A proteome-wide protein interaction map for Campylobacter jejuni (2007)
Parrish, Jodi R, Yu, Jingkai, Liu, Guozhen, Hines, Julie A, Chan, Jason E, Mangiola, Bernie A, ...
Abstract Background Data from large-scale protein interaction screens for humans and model eukaryotes have been invaluable for developing systems-level models of biological processes. Despite this...
A direct comparison of protein interaction confidence assignment schemes (2006)
Suthram, Silpa, Shlomi, Tomer, Ruppin, Eytan, Sharan, Roded, Ideker, Trey
Abstract Background Recent technological advances have enabled high-throughput measurements of protein-protein interactions in the cell, producing large protein interaction networks for various...
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Abstract Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions....
Integrated Assessment and Prediction of Transcription Factor Binding (2006)
Andreas Beyer, Christopher Workman, Jens Hollunder, Dörte Radke, Ulrich Möller, Thomas Wilhelm, ...
Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of...
Systematic identification of functional orthologs based on protein network comparison. (2006)
Bandyopadhyay, Sourav, Sharan, Roded, Ideker, Trey
Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying...
Interactome networks: the state of the science (2006)
Warner, Guy J, Adeleye, Yeyejide A, Ideker, Trey
A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005. High-throughput analyses are identifying the DNA, RNA, proteins and...
Validation and refinement of gene-regulatory pathways on a network of physical interactions (2005)
Yeang, Chen-Hsiang, Mak, H Craig, McCuine, Scott, Workman, Christopher, Jaakkola, Tommi, Ideker, Trey
Abstract As genome-scale measurements lead to increasingly complex models of gene regulation, systematic approaches are needed to validate and refine these models. Towards this goal, we describe an...
Integrating phenotypic and expression profiles to map arsenic-response networks (2004)
Haugen, Astrid C, Kelley, Ryan, Collins, Jennifer B, Tucker, Charles J, Deng, Changchun, Afshari, Cynthia A, ...
Abstract Background Arsenic is a nonmutagenic carcinogen affecting millions of people. The cellular impact of this metalloid in Saccharomyces cerevisiae was determined by profiling global gene...
Roded Sharan, Trey Ideker, Brian Kelley, Ron Shamir, Richard M. Karp
Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to nd complexes that are common to the yeast S. cerevisiae and the bacteria H. pylori. Our...
Identification of Protein Complexes by Comparative Analysis of (2003)
Roded Sharan, Trey Ideker, Brian Kelley, Ron Shamir, Richard M. Karp
Mounting evidence shows that many protein complexes are conserved in evolution. Here we use conservation to find complexes that are common to yeast S. Cerevisiae and bacteria H. pylori. Our analysis...
Visualization and Integration of Protein-Protein Interactions (2001)
CONTENTS INTRODUCTION ..........................................................................................................................................2 WHY DO WE NEED VISUALIZATION?...
Validation and refinement of genetic networks in yeast / (2001)
Thesis (Ph. D.)--University of Washington, 2001.
Offset correction techniques for imaging sensors using random dither information (1995)
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1995.
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1995.
Offset correction techniques for imaging sensors using random dither information (1995)
Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1995.
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
Kelley, Brian P., Sharan, Roded, Karp, Richard M., Sittler, Taylor, Root, David E., Stockwell, Brent R., ...
We implement a strategy for aligning two protein–protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and...
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Shannon, Paul, Markiel, Andrew, Ozier, Owen, Baliga, Nitin S., Wang, Jonathan T., Ramage, Daniel, ...
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework....
PathBLAST: a tool for alignment of protein interaction networks
Kelley, Brian P., Yuan, Bingbing, Lewitter, Fran, Sharan, Roded, Stockwell, Brent R., Ideker, Trey
PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic...
Integrating phenotypic and expression profiles to map arsenic-response networks
Haugen, Astrid C, Kelley, Ryan, Collins, Jennifer B, Tucker, Charles J, Deng, Changchun, Afshari, Cynthia A, ...
