Knowledge based identification of essential signaling from genome-scale siRNA experiments (2009)
Bankhead, Armand, Sach, Iliana, Ni, Chester, LeMeur, Nolwenn, Kruger, Mark, Ferrer, Marc, ...
Abstract Background A systems biology interpretation of genome-scale RNA interference (RNAi) experiments is complicated by scope, experimental variability and network signaling robustness. Over...
flowCore: a Bioconductor package for high throughput flow cytometry (2009)
Hahne, Florian, LeMeur, Nolwenn, Brinkman, Ryan R, Ellis, Byron, Haaland, Perry, Sarkar, Deepayan, ...
Abstract Background Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or...
rtracklayer: an R package for interfacing with genome browsers (2009)
Lawrence, Michael, Gentleman, Robert, Carey, Vincent
Summary: The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R. The user may (i) transfer annotation tracks to and from a genome...
arrayQualityMetrics--a bioconductor package for quality assessment of microarray data (2009)
Kauffmann, Audrey, Gentleman, Robert, Huber, Wolfgang
Summary:: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour...
Carey, Vincent J., Davis, Adam R., Lawrence, Michael F., Gentleman, Robert, Raby, Benjamin A.
Summary: Associations between DNA polymorphisms and mRNA abundance are a natural target of genetic investigations, and microarrays facilitate genome-wide and transcriptome-wide surveys of these...
Morgan, Martin, Anders, Simon, Lawrence, Michael, Aboyoun, Patrick, Pagès, Hervé, Gentleman, Robert
Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready...
iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor (2009)
Kyongryun Lee, Florian Hahne, Deepayan Sarkar, Robert Gentleman
Flow cytometry (FCM) has become an important analysis technology in health care and medical research, but the large volume of data produced by modern high-throughput experiments has presented...
Modeling synthetic lethality (2008)
Le Meur, Nolwenn, Gentleman, Robert
Abstract Background Synthetic lethality defines a genetic interaction where the combination of mutations in two or more genes leads to cell death. The implications of synthetic lethal screens have...
Analysis (A. Poustka) DKFZ Heidelberg Acknowledgements (2008)
Wolfgang Huber, Anja Von Heydebreck, Günther Sawitzki, Holger Sültmann, Klaus Steiner, Markus Vogt, ...
First analysis steps o quality control and optimization o calibration and error modeling o data transformations
Assessing The Role Of Multi-protein Complexes In Determining Phenotype (2008)
Le Meur, Nolwenn, Gentleman, Robert
Understanding regulatory mechanisms in complex biological systems is an important challenge, in particular to understand disease mechanisms, and to discover new therapies and drugs. In this paper, we...
Assessing The Role Of Multi-protein Complexes In Determining Phenotype (2008)
Le Meur, Nolwenn, Gentleman, Robert
Understanding regulatory mechanisms in complex biological systems is an important challenge, in particular to understand disease mechanisms, and to discover new therapies and drugs. In this paper, we...
Assessing The Role Of Multi-protein Complexes In Determining Phenotype (2008)
Le Meur, Nolwenn, Gentleman, Robert
Understanding regulatory mechanisms in complex biological systems is an important challenge, in particular to understand disease mechanisms, and to discover new therapies and drugs. In this paper, we...
Assessing The Role Of Multi-protein Complexes In Determining Phenotype (2008)
Le Meur, Nolwenn, Gentleman, Robert
Understanding regulatory mechanisms in complex biological systems is an important challenge, in particular to understand disease mechanisms, and to discover new therapies and drugs. In this paper, we...
Estimating node degree in bait-prey graphs (2008)
Scholtens, Denise, Chiang, Tony, Huber, Wolfgang, Gentleman, Robert
Motivation: Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for...
Gene set enrichment analysis using linear models and diagnostics (2008)
Oron, Assaf P., Jiang, Zhen, Gentleman, Robert
Motivation: Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential samples, and...
Chiang, Tony, Li, Nianhua, Orchard, Sandra, Kerrien, Samuel, Hermjakob, Henning, Gentleman, Robert, ...
Motivation: The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational...
The 1991 revision of the S language [2] introduced several new concepts. In this paper we show how three of these: dataframes, formulas, and object oriented programming can be used to simplify the...
Making the most of high-throughput protein-interaction data (2007)
Gentleman, Robert, Huber, Wolfgang
Abstract We review the estimation of coverage and error rate in high-throughput protein-protein interaction datasets and argue that reports of the low quality of such data are to a substantial extent...
Graphs in molecular biology (2007)
Huber, Wolfgang, Carey, Vincent J, Long, Li, Falcon, Seth, Gentleman, Robert
Abstract Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and...
