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List of works by Rafael Irizarry

A Guide to Teaching Data Science

scientific article published on 14 November 2018

A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

A benchmark for Affymetrix GeneChip expression measures

scientific article published in February 2004

A benchmark for RNA-seq quantification pipelines

scientific article

A framework for oligonucleotide microarray preprocessing.

scientific article

A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs

article

A gene expression bar code for microarray data

scientific article

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

scientific article published on 6 November 2015

A multilevel model to address batch effects in copy number estimation using SNP arrays.

scientific article

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

scientific article

A species-generalized probabilistic model-based definition of CpG islands

scientific article published on 24 September 2009

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

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

scientific article

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

scientific article published on 12 October 2017

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

scientific article

Accurate genome-scale percentage DNA methylation estimates from microarray data

scientific article

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

scientific article published on 16 April 2015

Air pollution sources and childhood asthma attacks in Catano, Puerto Rico

scientific article published on 17 February 2007

Analysis of Affymetrix GeneChip data using amplified RNA.

scientific article

Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray.

scientific article

Assessing affymetrix GeneChip microarray quality

scientific article

Author Correction: Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

scientific article published on 07 September 2020

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

scientific article published on 22 July 2020

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

scientific article

Bioconductor: open software development for computational biology and bioinformatics

scientific article

Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells

scientific article published on 26 January 2017

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

scientific article published in February 2012

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

scientific article published on May 1, 2013

Challenges and emerging directions in single-cell analysis

scientific article published on 8 May 2017

Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

scientific article

Circadian rhythm variation in activity, body temperature, and heart rate between C3H/HeJ and C57BL/6J inbred strains

scientific article published on 01 February 2002

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

scientific article published on 8 March 2011

Comparison of Affymetrix GeneChip expression measures.

scientific article published on 12 January 2006

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

scientific article

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

scientific article

Consolidated strategy for the analysis of microarray spike-in data

scientific article

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

scientific article published in February 2017

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

scientific article

DNA methylation alterations exhibit intraindividual stability and interindividual heterogeneity in prostate cancer metastases

scientific article published on January 2013

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

scientific article

Deficiency of different nitric oxide synthase isoforms activates divergent transcriptional programs in cardiac hypertrophy ⬇️

scientific article published on June 24, 2003

Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing

scientific article published on 22 February 2018

Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

scientific article published on 22 June 2020

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

scientific article

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

scientific article

Editor's note on Zheng et al. and Rahmani et al

scientific article published on 01 February 2017

Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis ⬇️

scientific article published on September 28, 2011

Effective detection of rare variants in pooled DNA samples using cross-pool tail-curve analysis.

scientific article published on 19 September 2011

Erratum to: A benchmark for RNA-seq quantification pipelines.

scientific article published on 30 September 2016

Erratum to: A benchmark for RNA-seq quantification pipelines.

scientific article published on 23 May 2016

Estimating genome-wide copy number using allele-specific mixture models

scientific article published on September 2008

Every Body Counts: Measuring Mortality From the COVID-19 Pandemic

scientific article published on 11 September 2020

Evolution in health and medicine Sackler colloquium: Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease

scientific article

Excess deaths associated with covid-19 pandemic in 2020: age and sex disaggregated time series analysis in 29 high income countries

scholarly article by Nazrul Islam published in 2021

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

scientific article

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

scientific article (publication date: April 2003)

Fast Wavelet Based Functional Models for Transcriptome Analysis with Tiling Arrays ⬇️

scientific article published on January 6, 2012

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

scientific article published on 23 December 2019

Feature-level exploration of a published Affymetrix GeneChip control dataset

scientific article published on January 2006

Flexible expressed region analysis for RNA-seq with derfinder

scientific article published on 29 September 2016

Flexible expressed region analysis for RNA-seq with derfinder

scholarly article published 19 February 2015

Frozen robust multiarray analysis (fRMA).

scientific article

Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK

retracted paper

Gene expression analysis of ischemic and nonischemic cardiomyopathy: shared and distinct genes in the development of heart failure

scientific article published on 15 March 2005

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

scientific article

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

scientific article published on July 2005

Gene set enrichment analysis made simple

scientific article published on December 2009

Generalized Additive Selection Models for the Analysis of Studies with Potentially Nonignorable Missing Outcome Data ⬇️

scientific article published on September 1, 2003

Genome-Wide DNA Methylation Scan in Major Depressive Disorder ⬇️

scientific article published on April 12, 2012

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

scientific article

Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions

scientific article

Global synthetic-lethality analysis and yeast functional profiling

scientific article

High-resolution spatial normalization for microarrays containing embedded technical replicates

scientific article published on 23 October 2006

High-throughput identification of RNA nuclear enrichment sequences

scientific article published on 15 January 2018

IVT-seq reveals extreme bias in RNA sequencing

scientific article

Identification of a gene expression profile that differentiates between ischemic and nonischemic cardiomyopathy

scientific article published on 22 November 2004

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

scientific article

Improved microarray methods for profiling the Yeast Knockout strain collection

scientific article

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

scientific article

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology

scientific article

Increased methylation variation in epigenetic domains across cancer types

scientific article published on 26 June 2011

Influence of host gene transcription level and orientation on HIV-1 latency in a primary-cell model

scientific article published on 23 March 2011

Intensity normalization improves color calling in SOLiD sequencing

scientific article published on May 2010

Intra-individual change over time in DNA methylation with familial clustering

scientific article

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

scientific article

Large histone H3 lysine 9 dimethylated chromatin blocks distinguish differentiated from embryonic stem cells

scientific article published on 18 January 2009

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

scientific article

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

scientific article published on 18 August 2020

Leydig cell gene expression: effects of age and caloric restriction

scientific article

Local Regression With Meaningful Parameters

MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens

scientific article

Measuring cell-type specific differential methylation in human brain tissue

scientific article published on 30 August 2013

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

scientific article

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

scientific article

Missing data and technical variability in single-cell RNA-sequencing experiments

scientific article

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

scientific article

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation

article

Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.

