarry, 2015, Genome Biology.

Improved microarray methods for profiling the yeast knockout strain collection

Rafael A. Irizarry, Daniel S. Yuan, Jef D. Boeke, 2005, Nucleic acids research.