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