Roth, Frederick P, Lipshitz, Howard D, Andrews, Brenda J
No abstract available.
An empirical framework for binary interactome mapping (2009)
Venkatesan, Kavitha, Rual, Jean-Francois, Vazquez, Alexei, Stelzl, Ulrich, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets....
An experimentally derived confidence score for binary protein-protein interactions (2009)
Braun, Pascal, Tasan, Murat, Dreze, Matija, Barrios-Rodiles, Miriam, Lemmens, Irma, Yu, Haiyuan, ...
Information on protein-protein interactions is of central importance for many areas of biomedical research. At present no method exists to systematically and experimentally assess the quality of...
Simonis, Nicolas, Rual, Jean-Francois, Carvunis, Anne-Ruxandra, Tasan, Murat, Lemmens, Irma, Hirozane-Kishikawa, Tomoko, ...
Abstract: To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards....
Next generation software for functional trend analysis (2009)
Berriz, Gabriel F., Beaver, John E., Cenik, Can, Tasan, Murat, Roth, Frederick P.
Summary: FuncAssociate is a web application that discovers properties enriched in lists of genes or proteins that emerge from large-scale experimentation. Here we describe an updated application with...
Martinez, Natalia J., Ow, Maria C., Barrasa, M. Inmaculada, Hammell, Molly, Sequerra, Reynaldo, Doucette-Stamm, Lynn, ...
MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both miRNAs and TFs, the transcriptional networks...
An en massephenotype and function prediction system for Mus musculus (2008)
Taşan, Murat, Tian, Weidong, Hill, David P, Gibbons, Francis D, Blake, Judith A, Roth, Frederick P
Abstract Background: Individual researchers are struggling to keep up with the accelerating emergence of high-throughput biological data, and to extract information that relates to their specific...
Tian, Weidong, Zhang, Lan V, Taşan, Murat, Gibbons, Francis D, King, Oliver D, Park, Julie, ...
Abstract Background: Learning the function of genes is a major goal of computational genomics. Methods for inferring gene function have typically fallen into two categories: 'guilt-by-profiling',...
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
Abstract Background: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of...
A race through the maze of genomic evidence (2008)
Hughes, Timothy R, Roth, Frederick P
No abstract available.
A Rich Probabilistic Model to Predict Yeast Gene Function (2008)
Lan V. Zhang, Oliver D. King, Zeba Wunderlich, Frederick P. Roth
interaction, protein domain, and gene ontology.
Probabilistic paths in protein interaction networks (2008)
Hailiang Huang, Lan V. Zhang, Frederick P. Roth, Joel S. Bader
Understanding how proteins are physically organized into complexes and pathways is increasingly based on observations from high-throughput experiments. Yeast is a widely used model for eukaryotic...
Functional Specificity among Ribosomal Proteins Regulates Gene Expression (2008)
Suzanne Komili, Natalie G. Farny, Frederick P. Roth, Pamela A. Silver
Duplicated genes escape gene loss by conferring a dosage benefit or evolving diverged functions. The yeast Saccharomyces cerevisiae contains many duplicated genes encoding ribosomal proteins. Prior...
Metabolomic Identification of Novel Biomarkers of (2008)
Myocardial Ischemia, Robert Mccarroll, Phd Roger Wieg, Phd Gabriel, F. Berriz, Frederick P. Roth, ...
Background—Recognition of myocardial ischemia is critical both for the diagnosis of coronary artery disease and the selection and evaluation of therapy. Recent advances in proteomic and metabolic...
808 RESEARCH ARTICLE Global Mapping of the Yeast Genetic Interaction Network (2008)
Amy Hin, Yan Tong, Guillaume Lesage, Gary D. Bader, Huiming Ding, Hong Xu, ...
A genetic interaction network containing �1000 genes and �4000 interactions was mapped by crossing mutations in 132 different query genes into a set of �4700 viable gene yeast deletion mutants...
PERSPECTIVE Downloaded from (2008)
Suzanne Komili, Frederick P. Roth
www.genesdev.org Genetic interaction screens advance in reverse
Probabilistic Paths for Protein Complex Inference (2008)
Hailiang Huang, Lan V. Zhang, Frederick P. Roth, Joel S. Bader
Abstract. Understanding how individual proteins are organized into complexes and pathways is a significant current challenge. We introduce new algorithms to infer protein complexes by combining seed...
