Frederick P. Roth

The genome-wide localization of Rsc9, a component of the RSC chromatin-remodeling complex, changes in response to stress.

Judging the quality of gene expression-based clustering methods using gene annotation.

Assessing experimentally derived interactions in a small world.

GoFish finds genes with combinations of Gene Ontology attributes.

Predicting gene function from patterns of annotation.

Regulating general mutation rates: examination of the hypermutable state model for Cairnsian adaptive mutation.

Predicting phenotype from patterns of annotation.

Latent herpes simplex virus infection of sensory neurons alters neuronal gene expression.

A non-parametric model for transcription factor binding sites.

Characterizing gene sets with FuncAssociate.

A map of the interactome network of the metazoan C. elegans.

Intensity-based protein identification by machine learning from a library of tandem mass spectra.

Global mapping of the yeast genetic interaction network.

Predicting co-complexed protein pairs using genomic and proteomic data integration.

Predicting protein complex membership using probabilistic network reliability.

SILVER helps assign peptides to tandem mass spectra using intensity-based scoring.

Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura.

Evidence for dynamically organized modularity in the yeast protein-protein interaction network.

Combining biological networks to predict genetic interactions.

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.

Discovering functional relationships: biochemistry versus genetics.

Transcriptional compensation for gene loss plays a minor role in maintaining genetic robustness in Saccharomyces cerevisiae.

Genomewide identification of Sko1 target promoters reveals a regulatory network that operates in response to osmotic stress in Saccharomyces cerevisiae.

Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis.

Towards a proteome-scale map of the human protein-protein interaction network.

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization.

Metabolomic identification of novel biomarkers of myocardial ischemia.

Query Chem: a Google-powered web search combining text and chemical structures.

Using high-throughput screening data to discriminate compounds with single-target effects from those with side effects.

Systematic genetics swims forward elegantly.

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants.

Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.

Genetic interaction screens advance in reverse.

Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans.

Confirmation of organized modularity in the yeast interactome.

Functional specificity among ribosomal proteins regulates gene expression.

Defining genetic interaction.

Challenges in translating plasma proteomics from bench to bedside: update from the NHLBI Clinical Proteomics Programs.

Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing.

A race through the maze of genomic evidence.

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function.

An en masse phenotype and function prediction system for Mus musculus.

A protein domain-based interactome network for C. elegans early embryogenesis.

The Synergizer service for translating gene, protein and other biological identifiers.

High-quality binary protein interaction map of the yeast interactome network.

Metabolite profiling of blood from individuals undergoing planned myocardial infarction reveals early markers of myocardial injury.

Chemical substructures that enrich for biological activity.

A C. elegans genome-scale microRNA network contains composite feedback motifs with high flux capacity.

An experimentally derived confidence score for binary protein-protein interactions.

An empirical framework for binary interactome mapping.

Literature-curated protein interaction datasets.

Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.

Q&A: epistasis.

Quantitative phenotyping via deep barcode sequencing.

Next generation software for functional trend analysis.

Large-scale RACE approach for proactive experimental definition of C. elegans ORFeome.

Pathways of the heart.

The genetic landscape of a cell.

Numerous conserved and divergent microRNAs expressed by herpes simplex viruses 1 and 2.

Interpreting metabolomic profiles using unbiased pathway models.

The tandem inversion duplication in Salmonella enterica: selection drives unstable precursors to final mutation types.

Genome-wide functional analysis of human 5' untranslated region introns.

Absence of evidence for MHC-dependent mate selection within HapMap populations.

FuncBase: a resource for quantitative gene function annotation.

Metabolic signatures of exercise in human plasma.

A genome-wide gene function prediction resource for Drosophila melanogaster.

Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes.

Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection.

Reconstitution of human RNA interference in budding yeast.

Next-generation sequencing to generate interactome datasets.

Genome analysis reveals interplay between 5'UTR introns and nuclear mRNA export for secretory and mitochondrial genes.

Discovering the targets of drugs via computational systems biology.

Independently evolved virulence effectors converge onto hubs in a plant immune system network.

Systematic exploration of synergistic drug pairs.

Personalized medicine: from genotypes and molecular phenotypes towards computed therapy.

A Resource of Quantitative Functional Annotation for Homo sapiens Genes.

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 for the MHC locus in human mate selection.

Genome rearrangements caused by depletion of essential DNA replication proteins in Saccharomyces cerevisiae.

Viral perturbations of host networks reflect disease etiology.

Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.

Introns in UTRs: Why we should stop ignoring them.

ChromoZoom: a flexible, fluid, web-based genome browser.