Coverage and error models of protein-protein interaction data by directed graph analysis (2007)
Chiang, Tony, Scholtens, Denise, Sarkar, Deepayan, Gentleman, Robert, Huber, Wolfgang
Abstract Using a directed graph model for bait to prey systems and a multinomial error model, we assessed the error statistics in all published large-scale datasets for Saccharomyces cerevisiae and...
Data Quality Assessment of Ungated Flow Cytometry Data in High (2007)
Le Meur, Nolwenn, Rossini, Anthony, Gasparetto, Maura, Smith, Clay, Brinkman, Ryan R, Gentleman, Robert
Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical...
Data Quality Assessment of Ungated Flow Cytometry Data in High (2007)
Le Meur, Nolwenn, Rossini, Anthony, Gasparetto, Maura, Smith, Clay, Brinkman, Ryan R, Gentleman, Robert
Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical...
Data Quality Assessment of Ungated Flow Cytometry Data in High (2007)
Le Meur, Nolwenn, Rossini, Anthony, Gasparetto, Maura, Smith, Clay, Brinkman, Ryan R, Gentleman, Robert
Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical...
Data Quality Assessment of Ungated Flow Cytometry Data in High (2007)
Le Meur, Nolwenn, Rossini, Anthony, Gasparetto, Maura, Smith, Clay, Brinkman, Ryan R, Gentleman, Robert
Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical...
GGtools: analysis of genetics of gene expression in bioconductor (2007)
Carey, Vincent J., Morgan, Martin, Falcon, Seth, Lazarus, Ross, Gentleman, Robert
Summary: This paper reviews the central concepts and implementation of data structures and methods for studying genetics of gene expression with the GGtools package of Bioconductor. Illustration with...
Extensions to gene set enrichment (2007)
Jiang, Zhen, Gentleman, Robert
Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture changes in the expression of pre-defined sets of genes. We propose number of extensions to GSEA, including the...
Extensions to Gene Set Enrichment (2006)
Jiang, Zhen, Gentleman, Robert
Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture moderate but coordinated changes in the expression of sets of functionally related genes. We propose number of...
Extensions to Gene Set Enrichment (2006)
Jiang, Zhen, Gentleman, Robert
Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture moderate but coordinated changes in the expression of sets of functionally related genes. We propose number of...
Extensions to Gene Set Enrichment (2006)
Jiang, Zhen, Gentleman, Robert
Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture moderate but coordinated changes in the expression of sets of functionally related genes. We propose number of...
Extensions to Gene Set Enrichment (2006)
Jiang, Zhen, Gentleman, Robert
Motivation: Gene Set Enrichment Analysis (GSEA) has been developed recently to capture moderate but coordinated changes in the expression of sets of functionally related genes. We propose number of...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
Visualizing Genomic Data (2006)
Gentleman, Robert, Hahne, Florian, Huber, Wolfgang
The advent of experimental techniques capable of probing biomolecules and cells at high levels of resolution has led to a rapid change in the methods used for the analysis of experimental molecular...
1 Overview HowTo: Querying online Data (2006)
This article demonstrates how you can make use of the tools that have been provided for on-line querying of data resources. These tools rely on others (such as the NLM and NCBI) providing and...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
On the Synthesis of Microarray Experiments (2005)
Gentleman, Robert, Ruschhaupt, Markus, Huber, Wolfgang
With many different investigators studying the same disease and with a strong commitment to publish supporting data in the scientific community, there are often many different datasets available for...
Reproducible Research: A Bioinformatics Case Study (2005)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Reproducible Research: A Bioinformatics Case Study (2005)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Reproducible Research: A Bioinformatics Case Study (2005)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Reproducible Research: A Bioinformatics Case Study (2005)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Making Sense of High-Throughput Protein-Protein Interaction Data (2005)
Scholtens, Denise, Gentleman, Robert
Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of...
Making Sense of High-Throughput Protein-Protein Interaction Data (2005)
Scholtens, Denise, Gentleman, Robert
Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of...
Making Sense of High-Throughput Protein-Protein Interaction Data (2005)
Scholtens, Denise, Gentleman, Robert
Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of...
Making Sense of High-Throughput Protein-Protein Interaction Data (2005)
Scholtens, Denise, Gentleman, Robert
Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of...
BIOINFORMATICS ORIGINAL PAPER Systems biology Local modeling of global interactome networks (2005)
Denise Scholtens, Marc Vidal, Robert Gentleman
Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and affinity–...
Local modeling of global interactome networks (2005)
Scholtens, Denise, Vidal, Marc, Gentleman, Robert
Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and...
Network structures and algorithms in Bioconductor (2005)
Carey, Vincent J., Gentry, Jeff, Whalen, Elizabeth, Gentleman, Robert
Summary: In this paper, we review the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T...
