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<!DOCTYPE html> <html> <head> <meta name="viewport" content="width=device-width,initial-scale=1.0"> <META NAME='keywords' CONTENT='Gary Bader, homepage, bioinformatics, computational biology, biological networks, pathways'><META NAME='description' CONTENT='Gary Bader c omputational biology lab homepage at the University of Toronto, Canada.'><meta http-equiv="Content-Type" content="text/html;charset=utf-8"> <meta name="robots" content="index,nofollow"> <title>Publications - Bader Lab @ The University of Toronto</title> <script type="text/javascript" src="/moin_static198/common/js/common.js"></script> <script type="text/javascript">  </script> <link rel="stylesheet" type="text/css" media="all" href="/moin_static198/memodump/css/bootstrap.min.css"> <link rel="stylesheet" type="text/css" media="all" href="/moin_static198/memodump/css/bootstrap-theme.min.css"> <link rel="stylesheet" type="text/css" media="all" href="/moin_static198/memodump/css/memodump.css"> <link rel="stylesheet" type="text/css" media="all" href="/moin_static198/memodump/css/moinizer.css">   <link rel="alternate" title="Bader Lab @ The University of Toronto: Publications" href="/Publications?diffs=1&show_att=1&action=rss_rc&unique=0&page=Publications&ddiffs=1" type="application/rss+xml"> <link rel="Start" href="/Home"> <link rel="Alternate" title="Wiki Markup" href="/Publications?action=raw"> <link rel="Alternate" media="print" title="Print View" href="/Publications?action=print"> <link rel="Appendix" title="2002_SeqHound_BMCBioinfo.pdf" href="/Publications?action=AttachFile&do=view&target=2002_SeqHound_BMCBioinfo.pdf"> <link rel="Appendix" title="2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf" href="/Publications?action=AttachFile&do=view&target=2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf"> <link rel="Appendix" title="2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf" href="/Publications?action=AttachFile&do=view&target=2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf"> <link rel="Appendix" title="2003_BaderHogue_MCODE.pdf" href="/Publications?action=AttachFile&do=view&target=2003_BaderHogue_MCODE.pdf"> <link rel="Appendix" title="2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf" href="/Publications?action=AttachFile&do=view&target=2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf"> <link rel="Appendix" title="2003_OsheaWeissmanReview_NatureBiotech.pdf" href="/Publications?action=AttachFile&do=view&target=2003_OsheaWeissmanReview_NatureBiotech.pdf"> <link rel="Appendix" title="2003_PeptideRecognitionModuleNetworks.pdf" href="/Publications?action=AttachFile&do=view&target=2003_PeptideRecognitionModuleNetworks.pdf"> <link rel="Appendix" title="2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf" href="/Publications?action=AttachFile&do=view&target=2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf"> <link rel="Appendix" title="2004_SGA_Hartwell_comment.pdf" href="/Publications?action=AttachFile&do=view&target=2004_SGA_Hartwell_comment.pdf"> <link rel="Appendix" title="2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf" href="/Publications?action=AttachFile&do=view&target=2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf"> <link rel="Appendix" title="2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf" href="/Publications?action=AttachFile&do=view&target=2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf"> <link rel="Appendix" title="2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf" href="/Publications?action=AttachFile&do=view&target=2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf"> <link rel="Appendix" title="2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf" href="/Publications?action=AttachFile&do=view&target=2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf"> <link rel="Appendix" title="2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf" href="/Publications?action=AttachFile&do=view&target=2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf"> <link rel="Appendix" title="2007_Cytoscape_Cline_NatureProtocols_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2007_Cytoscape_Cline_NatureProtocols_Oct.pdf"> <link rel="Appendix" title="2007_Germ-lineDNACopyNumberVariationFrequenciesInALargeNorthAmericanPopulation_Zogopoulos_Bader_Gallinder_HumanGenetics.pdf" href="/Publications?action=AttachFile&do=view&target=2007_Germ-lineDNACopyNumberVariationFrequenciesInALargeNorthAmericanPopulation_Zogopoulos_Bader_Gallinder_HumanGenetics.pdf"> <link rel="Appendix" title="2007_Kerrien_PSIMI_BMCBiology.pdf" href="/Publications?action=AttachFile&do=view&target=2007_Kerrien_PSIMI_BMCBiology.pdf"> <link rel="Appendix" title="2007_MIMIx_OrchardEtAl_NatBiotech_August.pdf" href="/Publications?action=AttachFile&do=view&target=2007_MIMIx_OrchardEtAl_NatBiotech_August.pdf"> <link rel="Appendix" title="2007_MatthewTaylorBader_TranslationalReview_PLoSCompBio_Feb.pdf" href="/Publications?action=AttachFile&do=view&target=2007_MatthewTaylorBader_TranslationalReview_PLoSCompBio_Feb.pdf"> <link rel="Appendix" title="2007_NetMatch-ACytoscapePluginForSearchingBiologicalNetworks_Ferro_Guigno_Bader_Shasha_Apr.pdf" href="/Publications?action=AttachFile&do=view&target=2007_NetMatch-ACytoscapePluginForSearchingBiologicalNetworks_Ferro_Guigno_Bader_Shasha_Apr.pdf"> <link rel="Appendix" title="2008_Ashkenazi_CytoscapeESP_Bioinformatics.pdf" href="/Publications?action=AttachFile&do=view&target=2008_Ashkenazi_CytoscapeESP_Bioinformatics.pdf"> <link rel="Appendix" title="2008_Skrabanek_MolBiotech_PPI.pdf" href="/Publications?action=AttachFile&do=view&target=2008_Skrabanek_MolBiotech_PPI.pdf"> <link rel="Appendix" title="2008_Tonikian_PDZSpecificityMap_PlosBiology.pdf" href="/Publications?action=AttachFile&do=view&target=2008_Tonikian_PDZSpecificityMap_PlosBiology.pdf"> <link rel="Appendix" title="2009_Ernst_PDZEvolution_ScienceSignaling_Sep.pdf" href="/Publications?action=AttachFile&do=view&target=2009_Ernst_PDZEvolution_ScienceSignaling_Sep.pdf"> <link rel="Appendix" title="2009_Koh_Drygin_NAR_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2009_Koh_Drygin_NAR_Oct.pdf"> <link rel="Appendix" title="2009_Merico_Primer_NatBiotech_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2009_Merico_Primer_NatBiotech_Oct.pdf"> <link rel="Appendix" title="2009_Tan_ComparativePhosphoProteomics_ScienceSignaling_Jul.pdf" href="/Publications?action=AttachFile&do=view&target=2009_Tan_ComparativePhosphoProteomics_ScienceSignaling_Jul.pdf"> <link rel="Appendix" title="2009_Tan_TyrosineLoss_Science.pdf" href="/Publications?action=AttachFile&do=view&target=2009_Tan_TyrosineLoss_Science.pdf"> <link rel="Appendix" title="2009_Tonikian_YeastSH3_PLoSBiology_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2009_Tonikian_YeastSH3_PLoSBiology_Oct.pdf"> <link rel="Appendix" title="2010_AutismNature.pdf" href="/Publications?action=AttachFile&do=view&target=2010_AutismNature.pdf"> <link rel="Appendix" title="2010_BaryshnikovaMyers-SGAScore_NatMethods.pdf" href="/Publications?action=AttachFile&do=view&target=2010_BaryshnikovaMyers-SGAScore_NatMethods.pdf"> <link rel="Appendix" title="2010_BurnsWallace_bioaccumulationWorms_May.pdf" href="/Publications?action=AttachFile&do=view&target=2010_BurnsWallace_bioaccumulationWorms_May.pdf"> <link rel="Appendix" title="2010_CeramiBaderSander-PathwayCommons_NAR.pdf" href="/Publications?action=AttachFile&do=view&target=2010_CeramiBaderSander-PathwayCommons_NAR.pdf"> <link rel="Appendix" title="2010_CostanzoBaryshnikova_GeneticLandscapeOfTheCell_Science_Jan.pdf" href="/Publications?action=AttachFile&do=view&target=2010_CostanzoBaryshnikova_GeneticLandscapeOfTheCell_Science_Jan.pdf"> <link rel="Appendix" title="2010_CytoscapeWeb_Lopes_Bioinformatics_Jul.pdf" href="/Publications?action=AttachFile&do=view&target=2010_CytoscapeWeb_Lopes_Bioinformatics_Jul.pdf"> <link rel="Appendix" title="2010_Demir_BioPAX_NatBiotech_Sep.pdf" href="/Publications?action=AttachFile&do=view&target=2010_Demir_BioPAX_NatBiotech_Sep.pdf"> <link rel="Appendix" title="2010_EM_proteomics.pdf" href="/Publications?action=AttachFile&do=view&target=2010_EM_proteomics.pdf"> <link rel="Appendix" title="2010_ErnstSidhu_PDZSpecificityEvolution_MBS_Aug.pdf" href="/Publications?action=AttachFile&do=view&target=2010_ErnstSidhu_PDZSpecificityEvolution_MBS_Aug.pdf"> <link rel="Appendix" title="2010_GeneMANIA_Cytoscape_Plugin_Montojo_Bioinformatics_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2010_GeneMANIA_Cytoscape_Plugin_Montojo_Bioinformatics_Oct.pdf"> <link rel="Appendix" title="2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf" href="/Publications?action=AttachFile&do=view&target=2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf"> <link