A protein domain-based interactome network for C. elegans early embryogenesis (2008)
Boxem, Mike, Maliga, Zoltan, Klitgord, Niels, Li, Na, Lemmens, Irma, Mana, Miyeko, ...
Many protein-protein interactions are mediated through independently folding modular domains. Proteome-wide efforts to model protein-protein interaction or "interactome" networks have largely ignored...
Martinez, Natalia J., Ow, Maria C., Barrasa, M. Inmaculada, Hammell, Molly, Sequerra, Reynaldo, Doucette-Stamm, Lynn, ...
MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both miRNAs and TFs, the transcriptional networks...
The Synergizer service for translating gene, protein and other biological identifiers (2008)
Berriz, Gabriel F., Roth, Frederick P.
Summary: The Synergizer is a database and web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively. Availability: The...
Chemical substructures that enrich for biological activity (2008)
Klekota, Justin, Roth, Frederick P.
Motivation: Certain chemical substructures are present in many drugs. This has led to the claim of ‘privileged’ substructures which are predisposed to bioactivity. Because bias in screening...
Insight/Outlook Bringing Out the Best Features of Expression Data (2007)
Scientists are constantly classifying objects based on observation: A Drosophila geneticist sexes flies; a taxonomist sorts butterflies according to genus and species; a physician interviews...
Methods Predicting Gene Function From Patterns of Annotation (2007)
Oliver D. King, Rebecca E. Foulger, Selina S. Dwight, James V. White, Frederick P. Roth
The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows the prediction of...
Methods Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation (2007)
Francis D. Gibbons, Frederick P. Roth
We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying...
Confirmation of Organized Modularity in the Yeast Interactome (2007)
Nicolas Bertin, Nicolas Simonis, Denis Dupuy, Michael E. Cusick, Hunter B. Fraser, ...
Query Chem: A Google-Powered Web Search Combining Text and Chemical Structures (2006)
Justin Klekota, Frederick P. Roth, Stuart L. Schreiber, Alfonso Valencia
Query Chem (www.QueryChem.com) is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google’s Web Application Program...
Query Chem: a Google-powered web search combining text and chemical structures (2006)
Klekota, Justin, Roth, Frederick P., Schreiber, Stuart L.
Summary: Query Chem (www.QueryChem.com) is a Web program that integrates chemical structure and text-based searching using publicly available chemical databases and Google's Web Application Program...
Gibbons, Francis D, Proft, Markus, Struhl, Kevin, Roth, Frederick P
Abstract Chromatin immunoprecipitation combined with microarray technology (Chip 2 ) allows genome-wide determination of protein-DNA binding sites. The current standard method for analyzing Chip 2...
Gibbons, Francis D., Proft, Markus, Struhl, Kevin, Roth, Frederick P.
The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2005/6/11/R96
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiaeinteraction network (2005)
Zhang, Lan V, King, Oliver D, Wong, Sharyl L, Goldberg, Debra S, Tong, Amy HY, Lesage, Guillaume, ...
Abstract Background Large-scale studies have revealed networks of various biological interaction types, such as protein-protein interaction, genetic interaction, transcriptional regulation, sequence...
Justin Klekota, Erik Brauner, Frederick P. Roth, Stuart L. Schreiber
The most desirable compound leads from high-throughput assays are those with novel biological activities resulting from their action on a single biological target. Valuable resources can be wasted on...
Markus Proft, Francis D. Gibbons, Matthew Copel, Frederick P. Roth, Kevin Struhl
In Saccharomyces cerevisiae, the ATF/CREB transcription factor Sko1 (Acr1) regulates the expression of genes induced by osmotic stress under the control of the high osmolarity glycerol (HOG)...
Francis D Gibbons, Markus Proft, Kevin Struhl, Frederick P Roth
Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization
Predicting co-complexed protein pairs using genomic and proteomic data integration (2004)
Zhang, Lan V, Wong, Sharyl L, King, Oliver D, Roth, Frederick P
Abstract Background Identifying all protein-protein interactions in an organism is a major objective of proteomics. A related goal is to know which protein pairs are present in the same protein...
