List of works by Frederick P. Roth

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

scientific article published on September 2008

A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis

A Resource of Quantitative Functional Annotation for Homo sapiens Genes

scientific article published on February 2012

A common class of transcripts with 5'-intron depletion, distinct early coding sequence features, and N1-methyladenosine modification

scientific article published on 19 December 2016

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

scientific article

A framework for exhaustively mapping functional missense variants.

scientific article published on 21 December 2017

A genome-wide gene function prediction resource for Drosophila melanogaster

scientific article

A highly conserved program of neuronal microexons is misregulated in autistic brains

scientific article published on December 2014

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

scientific article (publication date: 23 January 2004)

A proactive genotype-to-patient-phenotype map for cystathionine beta-synthase

scientific article published on 30 January 2020

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

scientific article

A proteome-scale map of the human interactome network

scientific article

A race through the maze of genomic evidence

scientific article

A reference map of the human binary protein interactome

scientific article published on 08 April 2020

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

scientific article

An empirical framework for binary interactome mapping

scientific article

An en masse phenotype and function prediction system for Mus musculus

scientific article published on 27 June 2008

An experimentally derived confidence score for binary protein-protein interactions

scientific article

An extended set of yeast-based functional assays accurately identifies human disease mutations

scientific article published on 14 March 2016

An inter-species protein-protein interaction network across vast evolutionary distance

scientific article (publication date: 22 April 2016)

An open-source platform to distribute and interpret data from multiplexed assays of variant effect

Assessing experimentally derived interactions in a small world

scientific article

Assessing predictions of fitness effects of missense mutations in SUMO-conjugating enzyme UBE2I.

scientific article published in September 2017

Bringing out the best features of expression data.

scientific article

CNTN5-/+ or EHMT2-/+ iPSC-Derived Neurons from Individuals with Autism Develop Hyperactive Neuronal Networks

CRISPR/Cas9 System as a Valuable Genome Editing Tool for Wine Yeasts with Application to Decrease Urea Production.

scientific article published on 9 November 2017

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

scientific article published on 2 May 2008

Characterizing gene sets with FuncAssociate

scientific article published on December 2003

Chemical substructures that enrich for biological activity

scientific article

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

scientific article published on 6 December 2012

Combining biological networks to predict genetic interactions

scholarly article

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

scientific article published on 27 June 2008

Confirmation of organized modularity in the yeast interactome

scientific article

Cross-species protein interactome mapping reveals species-specific wiring of stress response pathways

scientific article published on 21 May 2013

Defining genetic interaction

scholarly article

Discovering functional relationships: biochemistry versus genetics

article

Discovering the targets of drugs via computational systems biology

scientific article

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

scientific article

Erratum: Addendum: Literature-curated protein interaction datasets

scholarly article published in Nature Methods

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

scientific article

FuncBase: a resource for quantitative gene function annotation

scientific article

Functional specificity among ribosomal proteins regulates gene expression

scientific article published on November 2007

Genetic interaction screens advance in reverse

scientific article published on 01 January 2007

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

scientific article published in April 2011

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

scientific article published on 5 June 2012

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

scientific article published on 7 May 2007

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

scientific article

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

scientific article

Global mapping of the yeast genetic interaction network

scientific article

GoFish finds genes with combinations of Gene Ontology attributes

scientific article

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities.

scientific article published on 25 November 2015

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

scientific article

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

scientific article

Identifying pathogenicity of human variants via paralog-based yeast complementation.

scientific article

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

scientific article published in July 2011

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

scientific article

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

scientific journal article

Interpreting metabolomic profiles using unbiased pathway models

scientific article

Introns in UTRs: why we should stop ignoring them

scientific article

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

scientific article published on 15 June 2008

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

scientific article

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

scientific article

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

scientific article published on 2 October 2009

Large-scale identification and analysis of suppressive drug interactions

scientific article

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

scientific article published on September 2003

List of Contributors

Literature-curated protein interaction datasets.

scientific article published on January 2009

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

scientific article published on 24 September 2006

Mapping DNA damage-dependent genetic interactions in yeast via party mating and barcode fusion genetics.

scientific article

MaveRegistry: a collaboration platform for multiplexed assays of variant effect

scientific article published in 2021

Metabolic signatures of exercise in human plasma

scientific article

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

scientific article

Metabolomic identification of novel biomarkers of myocardial ischemia

scientific article

Modeling the impact of drug interactions on therapeutic selectivity

scientific article published in Nature Communications

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

scientific article

Multiplexed assays of variant effects contribute to a growing genotype-phenotype atlas

Multiplexed measurement of variant abundance and activity reveals VKOR topology, active site and human variant impact

scientific article published on 11 May 2020

Next generation software for functional trend analysis

scientific article

Next-generation sequencing to generate interactome datasets

scientific article

Novel cardiovascular gene functions revealed via systematic phenotype prediction in zebrafish

scientific article

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

scientific article

Pathways of the heart

scientific article published on August 2009

Pooled-matrix protein interaction screens using Barcode Fusion Genetics

scientific journal article

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

scientific article

Predicting gene function from patterns of annotation

scientific article published on 14 April 2003

Predicting phenotype from patterns of annotation

scientific article published on January 2003

Predicting protein complex membership using probabilistic network reliability

scientific article

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

scientific article published on 14 May 2004

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

scientific article published in August 2005

Prioritizing causal disease genes using unbiased genomic features

scientific article

Protein domain-level landscape of cancer-type-specific somatic mutations

scientific article

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism.

scientific article published on 11 April 2014

Q&A: epistasis

scientific article

Quantifying Immune-Based Counterselection of Somatic Mutations

Quantifying immune-based counterselection of somatic mutations ⬇️

scientific article published on 25 July 2019

Quantitative analysis of protein interaction network dynamics in yeast.

scientific article published on 13 July 2017

Quantitative phenotyping via deep barcode sequencing.

scientific article

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

scientific article published on 03 May 2006

RanBP2/Nup358 potentiates the translation of a subset of mRNAs encoding secretory proteins

scientific article

Reconstitution of human RNA interference in budding yeast

scientific article

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

scientific article

SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets.

scientific article

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

scientific article

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks

scientific article published on 22 December 2014

Systematic analysis of bypass suppression of essential genes

scientific article published on 01 September 2020

Systematic exploration of synergistic drug pairs

scientific article published on 8 November 2011

Systematic genetics swims forward elegantly

scientific article published on 12 September 2006

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

scientific article published on 07 January 2007

Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions

scientific article published on 23 March 2020

Systems biology and the analysis of genetic variation

scientific article

Taking Exception to Human Eugenics

scientific article published on October 2016

Target-independent prediction of drug synergies using only drug lipophilicity

scientific article published on August 2014

The Impact of Oncogenic EGFRvIII on the Proteome of Extracellular Vesicles Released from Glioblastoma Cells

scientific article published on 13 July 2018

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

scientific article published on 12 August 2008

The genetic landscape of a cell

scientific article

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

scientific article

The green monster process for the generation of yeast strains carrying multiple gene deletions

scientific article published on 15 December 2012

The insertion Green Monster (iGM) method for expression of multiple exogenous genes in yeast

scientific article published on 28 April 2014

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

scientific article

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

scientific article

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

scientific article published on 5 July 2005

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

scientific article

Viral perturbations of host networks reflect disease etiology

scientific article

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

scientific article published on February 2016

Widespread macromolecular interaction perturbations in human genetic disorders

scientific journal article

Paulina is supported by:

About Paulina

Help