rel="Appendix" title="2010_HuiBader-ProteomeScanningPDZ_BMCBioinformatics.pdf" href="/Publications?action=AttachFile&do=view&target=2010_HuiBader-ProteomeScanningPDZ_BMCBioinformatics.pdf"> <link rel="Appendix" title="2010_ICGC.pdf" href="/Publications?action=AttachFile&do=view&target=2010_ICGC.pdf"> <link rel="Appendix" title="2010_JainBader-SemanticSimilarityGO_BMCBioinformatics.pdf" href="/Publications?action=AttachFile&do=view&target=2010_JainBader-SemanticSimilarityGO_BMCBioinformatics.pdf"> <link rel="Appendix" title="2010_Kandasamy_NetPath_GenomeBiol_Jan.pdf" href="/Publications?action=AttachFile&do=view&target=2010_Kandasamy_NetPath_GenomeBiol_Jan.pdf"> <link rel="Appendix" title="2010_KirouacZandstra_DynamicCellCellInteractionNetworks_MSB_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2010_KirouacZandstra_DynamicCellCellInteractionNetworks_MSB_Oct.pdf"> <link rel="Appendix" title="2010_MericoIsserlinStuekerBader-EnrichmentMap_PLoSOne.pdf" href="/Publications?action=AttachFile&do=view&target=2010_MericoIsserlinStuekerBader-EnrichmentMap_PLoSOne.pdf"> <link rel="Appendix" title="2010_OkaSudol_YAP2_ZO2_BJ_Oct.pdf" href="/Publications?action=AttachFile&do=view&target=2010_OkaSudol_YAP2_ZO2_BJ_Oct.pdf"> <link rel="Appendix" title="2010_ShaoTanBader-PDZAffinity_Bioinformatics.pdf" href="/Publications?action=AttachFile&do=view&target=2010_ShaoTanBader-PDZAffinity_Bioinformatics.pdf"> <link rel="Appendix" title="2011_Gfeller.pdf" href="/Publications?action=AttachFile&do=view&target=2011_Gfeller.pdf"> <link rel="Appendix" title="2011_Michaut_Diso.pdf" href="/Publications?action=AttachFile&do=view&target=2011_Michaut_Diso.pdf"> <link rel="Appendix" title="2011_Michaut_Mono.pdf" href="/Publications?action=AttachFile&do=view&target=2011_Michaut_Mono.pdf"> <link rel="Appendix" title="2011_Raju-RANKL_Database.pdf" href="/Publications?action=AttachFile&do=view&target=2011_Raju-RANKL_Database.pdf"> <link rel="Appendix" title="2012_CytoscapePluginTravelGuide.pdf" href="/Publications?action=AttachFile&do=view&target=2012_CytoscapePluginTravelGuide.pdf"> <link rel="Appendix" title="2012_Xiong_ABI1_Oncogenesis.pdf" href="/Publications?action=AttachFile&do=view&target=2012_Xiong_ABI1_Oncogenesis.pdf"> <link rel="Appendix" title="2012_microRNAinfluence.pdf" href="/Publications?action=AttachFile&do=view&target=2012_microRNAinfluence.pdf"> <link rel="Appendix" title="2012_mir126andHSC.pdf" href="/Publications?action=AttachFile&do=view&target=2012_mir126andHSC.pdf"> <link rel="Appendix" title="AdvMater_July2019.pdf" href="/Publications?action=AttachFile&do=view&target=AdvMater_July2019.pdf"> <link rel="Appendix" title="Algorithm2015.pdf" href="/Publications?action=AttachFile&do=view&target=Algorithm2015.pdf"> <link rel="Appendix" title="Alshalalfa_PLOSONE.pdf" href="/Publications?action=AttachFile&do=view&target=Alshalalfa_PLOSONE.pdf"> <link rel="Appendix" title="Ammar_Ron_201311_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Ammar_Ron_201311_PhD_thesis.pdf"> <link rel="Appendix" title="Atwal_Gurnit_202106_PhD_Thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Atwal_Gurnit_202106_PhD_Thesis.pdf"> <link rel="Appendix" title="BIND_NAR_2001.pdf" href="/Publications?action=AttachFile&do=view&target=BIND_NAR_2001.pdf"> <link rel="Appendix" title="BIND_Spec_2000.pdf" href="/Publications?action=AttachFile&do=view&target=BIND_Spec_2000.pdf"> <link rel="Appendix" title="BMCCancer_Feb2024.pdf" href="/Publications?action=AttachFile&do=view&target=BMCCancer_Feb2024.pdf"> <link rel="Appendix" title="BMC_medicalgenom_Feb2018.pdf" href="/Publications?action=AttachFile&do=view&target=BMC_medicalgenom_Feb2018.pdf"> <link rel="Appendix" title="BaderHogueNBT2002.pdf" href="/Publications?action=AttachFile&do=view&target=BaderHogueNBT2002.pdf"> <link rel="Appendix" title="Baryshnikova_Anastasia_201303_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Baryshnikova_Anastasia_201303_PhD_thesis.pdf"> <link rel="Appendix" title="BioarxivOct282022.pdf" href="/Publications?action=AttachFile&do=view&target=BioarxivOct282022.pdf"> <link rel="Appendix" title="BiochemApr2015.pdf" href="/Publications?action=AttachFile&do=view&target=BiochemApr2015.pdf"> <link rel="Appendix" title="BioinfoFeb2016.pdf" href="/Publications?action=AttachFile&do=view&target=BioinfoFeb2016.pdf"> <link rel="Appendix" title="Bioinfo_June2019.pdf" href="/Publications?action=AttachFile&do=view&target=Bioinfo_June2019.pdf"> <link rel="Appendix" title="Bioinformadv_Nov2023.pdf" href="/Publications?action=AttachFile&do=view&target=Bioinformadv_Nov2023.pdf"> <link rel="Appendix" title="Bioinformatics_June2018.pdf" href="/Publications?action=AttachFile&do=view&target=Bioinformatics_June2018.pdf"> <link rel="Appendix" title="Biophyd_July2018.pdf" href="/Publications?action=AttachFile&do=view&target=Biophyd_July2018.pdf"> <link rel="Appendix" title="Biorxiv_Dec2023.pdf" href="/Publications?action=AttachFile&do=view&target=Biorxiv_Dec2023.pdf"> <link rel="Appendix" title="BloodCancer_Jan2021.pdf" href="/Publications?action=AttachFile&do=view&target=BloodCancer_Jan2021.pdf"> <link rel="Appendix" title="Blood_April2020.pdf" href="/Publications?action=AttachFile&do=view&target=Blood_April2020.pdf"> <link rel="Appendix" title="Blood_March2017.pdf" href="/Publications?action=AttachFile&do=view&target=Blood_March2017.pdf"> <link rel="Appendix" title="Blood_May2022.pdf" href="/Publications?action=AttachFile&do=view&target=Blood_May2022.pdf"> <link rel="Appendix" title="Blood_Sept2022.pdf" href="/Publications?action=AttachFile&do=view&target=Blood_Sept2022.pdf"> <link rel="Appendix" title="Bloodadv_Nov2020.pdf" href="/Publications?action=AttachFile&do=view&target=Bloodadv_Nov2020.pdf"> <link rel="Appendix" title="CCVF_June2023.pdf" href="/Publications?action=AttachFile&do=view&target=CCVF_June2023.pdf"> <link rel="Appendix" title="CancerCell2015.pdf" href="/Publications?action=AttachFile&do=view&target=CancerCell2015.pdf"> <link rel="Appendix" title="CancerCellFeb2016.pdf" href="/Publications?action=AttachFile&do=view&target=CancerCellFeb2016.pdf"> <link rel="Appendix" title="CancerCellJune2015.pdf" href="/Publications?action=AttachFile&do=view&target=CancerCellJune2015.pdf"> <link rel="Appendix" title="CancerCellJune2016.pdf" href="/Publications?action=AttachFile&do=view&target=CancerCellJune2016.pdf"> <link rel="Appendix" title="CancerCell_June2017.pdf" href="/Publications?action=AttachFile&do=view&target=CancerCell_June2017.pdf"> <link rel="Appendix" title="CancerDis_Dec2022.pdf" href="/Publications?action=AttachFile&do=view&target=CancerDis_Dec2022.pdf"> <link rel="Appendix" title="CancerDis_Sept2022.pdf" href="/Publications?action=AttachFile&do=view&target=CancerDis_Sept2022.pdf"> <link rel="Appendix" title="CancerDisc_Feb2020.pdf" href="/Publications?action=AttachFile&do=view&target=CancerDisc_Feb2020.pdf"> <link rel="Appendix" title="CancerResearch_March2017.pdf" href="/Publications?action=AttachFile&do=view&target=CancerResearch_March2017.pdf"> <link rel="Appendix" title="Cancers_July2022.pdf" href="/Publications?action=AttachFile&do=view&target=Cancers_July2022.pdf"> <link rel="Appendix" title="CelRep_March2019.pdf" href="/Publications?action=AttachFile&do=view&target=CelRep_March2019.pdf"> <link rel="Appendix" title="CellJan2016.pdf" href="/Publications?action=AttachFile&do=view&target=CellJan2016.pdf"> <link rel="Appendix" title="CellRe_December2017.pdf" href="/Publications?action=AttachFile&do=view&target=CellRe_December2017.pdf"> <link rel="Appendix" title="CellRep_March2022.pdf" href="/Publications?action=AttachFile&do=view&target=CellRep_March2022.pdf"> <link rel="Appendix" title="CellRep_Nov2022.pdf" href="/Publications?action=AttachFile&do=view&target=CellRep_Nov2022.pdf"> <link rel="Appendix" title="CellReports_April2020.pdf" href="/Publications?action=AttachFile&do=view&target=CellReports_April2020.pdf"> <link rel="Appendix" title="CellStemcell_Aug2021.pdf" href="/Publications?action=AttachFile&do=view&target=CellStemcell_Aug2021.pdf"> <link rel="Appendix" title="CellStemcell_July2021.pdf" href="/Publications?action=AttachFile&do=view&target=CellStemcell_July2021.pdf"> <link rel="Appendix" title="CellSys_April2020.pdf" href="/Publications?action=AttachFile&do=view&target=CellSys_April2020.pdf"> <link rel="Appendix" title="Cell_July2017.pdf" href="/Publications?action=AttachFile&do=view&target=Cell_July2017.pdf"> <link rel="Appendix" title="Cell_rep_Aug2020.pdf" href="/Publications?action=AttachFile&do=view&target=Cell_rep_Aug2020.pdf"> <link rel="Appendix" title="Cellrep_April2018.pdf" href="/Publications?action=AttachFile&do=view&target=Cellrep_April2018.pdf"> <link rel="Appendix" title="Cellstem_April2019.pdf" href="/Publications?action=AttachFile&do=view&target=Cellstem_April2019.pdf"> <link rel="Appendix" title="ChemicalInformationCytoscape_Wallace2011.pdf" href="/Publications?action=AttachFile&do=view&target=ChemicalInformationCytoscape_Wallace2011.pdf"> <link