Predicting protein complex membership using probabilistic network reliability (2004)
Saurabh Asthana, Oliver D. King, Francis D. Gibbons, Frederick P. Roth, Email Alerting, Saurabh Asthana, ...
data
SILVER Helps Assign Peptides to Tandem Mass Spectra Using Intensity-Based Scoring (2004)
Francis D. Gibbons, Joshua E. Elias, Steven P. Gygi, Frederick P. Roth
redicted for peptides in a genome-derived database. Software using the latter approach has been more commonly adopted, with SEQUEST [2] and Mascot [3] being popular examples. However, exhaustive...
Hy Tong, Guillaume Lesage, Brenda Andrews, Howard Bussey, Frederick P Roth
Research article Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Bmc Bioinformatics, Lan V Zhang, Sharyl L Wong, Oliver D King, Frederick P Roth, Lan V Zhang, ...
Predicting co-complexed protein pairs using genomic and
Predicting Protein Complex Membership Using Probabilistic Network Reliability (2004)
Saurabh Asthana, Oliver D. King, Francis D. Gibbons, Frederick P. Roth
this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this...
Predicting Protein Complex Membership Using Probabilistic Network Reliability (2004)
Asthana, Saurabh, King, Oliver D., Gibbons, Francis D., Roth, Frederick P.
Evidence for specific protein–protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are...
Grad, Yonatan H., Roth, Frederick P., Halfon, Marc S., Church, George M.
Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but...
Grad, Yonatan H., Roth, Frederick P., Halfon, Marc S., Church, George M.
Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but...
Predicting Protein Complex Membership Using Probabilistic Network Reliability (2004)
Asthana, Saurabh, King, Oliver D., Gibbons, Francis D., Roth, Frederick P.
Evidence for specific protein-protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are...
Grad, Yonatan H., Roth, Frederick P., Halfon, Marc S., Church, George M.
Motivation: To date, computational searches for cis-regulatory modules (CRMs) have relied on two methods. The first, phylogenetic footprinting, has been used to find CRMs in non-coding sequence, but...
Vol Suppl Pages, Oliver D. King, Jeffrey C. Lee, Aimée M. Dudley, Daniel M, George M. Church, ...
Motivation: Predicting the outcome of specific experiments (such as the growth of a particular mutant strain in a particular medium) has the potential to allow researchers to devote resources to...
Latent Herpes Simplex Virus Infection of Sensory Neurons Alters Neuronal Gene Expression (2003)
Neuronal Gene Expression, Martha F. Kramer, W. James Cook, Frederick P. Roth, Jia Zhu, Holly Holman, ...
ding potassium voltage-gated channels and a muscarinic acetylcholine receptor. We confirmed the neuronal localization of some of these transcripts by using in situ hybridization. To validate the...
Characterizing gene sets with FuncAssociate (2003)
Berriz, Gabriel F., King, Oliver D., Bryant, Barbara, Sander, Chris, Roth, Frederick P.
Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate...
A non-parametric model for transcription factor binding sites (2003)
King, Oliver D., Roth, Frederick P.
We introduce a non‐parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation...
Predicting Gene Function From Patterns of Annotation (2003)
King, Oliver D., Foulger, Rebecca E., Dwight, Selina S., White, James V., Roth, Frederick P.
The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows the prediction of...
Predicting Gene Function From Patterns of Annotation (2003)
King, Oliver D., Foulger, Rebecca E., Dwight, Selina S., White, James V., Roth, Frederick P.
Predicting phenotype from patterns of annotation (2003)
King, Oliver D., Lee, Jeffrey C., Dudley, Aimée M., Janse, Daniel M., Church, George M., Roth, Frederick P.
Motivation:Predicting the outcome of specific experiments (such as the growth of a particular mutant strain in a particular medium) has the potential to allow researchers to devote resources to...
Marc Damelin, Itamar Simon, Terence I. Moy, Boris Wilson, Suzanne Komili, Paul Tempst, ...
(Causton et al., 2001; Gasch et al., 2000). These studies also generalized the role of the transcriptional activators Msn2 and Msn4 in the stress response. One of the signaling pathways known to...
Latent Herpes Simplex Virus Infection of Sensory Neurons Alters Neuronal Gene Expression
Kramer, Martha F., Cook, W. James, Roth, Frederick P., Zhu, Jia, Holman, Holly, Knipe, David M., ...