Local modeling of global interactome networks (2005)
Scholtens, Denise, Vidal, Marc, Gentleman, Robert
Motivation: Systems biology requires accurate models of protein complexes, including physical interactions that assemble and regulate these molecular machines. Yeast two-hybrid (Y2H) and...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck,Anja, Huber,Wolfgang, Gentleman,Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these different data...
Statistical Analyses and Reproducible Research (2004)
Gentleman, Robert, Temple Lang, Duncan
For various reasons, it is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, etc. with the documents that describe...
Statistical Analyses and Reproducible Research (2004)
Gentleman, Robert, Temple Lang, Duncan
For various reasons, it is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, etc. with the documents that describe...
Statistical Analyses and Reproducible Research (2004)
Gentleman, Robert, Temple Lang, Duncan
For various reasons, it is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, etc. with the documents that describe...
Statistical Analyses and Reproducible Research (2004)
Gentleman, Robert, Temple Lang, Duncan
For various reasons, it is important, if not essential, to integrate the computations and code used in data analyses, methodological descriptions, simulations, etc. with the documents that describe...
A Model Based Background Adjustment for Oligonucleotide Expression Arrays (2004)
Wu, Zhijin, Irizarry, Rafael A, Gentleman, Robert, Murillo, Francisco Martinez, Spencer, Forrest
High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of...
A Model Based Background Adjustment for Oligonucleotide Expression Arrays (2004)
Wu, Zhijin, Irizarry, Rafael A, Gentleman, Robert, Murillo, Francisco Martinez, Spencer, Forrest
High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of...
A Model Based Background Adjustment for Oligonucleotide Expression Arrays (2004)
Wu, Zhijin, Irizarry, Rafael A, Gentleman, Robert, Murillo, Francisco Martinez, Spencer, Forrest
High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of...
A Model Based Background Adjustment for Oligonucleotide Expression Arrays (2004)
Wu, Zhijin, Irizarry, Rafael A, Gentleman, Robert, Murillo, Francisco Martinez, Spencer, Forrest
High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of...
Reproducible Research: A Bioinformatics Case Study (2004)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Reproducible Research: A Bioinformatics Case Study (2004)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Reproducible Research: A Bioinformatics Case Study (2004)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Reproducible Research: A Bioinformatics Case Study (2004)
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Classification Using Generalized Partial Least Squares (2004)
Ding, Beiying, Gentleman, Robert
The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in...
Classification Using Generalized Partial Least Squares (2004)
Ding, Beiying, Gentleman, Robert
The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in...
Classification Using Generalized Partial Least Squares (2004)
Ding, Beiying, Gentleman, Robert
The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in...
Classification Using Generalized Partial Least Squares (2004)
Ding, Beiying, Gentleman, Robert
The advances in computational biology have made simultaneous monitoring of thousands of features possible. The high throughput technologies not only bring about a much richer information context in...
Differential Expression with the Bioconductor Project (2004)
Von Heydebreck, Anja, Huber, Wolfgang, Gentleman, Robert
A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. We...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these...
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements (2004)
Huber, Wolfgang, Gentleman, Robert
Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation...
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements (2004)
Huber, Wolfgang, Gentleman, Robert
Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these...
Network structures and algorithms in Bioconductor (2004)
Carey, Vincent J., Gentry, Jeff, Whalen, Elizabeth, Gentleman, Robert
Summary: This paper reviews the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T...
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements (2004)
Huber, Wolfgang, Gentleman, Robert
Summary: The nucleotide sequences of the probes on a microarray can be used for a variety of purposes in the analysis of microarray experiments. We describe software and a paradigm for the creation...
Balasubramanian, Raji, LaFramboise, Thomas, Scholtens, Denise, Gentleman, Robert
Motivation: The last few years have seen the advent of high-throughput technologies to analyze various properties of the transcriptome and proteome of several organisms. The congruency of these...
Network structures and algorithms in Bioconductor (2004)
Carey, Vincent J., Gentry, Jeff, Whalen, Elizabeth, Gentleman, Robert
Summary: This paper reviews the central concepts and implementations of tools for working with network structures in Bioconductor. Interfaces to open source resources for visualization (AT&T...
Robert Gentleman, Sandrine Dudoit
– mailing list. • Bioconductor www.bioconductor.org – software, data, and documentation (vignettes); – training materials from short courses; – mailing list.
An extensible application for assembling annotation for genomic data (2003)
Zhang, Jianhua, Carey, Vincent, Gentleman, Robert
Summary: AnnBuilder is an R package for assembling genomic annotation data. The system currently provides parsers to process annotation data from LocusLink, Gene Ontology Consortium, and Human Gene...
Weak Order Partitioning of Interval Orders With Applications to Interval Censored Data (1998)
Alain C. Vandal, Robert Gentleman
We propose a method by which the set of linear extensions of an interval order may be partitioned into sets of linear extensions of weak orders, using so-called marked configurations of the interval...