rel="Appendix" title="ClinEpi_Mar2019.pdf" href="/Publications?action=AttachFile&do=view&target=ClinEpi_Mar2019.pdf"> <link rel="Appendix" title="ClinInvestAug20162016.pdf" href="/Publications?action=AttachFile&do=view&target=ClinInvestAug20162016.pdf"> <link rel="Appendix" title="CombineMar2015.pdf" href="/Publications?action=AttachFile&do=view&target=CombineMar2015.pdf"> <link rel="Appendix" title="CompBioNov2016.pdf" href="/Publications?action=AttachFile&do=view&target=CompBioNov2016.pdf"> <link rel="Appendix" title="Comp_struct_bio_July2020.pdf" href="/Publications?action=AttachFile&do=view&target=Comp_struct_bio_July2020.pdf"> <link rel="Appendix" title="Compling_Dec2023.pdf" href="/Publications?action=AttachFile&do=view&target=Compling_Dec2023.pdf"> <link rel="Appendix" title="CytoscapeCurrProtocolsProof-YeungBader_Sep2008.pdf" href="/Publications?action=AttachFile&do=view&target=CytoscapeCurrProtocolsProof-YeungBader_Sep2008.pdf"> <link rel="Appendix" title="Demir_paxtools_ploone.pdf" href="/Publications?action=AttachFile&do=view&target=Demir_paxtools_ploone.pdf"> <link rel="Appendix" title="EMBO_Jan2022.pdf" href="/Publications?action=AttachFile&do=view&target=EMBO_Jan2022.pdf"> <link rel="Appendix" title="Elife_Dec2021.pdf" href="/Publications?action=AttachFile&do=view&target=Elife_Dec2021.pdf"> <link rel="Appendix" title="Elife_July2021.pdf" href="/Publications?action=AttachFile&do=view&target=Elife_July2021.pdf"> <link rel="Appendix" title="EnrichmentMapsCytoscape_MericoIsserlin2011.pdf" href="/Publications?action=AttachFile&do=view&target=EnrichmentMapsCytoscape_MericoIsserlin2011.pdf"> <link rel="Appendix" title="EvodevoMarch2016.pdf" href="/Publications?action=AttachFile&do=view&target=EvodevoMarch2016.pdf"> <link rel="Appendix" title="F1000Apr2015.pdf" href="/Publications?action=AttachFile&do=view&target=F1000Apr2015.pdf"> <link rel="Appendix" title="F1000Nov2016.pdf" href="/Publications?action=AttachFile&do=view&target=F1000Nov2016.pdf"> <link rel="Appendix" title="F1000_June2021.pdf" href="/Publications?action=AttachFile&do=view&target=F1000_June2021.pdf"> <link rel="Appendix" title="Forster_Duncan_Terell_202311_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Forster_Duncan_Terell_202311_PhD_thesis.pdf"> <link rel="Appendix" title="FrontNeuro_Nov2022.pdf" href="/Publications?action=AttachFile&do=view&target=FrontNeuro_Nov2022.pdf"> <link rel="Appendix" title="Fronttrans_June2023.pdf" href="/Publications?action=AttachFile&do=view&target=Fronttrans_June2023.pdf"> <link rel="Appendix" title="GESTODIFFERENT.pdf" href="/Publications?action=AttachFile&do=view&target=GESTODIFFERENT.pdf"> <link rel="Appendix" title="Genome2NetworkReview.pdf" href="/Publications?action=AttachFile&do=view&target=Genome2NetworkReview.pdf"> <link rel="Appendix" title="GenomeMedMay2016.pdf" href="/Publications?action=AttachFile&do=view&target=GenomeMedMay2016.pdf"> <link rel="Appendix" title="GonzalezPerez_cancer_mutations_NatMeth.pdf" href="/Publications?action=AttachFile&do=view&target=GonzalezPerez_cancer_mutations_NatMeth.pdf"> <link rel="Appendix" title="HMS-PCI-Nature-Jan10_2002.pdf" href="/Publications?action=AttachFile&do=view&target=HMS-PCI-Nature-Jan10_2002.pdf"> <link rel="Appendix" title="HMS-PCINewsAndViews-NatureJan10_2002.pdf" href="/Publications?action=AttachFile&do=view&target=HMS-PCINewsAndViews-NatureJan10_2002.pdf"> <link rel="Appendix" title="HepatoCom_Nov2021.pdf" href="/Publications?action=AttachFile&do=view&target=HepatoCom_Nov2021.pdf"> <link rel="Appendix" title="Hu_Zhongming_ _202006_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Hu_Zhongming_+_202006_PhD_thesis.pdf"> <link rel="Appendix" title="Hui_Shirley_201311_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Hui_Shirley_201311_PhD_thesis.pdf"> <link rel="Appendix" title="Innes_Brendan_T_202406_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Innes_Brendan_T_202406_PhD_thesis.pdf"> <link rel="Appendix" title="IntbioNov2015.pdf" href="/Publications?action=AttachFile&do=view&target=IntbioNov2015.pdf"> <link rel="Appendix" title="InteBioinfo_July2019.pdf" href="/Publications?action=AttachFile&do=view&target=InteBioinfo_July2019.pdf"> <link rel="Appendix" title="IntegrativeBio_April2018.pdf" href="/Publications?action=AttachFile&do=view&target=IntegrativeBio_April2018.pdf"> <link rel="Appendix" title="IntergBioinform_july2024.pdf" href="/Publications?action=AttachFile&do=view&target=IntergBioinform_july2024.pdf"> <link rel="Appendix" title="Isserlin_f10002014.pdf" href="/Publications?action=AttachFile&do=view&target=Isserlin_f10002014.pdf"> <link rel="Appendix" title="JCB_June2018.pdf" href="/Publications?action=AttachFile&do=view&target=JCB_June2018.pdf"> <link rel="Appendix" title="JCI_August2017.pdf" href="/Publications?action=AttachFile&do=view&target=JCI_August2017.pdf"> 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href="/Publications?action=AttachFile&do=view&target=Mouseliver_BioarxivJuly2023.pdf"> <link rel="Appendix" title="MultipleGeneticInteractions.pdf" href="/Publications?action=AttachFile&do=view&target=MultipleGeneticInteractions.pdf"> <link rel="Appendix" title="NAR_June2018.pdf" href="/Publications?action=AttachFile&do=view&target=NAR_June2018.pdf"> <link rel="Appendix" title="NCB_News&Views.pdf" href="/Publications?action=AttachFile&do=view&target=NCB_News%26Views.pdf"> <link rel="Appendix" title="NanoLett_June2021.pdf" href="/Publications?action=AttachFile&do=view&target=NanoLett_June2021.pdf"> <link rel="Appendix" title="Nano_April2020.pdf" href="/Publications?action=AttachFile&do=view&target=Nano_April2020.pdf"> <link rel="Appendix" title="NatCellBio_Sept2022.pdf" href="/Publications?action=AttachFile&do=view&target=NatCellBio_Sept2022.pdf"> <link rel="Appendix" title="NatComm_Jan2020.pdf" href="/Publications?action=AttachFile&do=view&target=NatComm_Jan2020.pdf"> <link 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title="Nature_Sept2021.pdf" href="/Publications?action=AttachFile&do=view&target=Nature_Sept2021.pdf"> <link rel="Appendix" title="Nature_july2024.pdf" href="/Publications?action=AttachFile&do=view&target=Nature_july2024.pdf"> <link rel="Appendix" title="Naturecancer_Jan2021.pdf" href="/Publications?action=AttachFile&do=view&target=Naturecancer_Jan2021.pdf"> <link rel="Appendix" title="Northcott_Nature2012.pdf" href="/Publications?action=AttachFile&do=view&target=Northcott_Nature2012.pdf"> <link rel="Appendix" title="Northcott_Nature2014.pdf" href="/Publications?action=AttachFile&do=view&target=Northcott_Nature2014.pdf"> <link rel="Appendix" title="Nstemcellreports_April2017.pdf" href="/Publications?action=AttachFile&do=view&target=Nstemcellreports_April2017.pdf"> <link rel="Appendix" title="NucAcid_Oct2019.pdf" href="/Publications?action=AttachFile&do=view&target=NucAcid_Oct2019.pdf"> <link rel="Appendix" title="NuclAcid_May2024.pdf" 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rel="Appendix" title="Scireport_Mar2021.pdf" href="/Publications?action=AttachFile&do=view&target=Scireport_Mar2021.pdf"> <link rel="Appendix" title="Scireports_July2022.pdf" href="/Publications?action=AttachFile&do=view&target=Scireports_July2022.pdf"> <link rel="Appendix" title="SeminLiver_Aug2022.pdf" href="/Publications?action=AttachFile&do=view&target=SeminLiver_Aug2022.pdf"> <link rel="Appendix" title="Shih_J._H._David_201511_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Shih_J._H._David_201511_PhD_thesis.pdf"> <link rel="Appendix" title="Skowron_Patryk_ _202006_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Skowron_Patryk_+_202006_PhD_thesis.pdf"> <link rel="Appendix" title="StemCellJuly2016.pdf" href="/Publications?action=AttachFile&do=view&target=StemCellJuly2016.pdf"> <link rel="Appendix" title="StemCell_Aug2023.pdf" href="/Publications?action=AttachFile&do=view&target=StemCell_Aug2023.pdf"> <link rel="Appendix" title="StemCell_Sept2022.pdf" href="/Publications?action=AttachFile&do=view&target=StemCell_Sept2022.pdf"> <link rel="Appendix" title="Stemcell_Nov2018.pdf" href="/Publications?action=AttachFile&do=view&target=Stemcell_Nov2018.pdf"> <link rel="Appendix" title="Structure_September2017.pdf" href="/Publications?action=AttachFile&do=view&target=Structure_September2017.pdf"> <link rel="Appendix" title="Tamborero_SciRep_TCGA-pancancer.pdf" href="/Publications?action=AttachFile&do=view&target=Tamborero_SciRep_TCGA-pancancer.pdf"> <link rel="Appendix" title="Tan_SoonHeng_20126_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Tan_SoonHeng_20126_PhD_thesis.pdf"> <link rel="Appendix" title="Tran_Thinh_N_201911_MSc_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Tran_Thinh_N_201911_MSc_thesis.pdf"> <link rel="Appendix" title="WeileBMC.pdf" href="/Publications?action=AttachFile&do=view&target=WeileBMC.pdf"> <link rel="Appendix" title="Whitley_Owen_Kenneth