scientific article published on 26 September 2016

Mortality in Puerto Rico after Hurricane Maria

Multiple-laboratory comparison of microarray platforms

article

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

scientific article

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

scientific article published in May 2005

On time series analysis of public health and biomedical data

scientific article

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Orthologous gene-expression profiling in multi-species models: search for candidate genes

scientific article

Outcomes of adults with cystic fibrosis infected with antibiotic-resistant Pseudomonas aeruginosa

scientific article

Overcoming bias and systematic errors in next generation sequencing data

scientific article

Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification

scientific article published on 10 October 2008

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

scientific article

Performance evaluation of commercial miRNA expression array platforms

scientific article

Personalized epigenomic signatures that are stable over time and covary with body mass index

scientific article

Prenatal development of intrafetal and maternal-fetal synchrony

scientific article published in June 2006

Preprocessing of oligonucleotide array data

scientific article

Probabilistic gene expression signatures identify cell-types from single cell RNA-seq data ⬇️

journal article from 'bioRxiv' published in 2020

Proceedings of the second international molecular pathological epidemiology (MPE) meeting

scientific article

Proceedings of the third international molecular pathological epidemiology (MPE) meeting

scientific article

Processing of Agilent microRNA array data

scientific article

Progressive immune dysfunction with advancing disease stage in renal cell carcinoma

scientific article published on 11 March 2021

Promoter hypermethylation in MLL-r infant acute lymphoblastic leukemia: biology and therapeutic targeting.

scientific article

Quantifying the dynamics of migration after Hurricane Maria in Puerto Rico

scientific article published on 08 December 2020

Quantifying uncertainty in genotype calls

scientific article

Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers

scientific article published on 03 July 2020

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

scientific article published on 06 August 2009

Recommendations for the design and analysis of epigenome-wide association studies

scientific article published on October 2013

Redefining CpG islands using hidden Markov models

scientific article

Removing technical variability in RNA-seq data using conditional quantile normalization

scientific article

Response to Shields: ‘MIAME, we have a problem’

article

Reversible switching between epigenetic states in honeybee behavioral subcastes

scientific article

S-phase checkpoint genes safeguard high-fidelity sister chromatid cohesion

scientific article published on 23 January 2004

SMARCB1 is required for widespread BAF complex-mediated activation of enhancers and bivalent promoters

scientific article

SNP-specific array-based allele-specific expression analysis

scientific article

Salmon provides fast and bias-aware quantification of transcript expression

scientific article published on 6 March 2017

Sequencing technology does not eliminate biological variability

scientific article published on 11 July 2011

Serum protein MALDI profiling to distinguish upper aerodigestive tract cancer patients from control subjects

scientific article

Significance analysis and statistical dissection of variably methylated regions

scientific article published on 17 June 2011

Significance analysis for clustering with single-cell RNA-sequencing data

Smooth quantile normalization

scientific article published on 10 July 2017

Stacking the deck: double-tiled DNA microarrays

scientific article published on 01 November 2006

Statistical analysis of fitness data determined by TAG hybridization on microarrays.

scientific article

Stochastic models inspired by hybridization theory for short oligonucleotide arrays.

scientific article published in July 2005

Summaries of Affymetrix GeneChip probe level data

scientific article (publication date: 15 February 2003)

Tackling the widespread and critical impact of batch effects in high-throughput data

scientific article (publication date: October 2010)

Thawing Frozen Robust Multi-array Analysis (fRMA) ⬇️

scientific article published on September 16, 2011

The External RNA Controls Consortium: a progress report.

scientific article published in October 2005

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

scientific article

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

scientific article published on January 1, 2011

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

scientific article

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

scientific article

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

scientific article published on May 15, 2012

The psychophysiology of the maternal-fetal relationship.

scientific article published in July 2004

Top-down standards will not serve systems biology

scientific article published in Nature

Transposon insertion site profiling chip (TIP-chip).

scholarly article

Travelling waves in the occurrence of dengue haemorrhagic fever in Thailand

scientific article published on January 2004

Unstable heart rate and temperature regulation predict mortality in AKR/J mice

scientific article published on 10 October 2002

Use of mixture models in a microarray-based screening procedure for detecting differentially represented yeast mutants

scientific article published on 18 March 2003

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

scientific article published on May 2011

Vaginal microbiome topic modeling of laboring Ugandan women with and without fever

scientific article published on 10 September 2021

Validation and extension of an empirical Bayes method for SNP calling on Affymetrix microarrays

scientific article

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

scientific article

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

scientific article

methylCC: technology-independent estimation of cell type composition using differentially methylated regions

scientific article published on 29 November 2019

mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis

scientific article published on 13 June 2022

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

scientific article

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