The persistence of herpes simplex virus (HSV) and the diseases that it causes in the human population can be attributed to the maintenance of a latent infection within neurons in sensory ganglia....
Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation
Gibbons, Francis D., Roth, Frederick P.
We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying...
A non-parametric model for transcription factor binding sites
King, Oliver D., Roth, Frederick P.
We introduce a non-parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation smoothly...
Predicting co-complexed protein pairs using genomic and proteomic data integration
Zhang, Lan V, Wong, Sharyl L, King, Oliver D, Roth, Frederick P
Predicting Protein Complex Membership Using Probabilistic Network Reliability
Asthana, Saurabh, King, Oliver D., Gibbons, Francis D., Roth, Frederick P.
Evidence for specific protein–protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are...
Predicting Gene Function From Patterns of Annotation
King, Oliver D., Foulger, Rebecca E., Dwight, Selina S., White, James V., Roth, Frederick P.
The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows the prediction of...
Combining biological networks to predict genetic interactions
Wong, Sharyl L., Zhang, Lan V., Tong, Amy H. Y., Li, Zhijian, Goldberg, Debra S., King, Oliver D., ...
Genetic interactions define overlapping functions and compensatory pathways. In particular, synthetic sick or lethal (SSL) genetic interactions are important for understanding how an organism...
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Zhang, Lan V, King, Oliver D, Wong, Sharyl L, Goldberg, Debra S, Tong, Amy HY, Lesage, Guillaume, ...
Proft, Markus, Gibbons, Francis D., Copeland, Matthew, Roth, Frederick P., Struhl, Kevin
In Saccharomyces cerevisiae, the ATF/CREB transcription factor Sko1 (Acr1) regulates the expression of genes induced by osmotic stress under the control of the high osmolarity glycerol (HOG)...
Gibbons, Francis D, Proft, Markus, Struhl, Kevin, Roth, Frederick P
A new method, implemented in software as 'Chipper', is described that allows genome-wide determination of protein-DNA binding sites from chromatin immunoprecipitation microarrays.
Assessing experimentally derived interactions in a small world
Goldberg, Debra S., Roth, Frederick P.
Experimentally determined networks are susceptible to errors, yet important inferences can still be drawn from them. Many real networks have also been shown to have the small-world network properties...
Wong, Sharyl L., Roth, Frederick P.
If a gene is mutated and its function lost, are compensatory genes upregulated? We investigated whether genes are transcriptionally upregulated when their synthetic sick or lethal (SSL) partners are...
Roth, John R, Kofoid, Eric, Roth, Frederick P, Berg, Otto G, Seger, Jon, Andersson, Dan I
In the lac adaptive mutation system of Cairns, selected mutant colonies but not unselected mutant types appear to arise from a nongrowing population of Escherichia coli. The general mutagenesis...
Latent Herpes Simplex Virus Infection of Sensory Neurons Alters Neuronal Gene Expression
Kramer, Martha F., Cook, W. James, Roth, Frederick P., Zhu, Jia, Holman, Holly, Knipe, David M., ...
The persistence of herpes simplex virus (HSV) and the diseases that it causes in the human population can be attributed to the maintenance of a latent infection within neurons in sensory ganglia....
Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation
Gibbons, Francis D., Roth, Frederick P.
We compare several commonly used expression-based gene clustering algorithms using a figure of merit based on the mutual information between cluster membership and known gene attributes. By studying...
A non-parametric model for transcription factor binding sites
King, Oliver D., Roth, Frederick P.
We introduce a non-parametric representation of transcription factor binding sites which can model arbitrary dependencies between positions. As two parameters are varied, this representation smoothly...
Assessing experimentally derived interactions in a small world
Goldberg, Debra S., Roth, Frederick P.
Experimentally determined networks are susceptible to errors, yet important inferences can still be drawn from them. Many real networks have also been shown to have the small-world network properties...
Predicting co-complexed protein pairs using genomic and proteomic data integration
Zhang, Lan V, Wong, Sharyl L, King, Oliver D, Roth, Frederick P
Predicting Protein Complex Membership Using Probabilistic Network Reliability
Asthana, Saurabh, King, Oliver D., Gibbons, Francis D., Roth, Frederick P.