Nora_202211_PhD_thesis.pdf" href="/Publications?action=AttachFile&do=view&target=Whitley_Owen_Kenneth+Nora_202211_PhD_thesis.pdf"> <link rel="Appendix" title="Xin_SH3inter_MSB.pdf" href="/Publications?action=AttachFile&do=view&target=Xin_SH3inter_MSB.pdf"> <link rel="Appendix" title="Zuberi_genemanis_NAR.pdf" href="/Publications?action=AttachFile&do=view&target=Zuberi_genemanis_NAR.pdf"> <link rel="Appendix" title="abersold_prot.pdf" href="/Publications?action=AttachFile&do=view&target=abersold_prot.pdf"> <link rel="Appendix" title="anal_chem_April2023.pdf" href="/Publications?action=AttachFile&do=view&target=anal_chem_April2023.pdf"> <link rel="Appendix" title="automatedcopm.pdf" href="/Publications?action=AttachFile&do=view&target=automatedcopm.pdf"> <link rel="Appendix" title="bioarxiv.png" href="/Publications?action=AttachFile&do=view&target=bioarxiv.png"> <link rel="Appendix" title="bioinfoSept2015.pdf" href="/Publications?action=AttachFile&do=view&target=bioinfoSept2015.pdf"> 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title="f1000_Mar2019.pdf" href="/Publications?action=AttachFile&do=view&target=f1000_Mar2019.pdf"> <link rel="Appendix" title="f1000_Oct2020.pdf" href="/Publications?action=AttachFile&do=view&target=f1000_Oct2020.pdf"> <link rel="Appendix" title="genemania_ecoli.pdf" href="/Publications?action=AttachFile&do=view&target=genemania_ecoli.pdf"> <link rel="Appendix" title="gfeller_plosone2014.pdf" href="/Publications?action=AttachFile&do=view&target=gfeller_plosone2014.pdf"> <link rel="Appendix" title="hupo-bdhpp.pdf" href="/Publications?action=AttachFile&do=view&target=hupo-bdhpp.pdf"> <link rel="Appendix" title="iNatneuro_Oct2019.pdf" href="/Publications?action=AttachFile&do=view&target=iNatneuro_Oct2019.pdf"> <link rel="Appendix" title="iScience_Sept2019.pdf" href="/Publications?action=AttachFile&do=view&target=iScience_Sept2019.pdf"> <link rel="Appendix" title="integerbioinfo_Feb2017.pdf" href="/Publications?action=AttachFile&do=view&target=integerbioinfo_Feb2017.pdf"> <link rel="Appendix" title="iscience_Oct2023.pdf" href="/Publications?action=AttachFile&do=view&target=iscience_Oct2023.pdf"> <link rel="Appendix" title="jexm_May2020.pdf" href="/Publications?action=AttachFile&do=view&target=jexm_May2020.pdf"> <link rel="Appendix" title="leukemia_Feb2022.pdf" href="/Publications?action=AttachFile&do=view&target=leukemia_Feb2022.pdf"> <link rel="Appendix" title="leung_Bioinformatics2014.pdf" href="/Publications?action=AttachFile&do=view&target=leung_Bioinformatics2014.pdf"> <link rel="Appendix" title="mbs2014.pdf" href="/Publications?action=AttachFile&do=view&target=mbs2014.pdf"> <link rel="Appendix" title="montojoFrontgenet_2014.pdf" href="/Publications?action=AttachFile&do=view&target=montojoFrontgenet_2014.pdf"> <link rel="Appendix" title="musi-2011.pdf" href="/Publications?action=AttachFile&do=view&target=musi-2011.pdf"> <link rel="Appendix" title="nature_com_Aug2020.pdf" href="/Publications?action=AttachFile&do=view&target=nature_com_Aug2020.pdf"> <link rel="Appendix" title="nature_comment_Feb2011.pdf" href="/Publications?action=AttachFile&do=view&target=nature_comment_Feb2011.pdf"> <link rel="Appendix" title="netslim.pdf" href="/Publications?action=AttachFile&do=view&target=netslim.pdf"> <link rel="Appendix" title="omarwagih_thesis_msc.pdf" href="/Publications?action=AttachFile&do=view&target=omarwagih_thesis_msc.pdf"> <link rel="Appendix" title="pandeymay2014.pdf" href="/Publications?action=AttachFile&do=view&target=pandeymay2014.pdf"> <link rel="Appendix" title="pdz-struct-2013.pdf" href="/Publications?action=AttachFile&do=view&target=pdz-struct-2013.pdf"> <link rel="Appendix" title="phospholetter-2012.pdf" href="/Publications?action=AttachFile&do=view&target=phospholetter-2012.pdf"> <link rel="Appendix" title="pico_f10002014.pdf" href="/Publications?action=AttachFile&do=view&target=pico_f10002014.pdf"> <link rel="Appendix" title="plosgeneticsJan2015_Reimand.pdf" 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(Also, check out our latest publications in progress - <a href="/Publications#preprints">preprints</a>) <h1 id="Peer-reviewed_Articles">Peer-reviewed Articles</h1> <h2 id="A2024">2024</h2> <ol type="1"><li>Single-cell transcriptome analysis reveals CD34 as a marker of human sinoatrial node pacemaker cardiomyocytes Lim AA, Pouyabahar D, Ashraf M, Huang K, Lohbihler M, Murareanu BM, Chang ML, Kwan M, Alibhai FJ, Tran T, Mazine A, Laflamme MA, Bader GD, Laksman Z, Protze S <a class="https" href="https://www.nature.com/articles/s41467-024-54337-4">Nat Commun. 2024 Nov 27;15(1):10206</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/39604360/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_november2024_number2.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">The commitment of the human cell atlas to humanity Amit I, Ardlie K, Arzuaga F, Awandare G, Bader G, Bernier A, Carninci P, Donnelly S, Eils R, Forrest ARR, Greely HT, Guigo R, Hacohen N, Haniffa M, Kirby ES, Knoppers BM, Kriegstein A, Lein ES, Linnarsson S, Majumder PP, Merad M, Meyer K, Mhlanga MM, Nolan G, Ntusi NAB, Pe'er D, Prabhakar S, Raven-Adams M, Regev A, Rozenblatt-Rosen O, Saha S, Saltzman A, Shalek AK, Shin JW, Stunnenberg H, Teichmann SA, Tickle T, Villani AC, Wells C, Wold B, Yang H, Zhuang X <a class="https" href="https://www.nature.com/articles/s41467-024-54306-x">Nat Commun. 2024 Nov 20;15(1)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/39567491/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_november2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024 Golebiewski M, Bader G, Gleeson P, Gorochowski TE, Keating SM, König M, Myers CJ, Nickerson DP, Sommer B, Waltemath D, Schreiber F <a class="https" href="https://www.degruyter.com/document/doi/10.1515/jib-2024-0015/html">J Integr Bioinform. 2024 Jul 22;21(1)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/39026464/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=IntergBioinform_july2024.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap">Single-cell atlas of the human brain vasculature across development, adulthood and disease Wälchli T, Ghobrial M, Schwab M, Takada S, Zhong H, Suntharalingham S, Vetiska S, Gonzalez DR, Wu R, Rehrauer H, Dinesh A, Yu K, Chen ELY, Bisschop J, Farnhammer F, Mansur A, Kalucka J, Tirosh I, Regli L, Schaller K, Frei K, Ketela T, Bernstein M, Kongkham P, Carmeliet P, Valiante T, Dirks PB, Suva ML, Zadeh G, Tabar V, Schlapbach R, Jackson HW, De Bock K, Fish JE, Monnier PP, Bader GD, Radovanovic I <a class="https" href="https://www.nature.com/articles/s41586-024-07493-y">Nature. 2024 Aug;632(8025):603-613</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38987604/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nature_july2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Fatecode enables cell fate regulator prediction using classification-supervised autoencoder perturbation. Sadria M, Layton A, Goyal S, Bader GD <a class="https" href="https://www.cell.com/cell-reports-methods/fulltext/S2667-2375(24)00184-X">Cell Rep Methods. 2024 Jul 15;4(7):100819</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38986613/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=cellrepmethods_July2024.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/10.1101/2022.12.16.520772v1">arXiv</a> -<a class="https" href="https://www.biorxiv.org/content/10.1101/2022.12.16.520772v1.full.pdf">PDF</a> SINGLE CELL GENOMICS, SOFTWARE </li><li class="gap">Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J <a class="https" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10274948/">Nucleic Acids Res. 2024 Jul 5;52(W1):W481-W488</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38783119/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NuclAcid_May2024.pdf" title="PDF">PDF</a> <a class="https" href="https://arxiv.org/abs/2305.15453">arXiv</a> -<a class="https" href="https://arxiv.org/pdf/2305.15453">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Single-cell, single-nucleus, and spatial transcriptomics characterization of the immunological landscape in the healthy and PSC human liver Andrews TS, Nakib D, Perciani CT, Ma XZ, Liu L, Winter E, Camat D, Chung SW, Lumanto P, Manuel J, Mangroo S, Hansen B, Arpinder B, Thoeni C, Sayed B, Feld J, Gehring A, Gulamhusein A, Hirschfield GM, Ricciuto A, Bader GD, McGilvray ID, MacParland S <a class="https" href="https://www.journal-of-hepatology.eu/article/S0168-8278(24)00003-5/fulltext">J Hepatol. 