List of works - Robert Gentleman

A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

A graph-theoretic approach to testing associations between disparate sources of functional genomics data

scientific article

An extensible application for assembling annotation for genomic data

scientific article

An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription

scientific article published on 14 September 2011

Analyzing biological data using R: methods for graphs and networks

scientific article

Bayesian error-in-variable survival model for the analysis of GeneChip arrays

scientific article published in June 2005

Circulating microRNAs as stable blood-based markers for cancer detection

scientific article

Complex regulation of ADAR-mediated RNA-editing across tissues

scientific article

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

scientific article published on 2 September 2012

Coverage and error models of protein-protein interaction data by directed graph analysis

scientific article

Creating a data resource: what will it take to build a medical information commons?

scientific article published on 22 September 2017

DATABASE: A new forum for biological databases and curation

scientific article

Data quality assessment of ungated flow cytometry data in high throughput experiments

scientific article

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.

scientific article

Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery

scientific article published in November 2006

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

scientific article

Erratum: The anatomy of successful computational biology software

article

Estimating node degree in bait-prey graphs

article

Extensions to gene set enrichment

scientific article published on 24 November 2006

GGtools: analysis of genetics of gene expression in bioconductor.

scientific article published on 8 December 2006

Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.

scientific article

Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation

scientific article published on 01 October 2005

Gene set enrichment analysis using linear models and diagnostics

scientific article published on 11 September 2008

Graphs in molecular biology

scientific article

Independent filtering increases detection power for high-throughput experiments

scientific article

Knowledge based identification of essential signaling from genome-scale siRNA experiments

scientific article

Local modeling of global interactome networks

scientific article published on 5 July 2005

Making sense of high-throughput protein-protein interaction data

scientific article

Making the most of high-throughput protein-interaction data

scientific article

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries

scientific article

Modeling synthetic lethality.

scientific article published on 12 September 2008

Network structures and algorithms in Bioconductor

scientific article published on 5 August 2004

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Per-channel basis normalization methods for flow cytometry data

scientific article

Prediction and Quantification of Splice Events from RNA-Seq Data

scientific article

Querying genomic databases: refining the connectivity map.

scientific article published on 6 January 2012

R

programming language for statistical analysis

R

environment for statistical computing and graphics using the R programming language

R: A Language for Data Analysis and Graphics

scholarly article from 1996

Recurrent R-spondin fusions in colon cancer ⬇️

scientific article published on August 30, 2012

Reply to Talloen et al.: Independent filtering is a generic approach that needs domain specific adaptation

scientific article published on 8 November 2010

Reproducible research: a bioinformatics case study

scientific article published on 11 January 2005

Resampling Methods

article

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

scientific article

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

scientific article

Software for computing and annotating genomic ranges

scientific article

The anatomy of successful computational biology software

scientific article

The graft response to transplantation: a gene expression profile analysis ⬇️

scientific article published on September 29, 2003

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

scientific article

Top-down standards will not serve systems biology

scientific article published in Nature

Towards BioDBcore: a community-defined information specification for biological databases

scientific article

Towards BioDBcore: a community-defined information specification for biological databases

scientific article (publication date: 2011)

VariantTools: an extensible framework for developing and testing variant callers

scientific article published in October 2017

Wavelet thresholding with bayesian false discovery rate control

scientific article published in March 2005

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

scientific article

flowCore: a Bioconductor package for high throughput flow cytometry

scientific article

gCMAP: user-friendly connectivity mapping with R.

scientific article published on 15 October 2013

iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor

scientific article

rtracklayer: an R package for interfacing with genome browsers

scientific article published on 25 May 2009

List of works by Robert Gentleman

A Model-Based Background Adjustment for Oligonucleotide Expression Arrays

A graph-theoretic approach to testing associations between disparate sources of functional genomics data

An extensible application for assembling annotation for genomic data

An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription

Analyzing biological data using R: methods for graphs and networks

Bayesian error-in-variable survival model for the analysis of GeneChip arrays

Circulating microRNAs as stable blood-based markers for cancer detection

Complex regulation of ADAR-mediated RNA-editing across tissues

Comprehensive genomic analysis identifies SOX2 as a frequently amplified gene in small-cell lung cancer

Coverage and error models of protein-protein interaction data by directed graph analysis

Creating a data resource: what will it take to build a medical information commons?

DATABASE: A new forum for biological databases and curation

Data quality assessment of ungated flow cytometry data in high throughput experiments

Data structures and algorithms for analysis of genetics of gene expression with Bioconductor: GGtools 3.x.

Declining plasma fibrinogen alpha fragment identifies HER2-positive breast cancer patients and reverts to normal levels after surgery

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

Erratum: The anatomy of successful computational biology software

Estimating node degree in bait-prey graphs

Extensions to gene set enrichment

GGtools: analysis of genetics of gene expression in bioconductor.

Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival.

Gene expression profiles of B-lineage adult acute lymphocytic leukemia reveal genetic patterns that identify lineage derivation and distinct mechanisms of transformation

Gene set enrichment analysis using linear models and diagnostics

Graphs in molecular biology

Independent filtering increases detection power for high-throughput experiments

Knowledge based identification of essential signaling from genome-scale siRNA experiments

Local modeling of global interactome networks

Making sense of high-throughput protein-protein interaction data

Making the most of high-throughput protein-interaction data

MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries

Modeling synthetic lethality.

Network structures and algorithms in Bioconductor

Orchestrating high-throughput genomic analysis with Bioconductor

Per-channel basis normalization methods for flow cytometry data

Prediction and Quantification of Splice Events from RNA-Seq Data

Querying genomic databases: refining the connectivity map.

R

R

R: A Language for Data Analysis and Graphics

Recurrent R-spondin fusions in colon cancer ⬇️

Reply to Talloen et al.: Independent filtering is a generic approach that needs domain specific adaptation

Reproducible research: a bioinformatics case study

Resampling Methods

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

Software for computing and annotating genomic ranges

The anatomy of successful computational biology software

The graft response to transplantation: a gene expression profile analysis ⬇️

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Top-down standards will not serve systems biology

Towards BioDBcore: a community-defined information specification for biological databases

Towards BioDBcore: a community-defined information specification for biological databases

VariantTools: an extensible framework for developing and testing variant callers

Wavelet thresholding with bayesian false discovery rate control

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

flowCore: a Bioconductor package for high throughput flow cytometry

gCMAP: user-friendly connectivity mapping with R.

iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor

rtracklayer: an R package for interfacing with genome browsers