Evidence for specific protein–protein interactions is increasingly available from both small- and large-scale studies, and can be viewed as a network. It has previously been noted that errors are...
Predicting Gene Function From Patterns of Annotation
King, Oliver D., Foulger, Rebecca E., Dwight, Selina S., White, James V., Roth, Frederick P.
The Gene Ontology (GO) Consortium has produced a controlled vocabulary for annotation of gene function that is used in many organism-specific gene annotation databases. This allows the prediction of...
Combining biological networks to predict genetic interactions
Wong, Sharyl L., Zhang, Lan V., Tong, Amy H. Y., Li, Zhijian, Goldberg, Debra S., King, Oliver D., ...
Genetic interactions define overlapping functions and compensatory pathways. In particular, synthetic sick or lethal (SSL) genetic interactions are important for understanding how an organism...
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Zhang, Lan V, King, Oliver D, Wong, Sharyl L, Goldberg, Debra S, Tong, Amy HY, Lesage, Guillaume, ...
Proft, Markus, Gibbons, Francis D., Copeland, Matthew, Roth, Frederick P., Struhl, Kevin
In Saccharomyces cerevisiae, the ATF/CREB transcription factor Sko1 (Acr1) regulates the expression of genes induced by osmotic stress under the control of the high osmolarity glycerol (HOG)...
Gibbons, Francis D, Proft, Markus, Struhl, Kevin, Roth, Frederick P
A new method, implemented in software as 'Chipper', is described that allows genome-wide determination of protein-DNA binding sites from chromatin immunoprecipitation microarrays.
Wong, Sharyl L., Roth, Frederick P.
If a gene is mutated and its function lost, are compensatory genes upregulated? We investigated whether genes are transcriptionally upregulated when their synthetic sick or lethal (SSL) partners are...
Roth, John R, Kofoid, Eric, Roth, Frederick P, Berg, Otto G, Seger, Jon, Andersson, Dan I
In the lac adaptive mutation system of Cairns, selected mutant colonies but not unselected mutant types appear to arise from a nongrowing population of Escherichia coli. The general mutagenesis...
Confirmation of Organized Modularity in the Yeast Interactome
Bertin, Nicolas, Simonis, Nicolas, Dupuy, Denis, Cusick, Michael E, Han, Jing-Dong J, Fraser, Hunter B, ...
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
An en masse phenotype and function prediction system for Mus musculus
Taşan, Murat, Tian, Weidong, Hill, David P, Gibbons, Francis D, Blake, Judith A, Roth, Frederick P
Mani, Ramamurthy, St.Onge, Robert P., Hartman, John L., Giaever, Guri, Roth, Frederick P.
Sometimes mutations in two genes produce a phenotype that is surprising in light of each mutation's individual effects. This phenomenon, which defines genetic interaction, can reveal functional...
The Synergizer service for translating gene, protein and other biological identifiers
Berriz, Gabriel F., Roth, Frederick P.
Summary: The Synergizer is a database and web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively.
Lewis, Gregory D., Wei, Ru, Liu, Emerson, Yang, Elaine, Shi, Xu, Martinovic, Maryann, ...
Emerging metabolomic tools have created the opportunity to establish metabolic signatures of myocardial injury. We applied a mass spectrometry–based metabolite profiling platform to 36 patients...
Martinez, Natalia J., Ow, Maria C., Barrasa, M. Inmaculada, Hammell, Molly, Sequerra, Reynaldo, Doucette-Stamm, Lynn, ...
MicroRNAs (miRNAs) and transcription factors (TFs) are primary metazoan gene regulators. Whereas much attention has focused on finding the targets of both miRNAs and TFs, the transcriptional networks...
Gerszten, Robert E., Accurso, Frank, Bernard, Gordon R., Caprioli, Richard M., Klee, Eric W., Klee, George G., ...
The emerging scientific field of proteomics encompasses the identification, characterization, and quantification of the protein content or proteome of whole cells, tissues, or body fluids. The...
Chemical substructures that enrich for biological activity
Klekota, Justin, Roth, Frederick P.
Motivation: Certain chemical substructures are present in many drugs. This has led to the claim of ‘privileged’ substructures which are predisposed to bioactivity. Because bias in screening...