2024 May;80(5):730-743</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38199298/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Jhepatol_May2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Multimodal Medical Answer Generation using Large Language Models Toma A, Xie R, Palayew S, Bader GD, Wang B <a class="https" href="https://aclanthology.org/2024.clinicalnlp-1.60/">2024. WangLab at MEDIQA-M3G 2024: In Proceedings of the 6th Clinical Natural Language Processing Workshop, pages 624–634</a> <a class="https" href="https://aclanthology.org/2024.clinicalnlp-1.60/">Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Mediam3g_april2024_2.pdf" title="PDF">PDF</a> NATURAL LANGUAGE PROCESSING </li><li class="gap">The multimodality cell segmentation challenge: toward universal solutions Ma J, Xie R, Ayyadhury S, Ge C, Gupta A, Gupta R, Gu S, Zhang Y, Lee G, Kim J, Lou W, Li H, Upschulte E, Dickscheid T, de Almeida JG, Wang Y, Han L, Yang X, Labagnara M, Gligorovski V, Scheder M, Rahi SJ, Kempster C, Pollitt A, Espinosa L, Mignot T, Middeke JM, Eckardt JN, Li W, Li Z, Cai X, Bai B, Greenwald NF, Van Valen D, Weisbart E, Cimini BA, Cheung T, Brück O, Bader GD, Wang B <a class="https" href="https://www.nature.com/articles/s41592-024-02233-6">Nat Methods. 2024 Jun;21(6):1103-1113</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38532015/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatMethods_March2024.pdf" title="PDF">PDF</a> COMPUTER VISION,SINGLE CELL GENOMICS </li><li class="gap">Integrated transcriptomics uncovers an enhanced association between the prion protein gene expression and vesicle dynamics signatures in glioblastomas Boccacino JM, Dos Santos Peixoto R, Fernandes CFL, Cangiano G, Sola PR, Coelho BP, Prado MB, Melo-Escobar MI, de Sousa BP, Ayyadhury S, Bader GD, Shinjo SMO, Marie SKN, da Rocha EL, Lopes MH <a class="https" href="https://bmccancer.biomedcentral.com/articles/10.1186/s12885-024-11914-6">BMC Cancer. 2024 Feb 13;24(1):199</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38347462/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BMCCancer_Feb2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li></ol> <h2 id="A2023">2023</h2> <ol type="1"><li>Single-nucleus multiomic atlas of frontal cortex in amyotrophic lateral sclerosis with a deep learning-based decoding of alternative polyadenylation mechanisms McKeever PM, Sababi AM, Sharma R, Khuu N, Xu Z, Shen SY, Xiao S, McGoldrick P, Orouji E, Ketela T, Sato C, Moreno D, Visanji N, Kovacs GG, Keith J, Zinman L, Rogaeva E, Goodarzi H, Bader GD, Robertson J <a class="https" href="https://www.biorxiv.org/content/10.1101/2023.12.22.573083v1">bioRxiv [Preprint]. 2023 Dec 23,2023</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38187588/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Biorxiv_Dec2023.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Spatially Resolved Gene Expression Prediction from Histology Images via Bi-modal Contrastive Learning Xie R, Pang K, Chung SW, Perciani C, MacParland S, Wang B, Bader GD <a class="https" href="https://proceedings.neurips.cc/paper_files/paper/2023/hash/df656d6ed77b565e8dcdfbf568aead0a-Abstract-Conference.html">Proceedings of the Thirty-seventh Conference on Neural Information Processing Systems</a> - <a class="https" href="https://proceedings.neurips.cc/paper_files/paper/2023/file/df656d6ed77b565e8dcdfbf568aead0a-Paper-Conference.pdf">PDF</a> <a class="https" href="https://arxiv.org/abs/2306.01859">arXiv</a> -<a class="https" href="https://arxiv.org/pdf/2306.01859.pdf">PDF</a> <a class="https" href="https://neurips.cc/virtual/2023/poster/70961">Poster</a> SPATIAL TRANSCRIPTOMICS </li><li class="gap">Adversarial training improves model interpretability in single-cell RNA-seq analysis Sadria M, Layton A, Bader GD <a class="https" href="https://academic.oup.com/bioinformaticsadvances/article/3/1/vbad166/7444320">Bioinform Adv. 2023 Nov 23;3(1)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38099262/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Bioinformadv_Nov2023.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Open Domain Multi-document Summarization: A Comprehensive Study of Model Brittleness under Retrieval Giorgi J, Soldaini L, Wang B, Bader G, Lo K, Wang L, and Cohan A <a class="https" href="https://aclanthology.org/2023.findings-emnlp.549/">Findings of the Association for Computational Linguistics: EMNLP Dec 2023, pages 8177–8199</a> <a class="https" href="https://arxiv.org/abs/2212.10526">arXiv. 2022 Dec 20</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Compling_Dec2023.pdf" title="PDF">PDF</a> NATURAL LANGUAGE PROCESSING </li><li class="gap">A rat liver cell atlas reveals intrahepatic myeloid heterogeneity Pouyabahar D, Chung SW, Pezzutti OI, Perciani CT, Wang X, Ma XZ, Jiang C, Camat D, Chung T, Sekhon M, Manuel J, Chen XC, McGilvray ID, MacParland SA, Bader GD <a class="https" href="https://www.sciencedirect.com/science/article/pii/S2589004223022903">iScience. 2023 Oct 14;26(11):108213</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38026201/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=iscience_Oct2023.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Fate specification of GFAP-negative primitive neural stem cells and their progeny at clonal resolution Yammine S, Burns I, Gosio J, Peluso A, Merritt D, Innes B, Coles B, Yan WR, Bader GD, Morshead C, van der Kooy D <a class="https" href="https://www.liebertpub.com/doi/10.1089/scd.2023.0038">Stem Cells Dev. 2023 Oct;32(19-20):606-621</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/37551982/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=StemCell_Aug2023.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Distinct shared and compartment-enriched oncogenic networks drive primary versus metastatic breast cancer Jiang Z, Ju Y, Ali A, Chung PED, Skowron P, Wang DY, Shrestha M, Li H, Liu JC, Vorobieva I, Ghanbari-Azarnier R, Mwewa E, Koritzinsky M, Ben-David Y, Woodgett JR, Perou CM, Dupuy A, Bader GD, Egan SE, Taylor MD, Zacksenhaus E <a class="https" href="https://www.nature.com/articles/s41467-023-39935-y">Nat Commun. 2023 Jul 18;14(1):4313</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/37463901/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Natcomm_July2023.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Robust segregation of donor and recipient cells from single-cell RNA-sequencing of transplant samples Wilson GW, Duong A, Moshkelgosha S, Bader G, Keshavjee S, Martinu T, Juvet SC, Yeung JC <a class="https" href="https://www.frontiersin.org/articles/10.3389/frtra.2023.1161146/full">Front. Transplant., 12 June 2023 Volume 2 - 2023</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Fronttrans_June2023.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">MAESTER: Masked Autoencoder Guided Segmentation at Pixel Resolution for Accurate, Self-Supervised Subcellular Structure Recognition Xie R, Pang K, Bader GD, Wang B <a class="https" href="https://openaccess.thecvf.com/content/CVPR2023/html/Xie_MAESTER_Masked_Autoencoder_Guided_Segmentation_at_Pixel_Resolution_for_Accurate_CVPR_2023_paper.html">Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2023, pp. 3292-3301</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CCVF_June2023.pdf" title="PDF">PDF</a> COMPUTER VISION </li><li class="gap">Multiplatform molecular profiling uncovers two subgroups of malignant peripheral nerve sheath tumors with distinct therapeutic vulnerabilities Suppiah S, Mansouri S, Mamatjan Y, Liu JC, Bhunia MM, Patil V, Rath P, Mehani B, Heir P, Bunda S, Velez-Reyes GL, Singh O, Ijad N, Pirouzmand N, Dalcourt T, Meng Y, Karimi S, Wei Q, Nassiri F, Pugh TJ, Bader GD, Aldape KD, Largaespada DA, Zadeh G <a class="https" href="https://www.nature.com/articles/s41467-023-38432-6">Nat Commun. 2023 May 10;14(1):2696</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/37164978/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Natcomm_May2023.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Multi-scale systems genomics analysis predicts pathways, cell types, and drug targets involved in normative variation in peri-adolescent human cognition Pai S, Hui S, Weber P, Narayan S, Whitley O, Li P, Labrie V, Baumbach J, Wheeler AL, Bader GD <a class="https" href="https://academic.oup.com/cercor/advance-article/doi/10.1093/cercor/bhad142/7145898?login=false">Cereb Cortex. 2023 Apr 27</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/37106565/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=cereb_cortex_April2023.pdf" title="PDF">PDF</a> PRECISION MEDICINE </li><li class="gap">Genotyping SARS-CoV-2 Variants Using Ratiometric Nucleic Acid Barcode Panels Kozlowski HN, Malekjahani A, Li VYC, Lekuti AA, Perusini S, Bell NG, Voisin V, Pouyabahar D, Pai S, Bader GD, Mubareka S, Gubbay JB, Chan WCW <a class="https" href="https://pubs.acs.org/doi/10.1021/acs.analchem.2c04630">Anal Chem. 2023 Apr 11;95(14):5877-5885</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/37000033/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=anal_chem_April2023.pdf" title="PDF">PDF</a> COVID-19 </li><li class="gap">Cytoscape.js 2023 update: a graph theory library for visualisation and analysis. Bioinformatics Franz M, Lopes CT, Fong D, Kucera M, Cheung M, Siper MC, Huck G, Dong Y, Sumer O, Bader GD <a class="https" href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad031/6988031">Bioinformatics 2023 Jan 1;39(1)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36645249/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=bioinformatics_Jan2023.