Frederick P. Roth

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 13	2012

Other Publications

Article	Year
The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress. Molecular cell\| PubMed ID: 11931764	2002
Judging the quality of gene expression-based clustering methods using gene annotation. Genome research\| PubMed ID: 12368250	2002
Assessing experimentally derived interactions in a small world. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12676999	2003
GoFish finds genes with combinations of Gene Ontology attributes. Bioinformatics (Oxford, England)\| PubMed ID: 12691998	2003
Predicting gene function from patterns of annotation. Genome research\| PubMed ID: 12695322	2003
Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation. Genetics\| PubMed ID: 12702691	2003
Predicting phenotype from patterns of annotation. Bioinformatics (Oxford, England)\| PubMed ID: 12855456	2003
Latent herpes simplex virus infection of sensory neurons alters neuronal gene expression. Journal of virology\| PubMed ID: 12915567	2003
A non-parametric model for transcription factor binding sites. Nucleic acids research\| PubMed ID: 14500844	2003
Characterizing gene sets with FuncAssociate. Bioinformatics (Oxford, England)\| PubMed ID: 14668247	2003
A map of the interactome network of the metazoan C. elegans. Science (New York, N.Y.)\| PubMed ID: 14704431	2004
Intensity-based protein identification by machine learning from a library of tandem mass spectra. Nature biotechnology\| PubMed ID: 14730315	2004
Global mapping of the yeast genetic interaction network. Science (New York, N.Y.)\| PubMed ID: 14764870	2004
Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC bioinformatics\| PubMed ID: 15090078	2004
Predicting protein complex membership using probabilistic network reliability. Genome research\| PubMed ID: 15140827	2004
SILVER helps assign peptides to tandem mass spectra using intensity-based scoring. Journal of the American Society for Mass Spectrometry\| PubMed ID: 15144981	2004
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura. Bioinformatics (Oxford, England)\| PubMed ID: 15145800	2004
Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature\| PubMed ID: 15190252	2004
Combining biological networks to predict genetic interactions. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15496468	2004
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network. Journal of biology\| PubMed ID: 15982408	2005
Discovering functional relationships: biochemistry versus genetics. Trends in genetics : TIG\| PubMed ID: 15982781	2005
Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae. Genetics\| PubMed ID: 15998714	2005
Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae. Eukaryotic cell\| PubMed ID: 16087739	2005
Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature\| PubMed ID: 16094371	2005
Towards a proteome-scale map of the human protein-protein interaction network. Nature\| PubMed ID: 16189514	2005
Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. Genome biology\| PubMed ID: 16277751	2005
Metabolomic identification of novel biomarkers of myocardial ischemia. Circulation\| PubMed ID: 16344383	2005
Query Chem: a Google-powered web search combining text and chemical structures. Bioinformatics (Oxford, England)\| PubMed ID: 16672261	2006
Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects. Journal of chemical information and modeling\| PubMed ID: 16859287	2006
Systematic genetics swims forward elegantly. Molecular systems biology\| PubMed ID: 16969340	2006
Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nature genetics\| PubMed ID: 16998490	2006
Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions. Nature genetics\| PubMed ID: 17206143	2007
Genetic interaction screens advance in reverse. Genes & development\| PubMed ID: 17234880	2007
Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nature biotechnology\| PubMed ID: 17486083	2007
Confirmation of organized modularity in the yeast interactome. PLoS biology\| PubMed ID: 17564493	2007
Functional specificity among ribosomal proteins regulates gene expression. Cell\| PubMed ID: 17981122	2007
Defining genetic interaction. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 18305163	2008
Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs. American journal of physiology. Lung cellular and molecular physiology\| PubMed ID: 18456800	2008
Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing. Nature methods\| PubMed ID: 18552854	2008
A race through the maze of genomic evidence. Genome biology\| PubMed ID: 18613945	2008
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome biology\| PubMed ID: 18613946	2008
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. Genome biology\| PubMed ID: 18613951	2008
