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Author Details

Ruth Isserlin
University of Toronto
2002
49
27
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
34212855Control of tissue development and cell diversity by cell cycle-dependent transcriptional filtering.Elife2021
33758253Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer.Sci Rep2021
32867540Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment.Epigenomics2020
30664679Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap.Nat Protoc2019
31551601Single-cell transcriptomic profiling of the aging mouse brain.Nat Neurosci2019
30917865Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression.Clin Epigenetics2019
31115870Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells.J Neurooncol2019
30872331netDx: interpretable patient classification using integrated patient similarity networks.Mol Syst Biol2019
30446205The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety.Biol Psychiatry2019
29921600Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities.J Cell Biol2018
28826663Exercise-responsive phosphoproteins in the heart.J Mol Cell Cardiol2017
28314784Integrative Cancer Pharmacogenomics to Infer Large-Scale Drug Taxonomy.Cancer Res2017
26981160Dynamic interplay between locus-specific DNA methylation and hydroxymethylation regulates distinct biological pathways in prostate carcinogenesis.Clin Epigenetics2016
27830058AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations.F1000Res2016
27742792Global phosphoproteomic profiling reveals perturbed signaling in a mouse model of dilated cardiomyopathy.Proc Natl Acad Sci U S A2016
27424784Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors.Cell Stem Cell2016
27070706miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.Cancer Cell2016
26832662miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells.Cancer Cell2016
25361207Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy.Mol Biosyst2015
26261332Unbiased phosphoproteomic method identifies the initial effects of a methacrylic acid copolymer on macrophages.Proc Natl Acad Sci U S A2015
26232220A Call for Systematic Research on Solute Carriers.Cell2015
26098549Cardioprotective Signature of Short-Term Caloric Restriction.PLoS One2015
26227301Phosphoproteomic network analysis in the sea urchin Strongylocentrotus purpuratus reveals new candidates in egg activation.Proteomics2015
25915851Metabolomic profiling in liver of adiponectin-knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action.Biochem J2015
24361864Discovery of novel disease-specific and membrane-associated candidate markers in a mouse model of multiple sclerosis.Mol Cell Proteomics2014
25384593Large-scale label-free phosphoproteomics: from technology to data interpretation.Bioanalysis2014
25075306Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results.F1000Res2014
24870542A draft map of the human proteome.Nature2014
23401153Integrative network analysis of signaling in human CD34(+) hematopoietic progenitor cells by global phosphoproteomic profiling using TiO2 enrichment combined with 2D LC-MS/MS and pathway mapping.Proteomics2013
23606248Global proteomic profiling and enrichment maps of dilated cardiomyopathy.Methods Mol Biol2013
21233089The Biomolecular Interaction Network Database in PSI-MI 2.5.Database (Oxford)2011
21840481Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma.Cancer Cell2011
21877285Visualizing gene-set enrichment results using the Cytoscape plug-in enrichment map.Methods Mol Biol2011
21716279PSICQUIC and PSISCORE: accessing and scoring molecular interactions.Nat Methods2011
21307913Too many roads not taken.Nature2011
21473782WordCloud: a Cytoscape plugin to create a visual semantic summary of networks.Source Code Biol Med2011
20305087A lentiviral functional proteomics approach identifies chromatin remodeling complexes important for the induction of pluripotency.Mol Cell Proteomics2010
21085593Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.PLoS One2010
20937869Constitutively active calcineurin induces cardiac endoplasmic reticulum stress and protects against apoptosis that is mediated by alpha-crystallin-B.Proc Natl Acad Sci U S A2010
20127684Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps.Proteomics2010
19714876Large-scale characterization and analysis of the murine cardiac proteome.J Proteome Res2009
18056057Comparative proteomics profiling of a phospholamban mutant mouse model of dilated cardiomyopathy reveals progressive intracellular stress responses.Mol Cell Proteomics2008
18535930Interpretation of large-scale quantitative shotgun proteomic profiles for biomarker discovery.Curr Opin Mol Ther2008
17892321Structure-templated predictions of novel protein interactions from sequence information.PLoS Comput Biol2007
21136765Nine steps to proteomic wisdom: A practical guide to using protein-protein interaction networks and molecular pathways as a framework for interpreting disease proteomic profiles.Proteomics Clin Appl2007
17947979Integration of biological networks and gene expression data using Cytoscape.Nat Protoc2007
15608229The Biomolecular Interaction Network Database and related tools 2005 update.Nucleic Acids Res2005
15262781Analysis of domain correlations in yeast protein complexes.Bioinformatics2004
12401134SeqHound: biological sequence and structure database as a platform for bioinformatics research.BMC Bioinformatics2002
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Collaborators

Gary D Bader
University of Toronto
Co-authored papers 31
Andrew Emili
Boston University School of Medicine, Boston University
Co-authored papers 16
Hongbo Guo
Beihang University
Co-authored papers 6
Anthony O Gramolini
University of Toronto, University Avenue
Co-authored papers 6
Thomas Kislinger
Princess Margaret Cancer Centre, University Health Network, University of Toronto
Co-authored papers 5
Christopher W V Hogue
National University of Singapore
Co-authored papers 4
Bharati Bapat
Mt Sinai Hospital
Co-authored papers 4
Neil E Fleshner
University of Toronto
Co-authored papers 4
John E Dick
Princess Margaret Cancer Centre, University Health Network
Co-authored papers 3
Peter W Zandstra
Co-authored papers 3
Jun Lu
Yale University
Co-authored papers 2
Benjamin L Ebert
Co-authored papers 2
Keiichiro Ono
university of california san diego
Co-authored papers 2
Alexandre R Zlotta
University Health Network, Princess Margaret Cancer Center, University of Toronto
Co-authored papers 2
Mike Tyers
Institute for Research in Immunology and Cancer (IRIC), Universite de Montreal
Co-authored papers 2
Theodorus H van der Kwast
University Health Network, University of Toronto
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Mike Kucera
University of Toronto
Co-authored papers 2
Ankit Sinha
Max Planck Institute of Biochemistry
Co-authored papers 2
Ian M Donaldson
Samuel Lunenfeld Research Institute
Co-authored papers 2
Aled M Edwards
University of Toronto
Co-authored papers 2
Todd R Golub
Broad Institute of MIT and Harvard
Co-authored papers 2
Luigi Naldini
Vita-Salute San Raffaele University
Co-authored papers 2
Michel Dumontier
Institute of Data Science, Maastricht University
Co-authored papers 2
Peter P Liu
Co-authored papers 2
Sara Arab
Co-authored papers 2
David H MacLennan
Co-authored papers 2
Björn Nilsson
Co-authored papers 2
Jason Moffat
University of Toronto
Co-authored papers 2
Martin Hirst
University of British Columbia
Co-authored papers 2
Kolja Eppert
McGill University
Co-authored papers 2
Release 1.2