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2022">2022</h2> <ol type="1"><li>Single-cell profiling of healthy human kidney reveals features of sex-based transcriptional programs and tissue-specific immunity McEvoy CM, Murphy JM, Zhang L, Clotet-Freixas S, Mathews JA, An J, Karimzadeh M, Pouyabahar D, Su S, Zaslaver O, Röst H, Arambewela R, Liu LY, Zhang S, Lawson KA, Finelli A, Wang B, MacParland SA, Bader GD, Konvalinka A, Crome SQ <a class="https" href="https://www.nature.com/articles/s41467-022-35297-z">Nat Commun. 2022 Dec 10;13(1):7634</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36496458/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_Dec2022.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD, Egan SE, Cescon DW, Sørlie T, Wrana JL, Jackson HW, Wilson MD, Witkiewicz AK, Knudsen ES, Pujana MA, Wahl GM, Schramek D <a class="https" href="https://aacrjournals.org/cancerdiscovery/article/12/12/2930/711188/Loss-of-Epigenetic-Regulation-Disrupts-Lineage">Cancer Discov. 2022 Dec 2;12(12):2930-2953</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36108220/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerDis_Dec2022.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease-relevant pathologies Murtaza N, Cheng AA, Brown CO, Meka DP, Hong S, Uy JA, El-Hajjar J, Pipko N, Unda BK, Schwanke B, Xing S, Thiruvahindrapuram B, Engchuan W, Trost B, Deneault E, Calderon de Anda F, Doble BW, Ellis J, Anagnostou E, Bader GD, Scherer SW, Lu Y, Singh KK <a class="https" href="https://www.cell.com/cell-reports/fulltext/S2211-1247(22)01552-2">Cell Rep. 2022 Nov 22;41(8):111678</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36417873/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellRep_Nov2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Neurons and glial cells acquire a senescent signature after repeated mild traumatic brain injury in a sex-dependent manner Schwab N, Taskina D, Leung E, Innes BT, Bader GD, Hazrati LN <a class="https" href="https://www.frontiersin.org/articles/10.3389/fnins.2022.1027116/full#:~:text=all%206%20Articles-,Neurons%20and%20glial%20cells%20acquire%20a%20senescent%20signature%20after%20repeated,in%20a%20sex%2Ddependent%20manner&text=Mild%20traumatic%20brain%20injury%20(mTBI,and%20risk%20of%20neurodegenerative%20disease.">Front Neurosci. 2022 Nov 3;16:1027116</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36408415/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=FrontNeuro_Nov2022.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">BIONIC: biological network integration using convolutions Forster DT, Li SC, Yashiroda Y, Yoshimura M, Li Z, Isuhuaylas LAV, Itto-Nakama K, Yamanaka D, Ohya Y, Osada H, Wang B, Bader GD, Boone C <a class="https" href="https://www.nature.com/articles/s41592-022-01616-x">Nat Methods. 2022 Oct;19(10):1250-1261</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36192463/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatMethodsOct2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Single-cell atlas of human liver development reveals pathways directing hepatic cell fates Wesley BT, Ross ADB, Muraro D, Miao Z, Saxton S, Tomaz RA, Morell CM, Ridley K, Zacharis ED, Petrus-Reurer S, Kraiczy J, Mahbubani KT, Brown S, Garcia-Bernardo J, Alsinet C, Gaffney D, Horsfall D, Tysoe OC, Botting RA, Stephenson E, Popescu DM, MacParland S, Bader G, McGilvray ID, Ortmann D, Sampaziotis F, Saeb-Parsy K, Haniffa M, Stevens KR, Zilbauer M, Teichmann SA, Vallier L <a class="https" href="https://www.nature.com/articles/s41556-022-00989-7">Nat Cell Biol. 2022 Oct;24(10):1487-1498</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36109670/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatCellBio_Sept2022.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">PLAG1 dampens protein synthesis to promote human hematopoietic stem cell self-renewal Keyvani Chahi A, Belew MS, Xu J, Chen HTT, Rentas S, Voisin V, Krivdova G, Lechman E, Marhon SA, De Carvalho DD, Dick JE, Bader GD, Hope KJ <a class="https" href="https://ashpublications.org/blood/article/140/9/992/485426/PLAG1-dampens-protein-synthesis-to-promote-human">Blood. 2022 Sep 1;140(9):992-1008</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36055193/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Blood_Sept2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Modeling human multi-lineage heart field development with pluripotent stem cells Yang D, Gomez-Garcia J, Funakoshi S, Tran T, Fernandes I, Bader GD, Laflamme MA, Keller GM <a class="https" href="https://www.sciencedirect.com/science/article/pii/S1934590922003435?via%3Dihub">Cell Stem Cell. 2022 Sep 1;29(9):1382-1401</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36055193/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=StemCell_Sept2022.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Unraveling the Complexity of Liver Disease One Cell at a Time Atif J, Thoeni C, Bader GD, McGilvray ID, MacParland SA <a class="https" href="https://www.thieme-connect.com/products/ejournals/abstract/10.1055/s-0042-1755272">Semin Liver Dis. 2022 Aug;42(3):250-270</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/36008091/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=SeminLiver_Aug2022.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Genome Of The Netherlands Project, Ghs Study Group, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J <a class="https" href="https://www.mdpi.com/2072-6694/14/14/3363">Cancers (Basel). 2022 Jul 11;14(14)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35884425/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Cancers_July2022.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Comprehensive multi-cohort transcriptional meta-analysis of muscle diseases identifies a signature of disease severity Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Khatri P, Dos Santos CC <a class="https" href="https://www.nature.com/articles/s41598-022-15003-1">Sci Rep. 2022 Jul 4;12(1):11260</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35789175/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Scireports_July2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">OpenPIP: An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data Helmy M, Mee M, Ranjan A, Hao T, Vidal M, Calderwood MA, Luck K, Bader GD <a class="https" href="https://www.sciencedirect.com/science/article/pii/S0022283622001838">J Mol Biol. 2022 Jun 15;434(11):167603</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35662469/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=JMB_June2022.pdf" title="PDF">PDF</a> PROTEIN INTERACTION </li><li class="gap">The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness Thomas GE, Egan G, García-Prat L, Botham A, Voisin V, Patel PS, Hoff FW, Chin J, Nachmias B, Kaufmann KB, Khan DH, Hurren R, Wang X, Gronda M, MacLean N, O'Brien C, Singh RP, Jones CL, Harding SM, Raught B, Arruda A, Minden MD, Bader GD, Hakem R, Kornblau S, Dick JE, Schimmer AD <a class="https" href="https://www.nature.com/articles/s41556-022-00925-9">Nat Cell Biol. 2022 Jun 6</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35668135/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCellBio_June2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A sequence-to-sequence approach for document-level relation extraction Giorgi, John and Bader, Gary and Wang, Bo <a class="https" href="https://aclweb.org/aclwiki/BioNLP_Workshop">BioNLP @ ACL May 2022</a> <a class="https" href="https://aclanthology.org/2022.bionlp-1.2/">ACL Anthology</a> - <a class="https" href="https://aclanthology.org/2022.bionlp-1.2.pdf">PDF</a> NATURAL LANGUAGE PROCESSING </li><li class="gap">Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML Krivdova G, Voisin V, Schoof EM, Marhon SA, Murison A, McLeod JL, Gabra MM, Zeng AGX, Aigner S, Yee BA, Shishkin AA, Van Nostrand EL, Hermans KG, Trotman-Grant AC, Mbong N, Kennedy JA, Gan OI, Wagenblast E, De Carvalho DD, Salmena L, Minden MD, Bader GD, Yeo GW, Dick JE, Lechman ER <a class="https" href="https://www.cell.com/cell-reports/fulltext/S2211-1247(22)00214-5">Cell Rep. 2022 Mar 8;38(10)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35263585/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellRep_March2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">IPO11 regulates the nuclear import of BZW1/2 and is necessary for AML cells and stem cells Nachmias B, Khan DH, Voisin V, Mer AS, Thomas GE, Segev N, St-Germain J, Hurren R, Gronda M, Botham A, Wang X, Maclean N, Seneviratne AK, Duong N, Xu C, Arruda A, Orouji E, Algouneh A, Hakem R, Shlush L, Minden MD, Raught B, Bader GD, Schimmer AD <a class="https" href="https://www.nature.com/articles/s41375-022-01513-4">Leukemia. 