An en masse phenotype and function prediction system for Mus musculus. Genome biology\| PubMed ID: 18613952	2008
A protein domain-based interactome network for C. elegans early embryogenesis. Cell\| PubMed ID: 18692475	2008
The Synergizer service for translating gene, protein and other biological identifiers. Bioinformatics (Oxford, England)\| PubMed ID: 18697767	2008
High-quality binary protein interaction map of the yeast interactome network. Science (New York, N.Y.)\| PubMed ID: 18719252	2008
Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury. The Journal of clinical investigation\| PubMed ID: 18769631	2008
Chemical substructures that enrich for biological activity. Bioinformatics (Oxford, England)\| PubMed ID: 18784118	2008
A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity. Genes & development\| PubMed ID: 18794350	2008
An experimentally derived confidence score for binary protein-protein interactions. Nature methods\| PubMed ID: 19060903	2009
An empirical framework for binary interactome mapping. Nature methods\| PubMed ID: 19060904	2009
Literature-curated protein interaction datasets. Nature methods\| PubMed ID: 19116613	2009
Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network. Nature methods\| PubMed ID: 19123269	2009
Q&A: epistasis. Journal of biology\| PubMed ID: 19486505	2009
Quantitative phenotyping via deep barcode sequencing. Genome research\| PubMed ID: 19622793	2009
Next generation software for functional trend analysis. Bioinformatics (Oxford, England)\| PubMed ID: 19717575	2009
Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome. Genome research\| PubMed ID: 19801531	2009
Pathways of the heart. Circulation. Cardiovascular genetics\| PubMed ID: 20031600	2009
The genetic landscape of a cell. Science (New York, N.Y.)\| PubMed ID: 20093466	2010
Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2. Journal of virology\| PubMed ID: 20181707	2010
Interpreting metabolomic profiles using unbiased pathway models. PLoS computational biology\| PubMed ID: 20195502	2010
The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types. Genetics\| PubMed ID: 20215473	2010
Genome-wide functional analysis of human 5' untranslated region introns. Genome biology\| PubMed ID: 20222956	2010
Absence of evidence for MHC-dependent mate selection within HapMap populations. PLoS genetics\| PubMed ID: 20442868	2010
FuncBase: a resource for quantitative gene function annotation. Bioinformatics (Oxford, England)\| PubMed ID: 20495000	2010
Metabolic signatures of exercise in human plasma. Science translational medicine\| PubMed ID: 20505214	2010
A genome-wide gene function prediction resource for Drosophila melanogaster. PloS one\| PubMed ID: 20711346	2010
Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes. The Journal of biological chemistry\| PubMed ID: 21051541	2011
Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nature methods\| PubMed ID: 21217751	2011
Reconstitution of human RNA interference in budding yeast. Nucleic acids research\| PubMed ID: 21252293	2011
Next-generation sequencing to generate interactome datasets. Nature methods\| PubMed ID: 21516116	2011
Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes. PLoS genetics\| PubMed ID: 21533221	2011
Discovering the targets of drugs via computational systems biology. The Journal of biological chemistry\| PubMed ID: 21566122	2011
Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science (New York, N.Y.)\| PubMed ID: 21798943	2011
Systematic exploration of synergistic drug pairs. Molecular systems biology\| PubMed ID: 22068327	2011
Personalized medicine: from genotypes and molecular phenotypes towards computed therapy. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing\| PubMed ID: 22174287	2012
A Resource of Quantitative Functional Annotation for Homo sapiens Genes. G3 (Bethesda, Md.)\| PubMed ID: 22384401	2012
Response to "MHC-dependent mate choice in humans: Why genomic patterns from the HapMap European American data set support the hypothesis". HapMap genotypes do not confidently support a role ... BioEssays : news and reviews in molecular, cellular and developmental biology\| PubMed ID: 22467222	2012
Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae. Genetics\| PubMed ID: 22673806	2012
Viral perturbations of host networks reflect disease etiology. PLoS computational biology\| PubMed ID: 22761553	2012
Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature\| PubMed ID: 22810586	2012
Introns in UTRs: Why we should stop ignoring them. BioEssays : news and reviews in molecular, cellular and developmental biology\| PubMed ID: 23108796	2012
ChromoZoom: a flexible, fluid, web-based genome browser. Bioinformatics (Oxford, England)\| PubMed ID: 23220575	2012