By integrating phenotypic and transcriptional profiling and mapping the data onto metabolic and regulatory networks, it was shown that arsenic probably channels sulfur into glutathione for...
Conserved patterns of protein interaction in multiple species
Sharan, Roded, Suthram, Silpa, Kelley, Ryan M., Kuhn, Tanja, McCuine, Scott, Uetz, Peter, ...
To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein–protein interaction networks of Caenorhabditis elegans, Drosophila...
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
Hsiao, Albert, Ideker, Trey, Olefsky, Jerrold M., Subramaniam, Shankar
Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether...
Validation and refinement of gene-regulatory pathways on a network of physical interactions
Yeang, Chen-Hsiang, Mak, H Craig, McCuine, Scott, Workman, Christopher, Jaakkola, Tommi, Ideker, Trey
A new automated procedure for prioritizing genetic perturbations was used to evaluate 38 candidate regulatory networks in yeast. Further analysis of four high-priority gene knockout experiments...
Interactome networks: the state of the science
Warner, Guy J, Adeleye, Yeyejide A, Ideker, Trey
A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005.
Integrated Assessment and Prediction of Transcription Factor Binding
Beyer, Andreas, Workman, Christopher, Hollunder, Jens, Radke, Dörte, Möller, Ulrich, Wilhelm, Thomas, ...
Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of...
A direct comparison of protein interaction confidence assignment schemes
Suthram, Silpa, Shlomi, Tomer, Ruppin, Eytan, Sharan, Roded, Ideker, Trey
Systematic identification of functional orthologs based on protein network comparison
Bandyopadhyay, Sourav, Sharan, Roded, Ideker, Trey
Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying...
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Conserved pathways within bacteria and yeast as revealed by global protein network alignment
Kelley, Brian P., Sharan, Roded, Karp, Richard M., Sittler, Taylor, Root, David E., Stockwell, Brent R., ...
We implement a strategy for aligning two protein–protein interaction networks that combines interaction topology and protein sequence similarity to identify conserved interaction pathways and...
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Shannon, Paul, Markiel, Andrew, Ozier, Owen, Baliga, Nitin S., Wang, Jonathan T., Ramage, Daniel, ...
Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework....
PathBLAST: a tool for alignment of protein interaction networks
Kelley, Brian P., Yuan, Bingbing, Lewitter, Fran, Sharan, Roded, Stockwell, Brent R., Ideker, Trey
PathBLAST is a network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution. The basic...
Integrating phenotypic and expression profiles to map arsenic-response networks
Haugen, Astrid C, Kelley, Ryan, Collins, Jennifer B, Tucker, Charles J, Deng, Changchun, Afshari, Cynthia A, ...
By integrating phenotypic and transcriptional profiling and mapping the data onto metabolic and regulatory networks, it was shown that arsenic probably channels sulfur into glutathione for...
Conserved patterns of protein interaction in multiple species
Sharan, Roded, Suthram, Silpa, Kelley, Ryan M., Kuhn, Tanja, McCuine, Scott, Uetz, Peter, ...
To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein–protein interaction networks of Caenorhabditis elegans, Drosophila...
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
VAMPIRE microarray suite: a web-based platform for the interpretation of gene expression data
Hsiao, Albert, Ideker, Trey, Olefsky, Jerrold M., Subramaniam, Shankar
Microarrays are invaluable high-throughput tools used to snapshot the gene expression profiles of cells and tissues. Among the most basic and fundamental questions asked of microarray data is whether...
Validation and refinement of gene-regulatory pathways on a network of physical interactions
Yeang, Chen-Hsiang, Mak, H Craig, McCuine, Scott, Workman, Christopher, Jaakkola, Tommi, Ideker, Trey
A new automated procedure for prioritizing genetic perturbations was used to evaluate 38 candidate regulatory networks in yeast. Further analysis of four high-priority gene knockout experiments...