Order Theory and Nonparametric Maximum Likelihood for Interval Censored Data (1998)
Alain C. Vandal, Robert Gentleman
Interval censored data arises when individuals can be subjected to periodic inspection at possibly random moments, and their status (e.g. failed or functioning) is ascertained at each inspection. We...
Minimal Covers of Maximal Antichains for Interval Orders (1997)
Alain C. Vandal, Robert Gentleman
We address the problem of determining all sets which form minimal covers of maximal antichains for interval orders, i.e., sets no proper subsets of which form an element cover of the ordered set....
Maximum likelihood for interval censored data: Consistency and computation (1994)
GENTLEMAN, ROBERT, GEYER, CHARLES J.
Standard convex optimization techniques are applied to the analysis of interval censored data. These methods provide easily verifiable conditions for the self-consistent estimator proposed by...
Huber, Wolfgang, Carey, Vincent J, Long, Li, Falcon, Seth, Gentleman, Robert
Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas...
Making the most of high-throughput protein-interaction data
Gentleman, Robert, Huber, Wolfgang
Better methods of statistical analysis could make large-scale protein-interaction data more useful.
A Model-Based Background Adjustment for Oligonucleotide Expression Arrays
Zhijin Wu, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez-Murillo, Forrest Spencer
Reproducible Research: A Bioinformatics Case Study
While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has...
Making Sense of High-Throughput Protein-Protein Interaction Data
Denise Scholtens, Robert Gentleman
Accurate systems biology modeling requires a complete catalog of protein complexes and their constituent proteins. We discuss a graph-theoretic/statistical algorithm for local dynamic modeling of...
A Model Based Background Adjustment for Oligonucleotide Expression Arrays
Zhijin Wu, Rafael Irizarry, Robert Gentleman, Francisco Martinez Murillo, Forrest Spencer
High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of...
Coverage and error models of protein-protein interaction data by directed graph analysis
Chiang, Tony, Scholtens, Denise, Sarkar, Deepayan, Gentleman, Robert, Huber, Wolfgang
Directed graph and multinomial error models were used to assess and characterize the error statistics in all published large-scale datasets for Saccharomyces cerevisiae
Le Meur, Nolwenn, Gentleman, Robert
Using new computational tools in yeast, multi-protein complexes were identified that share an unusually high number of synthetic genetic interactions.
Analyzing factorial designed microarray experiments
Scholtens, Denise, Miron, Alexander, M. Merchant, Faisal, Miller, Arden, L. Miron, Penelope, Dirk Iglehart, J., ...
High-throughput quantification of gene expression using microarray technology has dramatically changed biological investigation into the roles of genes in normal cell functioning, as well as the...
Circulating microRNAs as stable blood-based markers for cancer detection
Mitchell, Patrick S., Parkin, Rachael K., Kroh, Evan M., Fritz, Brian R., Wyman, Stacia K., Pogosova-Agadjanyan, Era L., ...
Improved approaches for the detection of common epithelial malignancies are urgently needed to reduce the worldwide morbidity and mortality caused by cancer. MicroRNAs (miRNAs) are small (≈22 nt)...
arrayQualityMetrics—a bioconductor package for quality assessment of microarray data
Kauffmann, Audrey, Gentleman, Robert, Huber, Wolfgang
Summary:: The assessment of data quality is a major concern in microarray analysis. arrayQualityMetrics is a Bioconductor package that provides a report with diagnostic plots for one or two colour...
flowCore: a Bioconductor package for high throughput flow cytometry
Hahne, Florian, LeMeur, Nolwenn, Brinkman, Ryan R, Ellis, Byron, Haaland, Perry, Sarkar, Deepayan, ...
rtracklayer: an R package for interfacing with genome browsers
Lawrence, Michael, Gentleman, Robert, Carey, Vincent
Summary: The rtracklayer package supports the integration of existing genome browsers with experimental data analyses performed in R. The user may (i) transfer annotation tracks to and from a genome...
Knowledge based identification of essential signaling from genome-scale siRNA experiments
Bankhead, Armand, Sach, Iliana, Ni, Chester, LeMeur, Nolwenn, Kruger, Mark, Ferrer, Marc, ...
Morgan, Martin, Anders, Simon, Lawrence, Michael, Aboyoun, Patrick, Pagès, Hervé, Gentleman, Robert
Summary: ShortRead is a package for input, quality assessment, manipulation and output of high-throughput sequencing data. ShortRead is provided in the R and Bioconductor environments, allowing ready...
Gene set enrichment analysis using linear models and diagnostics
Oron, Assaf P., Jiang, Zhen, Gentleman, Robert
Motivation: Gene-set enrichment analysis (GSEA) can be greatly enhanced by linear model (regression) diagnostic techniques. Diagnostics can be used to identify outlying or influential samples, and...