2022 Feb 12</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35152270/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=leukemia_Feb2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A Shared Transcriptional Identity for Forebrain and Dentate Gyrus Neural Stem Cells from Embryogenesis to Adulthood Borrett MJ, Tahmasian N, Innes BT, Bader GD, Kaplan DR, Miller FD <a class="https" href="https://www.eneuro.org/content/early/2022/01/12/ENEURO.0271-21.2021.long">eNeuro. 2022 Jan 13:ENEURO.0271-21.2021</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35027446/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=eneuro_Jan2022.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Hypophosphorylated pRb knock-in mice exhibit hallmarks of aging and vitamin C-preventable diabetes Jiang Z, Li H, Schroer SA, Voisin V, Ju Y, Pacal M, Erdmann N, Shi W, Chung PED, Deng T, Chen NJ, Ciavarra G, Datti A, Mak TW, Harrington L, Dick FA, Bader GD, Bremner R, Woo M, Zacksenhaus E <a class="https" href="https://www.embopress.org/doi/full/10.15252/embj.2020106825">EMBO J. 2022 Jan 13</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35023164/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=EMBO_Jan2022.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2021">2021</h2> <ol type="1"><li>Temporal profiling of therapy resistance in human medulloblastoma identifies novel targetable drivers of recurrence Bakhshinyan D, Adile AA, Liu J, Gwynne WD, Suk Y, Custers S, Burns I, Singh M, McFarlane N, Subapanditha MK, Qazi MA, Vora P, Kameda-Smith MM, Savage N, Desmond KL, Tatari N, Tran D, Seyfrid M, Hope K, Bock NA, Venugopal C, Bader GD, Singh SK <a class="https" href="https://www.science.org/doi/full/10.1126/sciadv.abi5568?af=R">Sci Adv. 2021 Dec 10;7(50)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34878832/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=SciAdv_Dec2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Author-sourced capture of pathway knowledge in computable form using Biofactoid Wong JV, Franz M, Siper MC, Fong D, Durupinar F, Dallago C, Luna A, Giorgi J, Rodchenkov I, Babur Ö, Bachman JA, Gyori BM, Demir E, Bader GD, Sander C <a class="https" href="https://elifesciences.org/articles/68292">Elife. 2021 Dec 3;10</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34860157/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Elife_Dec2021.pdf" title="PDF">PDF</a> SOFTWARE </li><li class="gap">Single-Cell, Single-Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity Andrews TS, Atif J, Liu JC, Perciani CT, Ma XZ, Thoeni C, Slyper M, Eraslan G, Segerstolpe A, Manuel J, Chung S, Winter E, Cirlan I, Khuu N, Fischer S, Rozenblatt-Rosen O, Regev A, McGilvray ID, Bader GD, MacParland SA <a class="https" href="https://aasldpubs.onlinelibrary.wiley.com/doi/full/10.1002/hep4.1854">Hepatol Commun. 2021 Nov 18</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34792289/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=HepatoCom_Nov2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">The Reactome pathway knowledgebase 2022 Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D'Eustachio P <a class="https" href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab1028/6426058">Nucleic Acids Res. 2021 Nov 12</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34788843/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NucleicAcid_Nov2021.pdf" title="PDF">PDF</a> PATHWAY DATABASE </li><li class="gap">A flexible search system for high-accuracy identification of biological entities and molecules Franz M, Wong JV, Siper MC, Dallago C,Giorgi J, Demir E, Chris Sander C, Bader GD <a class="https" href="https://joss.theoj.org/papers/10.21105/joss.03756#">Journal of Open Source Software, 6(67), 3756</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34860157/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=JOSS_Nov2021.pdf" title="PDF">PDF</a> SOFTWARE </li><li class="gap">A microfluidic platform enables comprehensive gene expression profiling of mouse retinal stem cells Coles BLK, Labib M, Poudineh M, Innes BT, Belair-Hickey J, Gomis S, Wang Z, Bader GD, Sargent EH, Kelley SO, van der Kooy D <a class="https" href="https://pubs.rsc.org/en/content/articlelanding/2021/lc/d1lc00790d">Lab Chip. 2021 Oct 15</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34651637/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=LabChip_Oct2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">A roadmap for the Human Developmental Cell Atlas Haniffa M, Taylor D, Linnarsson S, Aronow BJ, Bader GD, Barker RA, Camara PG, Camp JG, Chédotal A, Copp A, Etchevers HC, Giacobini P, Göttgens B, Guo G, Hupalowska A, James KR, Kirby E, Kriegstein A, Lundeberg J, Marioni JC, Meyer KB, Niakan KK, Nilsson M, Olabi B, Pe'er D, Regev A, Rood J, Rozenblatt-Rosen O, Satija R, Teichmann SA, Treutlein B, Vento-Tormo R, Webb S <a class="https" href="https://www.nature.com/articles/s41586-021-03620-1">Nature. 2021 Sep;597(7875):196-205</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34497388/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nature_Sept2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">A clinically applicable integrative molecular classification of meningiomas Nassiri F, Liu J, Patil V, Mamatjan Y, Wang JZ, Hugh-White R, Macklin AM, Khan S, Singh O, Karimi S, Corona RI, Liu LY, Chen CY, Chakravarthy A, Wei Q, Mehani B, Suppiah S, Gao A, Workewych AM, Tabatabai G, Boutros PC, Bader GD, de Carvalho DD, Kislinger T, Aldape K, Zadeh G <a class="https" href="https://www.nature.com/articles/s41586-021-03850-3">Nature. 2021 Aug 25</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34433969/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nature_Aug2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">DeCLUTR: Deep Contrastive Learning for Unsupervised Textual Representations John Giorgi, Osvald Nitski, Bo Wang, Gary Bader <a class="https" href="https://aclanthology.org/2021.acl-long.72/">ACL/IJCNLP. 2021 Aug 1</a> <a class="https" href="https://aclanthology.org/2021.acl-long.72/">ACL Anthology</a> - <a class="https" href="https://aclanthology.org/2021.acl-long.72.pdf">PDF</a> NATURAL LANGUAGE PROCESSING </li><li class="gap">TFEB-mediated endolysosomal activity controls human hematopoietic stem cell fate García-Prat L, Kaufmann KB, Schneiter F, Voisin V, Murison A, Chen J, Chan-Seng-Yue M, Gan OI, McLeod JL, Smith SA, Shoong MC, Parris D, Pan K, Zeng AGX, Krivdova G, Gupta K, Takayanagi SI, Wagenblast E, Wang W, Lupien M, Schroeder T, Xie SZ, Dick JE <a class="https" href="https://www.sciencedirect.com/science/article/pii/S1934590921002885?via=ihub">Cell Stem Cell. 2021 Jul 28:S1934-5909(21)00288-5.</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34343492/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellStemcell_Aug2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Nicotinamide phosphoribosyltransferase inhibitors selectively induce apoptosis of AML stem cells by disrupting lipid homeostasis Subedi A, Liu Q, Ayyathan DM, Sharon D, Cathelin S, Hosseini M, Xu C, Voisin V, Bader GD, D'Alessandro A, Lechman ER, Dick JE, Minden MD, Wang JCY, Chan SM <a class="https" href="https://www.sciencedirect.com/science/article/pii/S1934590921002745">Cell Stem Cell. 2021 Jul 12:S1934-5909(21)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34293334/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellStemcell_July2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Control of tissue development and cell diversity by cell cycle dependent transcriptional filtering Abou Chakra M, Isserlin R, Tran TN, Bader GD <a class="https" href="https://elifesciences.org/articles/64951">Elife. 