Systematic identification of functional orthologs based on protein network comparison
Bandyopadhyay, Sourav, Sharan, Roded, Ideker, Trey
Annotating protein function across species is an important task that is often complicated by the presence of large paralogous gene families. Here, we report a novel strategy for identifying...
Interactome networks: the state of the science
Warner, Guy J, Adeleye, Yeyejide A, Ideker, Trey
A report on the joint Cold Spring Harbor/Wellcome Trust Meeting 'Interactome Networks', Hinxton, UK, 31 August-4 September 2005.
Integrated Assessment and Prediction of Transcription Factor Binding
Beyer, Andreas, Workman, Christopher, Hollunder, Jens, Radke, Dörte, Möller, Ulrich, Wilhelm, Thomas, ...
Systematic chromatin immunoprecipitation (chIP-chip) experiments have become a central technique for mapping transcriptional interactions in model organisms and humans. However, measurement of...
A direct comparison of protein interaction confidence assignment schemes
Suthram, Silpa, Shlomi, Tomer, Ruppin, Eytan, Sharan, Roded, Ideker, Trey
Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C, Myers, Chad L, ...
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri
Feist, Adam M, Scholten, Johannes C M, Palsson, Bernhard Ø, Brockman, Fred J, Ideker, Trey
We present a genome-scale metabolic model for the archaeal methanogen Methanosarcina barkeri. We characterize the metabolic network and compare it to reconstructions from the prokaryotic, eukaryotic...
CellCircuits: a database of protein network models
Mak, H. Craig, Daly, Mike, Gruebel, Bianca, Ideker, Trey
CellCircuits () is an open-access database of molecular network models, designed to bridge the gap between databases of individual pairwise molecular interactions and databases of validated pathways....
Transcriptional regulation of protein complexes within and across species
Tan, Kai, Shlomi, Tomer, Feizi, Hoda, Ideker, Trey, Sharan, Roded
Yeast two-hybrid and coimmunoprecipitation experiments have defined large-scale protein–protein interaction networks for many model species. Separately, systematic chromatin immunoprecipitation...
Network-based classification of breast cancer metastasis
Chuang, Han-Yu, Lee, Eunjung, Liu, Yu-Tsueng, Lee, Doheon, Ideker, Trey
Mapping the pathways that give rise to metastasis is one of the key challenges of breast cancer research. Recently, several large-scale studies have shed light on this problem through analysis of...
eQED: an efficient method for interpreting eQTL associations using protein networks
Suthram, Silpa, Beyer, Andreas, Karp, Richard M, Eldar, Yonina, Ideker, Trey
Analysis of expression quantitative trait loci (eQTLs) is an emerging technique in which individuals are genotyped across a panel of genetic markers and, simultaneously, phenotyped using DNA...
Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data
Bandyopadhyay, Sourav, Kelley, Ryan, Krogan, Nevan J., Ideker, Trey
Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS...
A proteome-wide protein interaction map for Campylobacter jejuni
Parrish, Jodi R, Yu, Jingkai, Liu, Guozhen, Hines, Julie A, Chan, Jason E, Mangiola, Bernie A, ...
'Systematic identification of protein interactions for the bacterium Campylobacter jejuni using high-throughput yeast two-hybrid screens detected interactions for 80% of the organism's proteins.
Transcriptome profiling to identify genes involved in peroxisome assembly and function
Smith, Jennifer J., Marelli, Marcello, Christmas, Rowan H., Vizeacoumar, Franco J., Dilworth, David J., Ideker, Trey, ...
Yeast cells were induced to proliferate peroxisomes, and microarray transcriptional profiling was used to identify PEX genes encoding peroxins involved in peroxisome assembly and genes involved in...
Inferring Pathway Activity toward Precise Disease Classification
Lee, Eunjung, Chuang, Han-Yu, Kim, Jong-Won, Ideker, Trey, Lee, Doheon
The advent of microarray technology has made it possible to classify disease states based on gene expression profiles of patients. Typically, marker genes are selected by measuring the power of their...