2021 Jul 2;10:e64951</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34212855/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Elife_July2021.pdf" title="PDF">PDF</a> MATHEMATICAL MODELLING </li><li class="gap">scNetViz: from single cells to networks using Cytoscape Choudhary K, Meng EC, Diaz-Mejia JJ, Bader GD, Pico AR, Morris JH <a class="https" href="https://f1000research.com/articles/10-448">F1000Res. 2021 Jun 7;10:ISCB Comm J-448</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34912541/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=F1000_June2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Surveilling and Tracking COVID-19 Patients Using a Portable Quantum Dot Smartphone Device Zhang Y, Malekjahani A, Udugama BN, Kadhiresan P, Chen H, Osborne M, Franz M, Kucera M, Plenderleith S, Yip L, Bader GD, Tran V, Gubbay JB, McGeer A, Mubareka S, Chan WCW <a class="https" href="https://pubs.acs.org/doi/10.1021/acs.nanolett.1c01280">Nano Lett. 2021 Jun 10</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34110166/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NanoLett_June2021.pdf" title="PDF">PDF</a> COVID-19 </li><li class="gap">Generation of mature compact ventricular cardiomyocytes from human pluripotent stem cells Funakoshi S, Fernandes I, Mastikhina O, Wilkinson D, Tran T, Dhahri W, Mazine A, Yang D, Burnett B, Lee J, Protze S, Bader GD, Nunes SS, Laflamme M, Keller G <a class="https" href="https://www.nature.com/articles/s41467-021-23329-z">Nat Commun. 2021 May 26;12(1):3155</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34039977/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureComm_May2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods Clarke ZA, Andrews TS, Atif J, Pouyabahar D, Innes BT, MacParland SA, Bader GD <a class="https" href="https://www.nature.com/articles/s41596-021-00534-0">Nat Protoc. 2021 May 24.</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/34031612/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureProt_May2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks Rougny A, Touré V, Albanese J, Waltemath D, Shirshov D, Sorokin A, Bader GD, Blinov ML, Mazein A <a class="https" href="https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbab049/6184415">Brief Bioinform. 2021 Mar 24</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33758926/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=briefbioinfo_Mar2021.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap">Distinct DNA methylation patterns associated with treatment resistance in metastatic castration resistant prostate cancer Peter MR, Bilenky M, Davies A, Isserlin R, Bader GD, Fleshner NE, Hirst M, Zoubeidi A, Bapat B <a class="https" href="https://www.nature.com/articles/s41598-021-85812-3">Sci Rep. 2021 Mar 23;11(1):6630</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33758253/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Scireport_Mar2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">The transcriptional landscape of Shh medulloblastoma Skowron P, Farooq H, Cavalli FMG, Morrissy AS, Ly M, Hendrikse LD, Wang EY, Djambazian H, Zhu H, Mungall KL, Trinh QM, Zheng T, Dai S, Stucklin ASG, Vladoiu MC, Fong V, Holgado BL, Nor C, Wu X, Abd-Rabbo D, Bérubé P, Wang YC, Luu B, Suarez RA, Rastan A, Gillmor AH, Lee JJY, Zhang XY, Daniels C, Dirks P, Malkin D, Bouffet E, Tabori U, Loukides J, Doz FP, Bourdeaut F, Delattre OO, Masliah-Planchon J, Ayrault O, Kim SK, Meyronet D, Grajkowska WA, Carlotti CG, de Torres C, Mora J, Eberhart CG, Van Meir EG, Kumabe T, French PJ, Kros JM, Jabado N, Lach B, Pollack IF, Hamilton RL, Rao AAN, Giannini C, Olson JM, Bognár L, Klekner A, Zitterbart K, Phillips JJ, Thompson RC, Cooper MK, Rubin JB, Liau LM, Garami M, Hauser P, Li KKW, Ng HK, Poon WS, Yancey Gillespie G, Chan JA, Jung S, McLendon RE, Thompson EM, Zagzag D, Vibhakar R, Ra YS, Garre ML, Schüller U, Shofuda T, Faria CC, López-Aguilar E, Zadeh G, Hui CC, Ramaswamy V, Bailey SD, Jones SJ, Mungall AJ, Moore RA, Calarco JA, Stein LD, Bader GD, Reimand J, Ragoussis J, Weiss WA, Marra MA, Suzuki H, Taylor MD <a class="https" href="https://www.nature.com/articles/s41467-021-21883-0">Nat Commun. 2021 Mar 19;12(1):1749</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33741928/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_Mar2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Biological and therapeutic implications of a unique subtype of NPM1 mutated AML Mer AS, Heath EM, Madani Tonekaboni SA, Dogan-Artun N, Nair SK, Murison A, Garcia-Prat L, Shlush L, Hurren R, Voisin V, Bader GD, Nislow C, Rantalainen M, Lehmann S, Gower M, Guidos CJ, Lupien M, Dick JE, Minden MD, Schimmer AD, Haibe-Kains B <a class="https" href="https://www.nature.com/articles/s41467-021-21233-0">Nat Commun. 2021 Feb 16;12(1):1054</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33594052/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_Feb2021_2.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">PRMT5 inhibition disrupts splicing and stemness in glioblastoma Sachamitr P, Ho JC, Ciamponi FE, Ba-Alawi W, Coutinho FJ, Guilhamon P, Kushida MM, Cavalli FMG, Lee L, Rastegar N, Vu V, Sánchez-Osuna M, Coulombe-Huntington J, Kanshin E, Whetstone H, Durand M, Thibault P, Hart K, Mangos M, Veyhl J, Chen W, Tran N, Duong BC, Aman AM, Che X, Lan X, Whitley O, Zaslaver O, Barsyte-Lovejoy D, Richards LM, Restall I, Caudy A, Röst HL, Bonday ZQ, Bernstein M, Das S, Cusimano MD, Spears J, Bader GD, Pugh TJ, Tyers M, Lupien M, Haibe-Kains B, Artee Luchman H, Weiss S, Massirer KB, Prinos P, Arrowsmith CH, Dirks PB <a class="https" href="https://www.nature.com/articles/s41467-021-21204-5">Nat Commun. 2021 Feb 12;12(1):979</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33579912/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_Feb2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Sphingosine-1-phosphate receptor 3 potentiates inflammatory programs in normal and leukemia stem cells to promote differentiation Xie SZ, Kaufmann KB, Wang W, Chan-Seng-Yue M, Gan OI, Laurenti E, Garcia-Prat L, Takayanagi SI, Ng SWK, Xu C, Zeng AGX, Jin L, <a class="nonexistent" href="/McLeod">McLeod</a> J, Wagenblast E, Mitchell A, Kennedy JA, Liu Q, Boutzen H, Kleinau M, Jargstorf J, Holmes G, Zhang Y, Voisin V, Bader GD, Wang JCY, Hannun YA, Luberto C, Schroeder T, Minden MD, Dick JE <a class="https" href="https://bloodcancerdiscov.aacrjournals.org/content/2/1/32">Blood Cancer Discov. 2021 Jan 1;2(1):32-53</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33458693/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BloodCancer_Jan2021.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Gradient of Developmental and Injury Response transcriptional states defines functional vulnerabilities underpinning glioblastoma heterogeneity Richards LM,Whitley OKN, MacLeod G, Cavalli FMG, Coutinho F, Jaramillo J, Svergun N, Riverin M, Croucher D, Kushida M, Yu K, Guilhamon P, Rastegar N, Ahmadi M, Bhatti J, Bozek D, Li N, Lee L, Che C, Luis E, Park N, Xu Z, Ketela T, Moore R, Marra M, Spears, Cusimano M, Das S, Bernstein M, Haibe-Kains B, Lupien M, Luchman H, Weiss S, Angers S, Dirks PB, Bader GD, Pugh TJ. <a class="https" href="https://www.nature.com/articles/s43018-020-00154-9">Nature Cancer 2021 Feb;2(2):157-173</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/35122077/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Naturecancer_Jan2021.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li></ol> <h2 id="A2020">2020</h2> <ol type="1"><li>Large-scale survey and database of high affinity ligands for peptide recognition modules Teyra J, Kelil A, Jain S, Helmy M, Jajodia R, Hooda Y, Gu J, D'Cruz AA, Nicholson SE, Min J, Sudol M, Kim PM, Bader GD, Sidhu SS <a class="https" href="https://www.embopress.org/doi/full/10.15252/msb.20199310">Mol Syst Biol. 2020 Dec;16(12)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33438817/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=MolSysBio_Dec2020.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">CD200 expression marks leukemia stem cells in human AML Ho JM, Dobson SM, Voisin V, McLeod J, Kennedy JA, Mitchell A, Jin L, Eppert K, Bader G, Minden MD, Dick JE, Wang JCY <a class="https" href="https://ashpublications.org/bloodadvances/article/4/21/5402/469828/CD200-expression-marks-leukemia-stem-cells-in">Blood Adv. 2020 Nov 10;4(21):5402-5413</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33147339/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Bloodadv_Nov2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">netDx: Software for building interpretable patient classifiers by multi-'omic data integration using patient similarity networks Pai S, Weber P, Isserlin R, Kaka H, Hui S, Shah MA, Giudice L, Giugno R, Nøhr AK, Baumbach J, Bader GD <a class="https" href="https://f1000research.com/articles/9-1239/v2">F1000Res. 2020 Oct 15;9:1239</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/33628435/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=f1000_Oct2020.pdf" title="PDF">PDF</a> PRECISION MEDICINE </li><li class="gap">Functional genomic landscape of cancer-intrinsic evasion of killing by T cells Lawson KA, Sousa CM, Zhang X, Kim E, Akthar R, Caumanns JJ, Yao Y, Mikolajewicz N, Ross C, Brown KR, Zid AA, Fan ZP, Hui S, Krall JA, Simons DM, Slater CJ, De Jesus V, Tang L, Singh R, Goldford JE, Martin S, Huang Q, Francis EA, Habsid A, Climie R, Tieu D, Wei J, Li R, Tong AHY, Aregger M, Chan KS, Han H, Wang X, Mero P, Brumell JH, Finelli A, Ailles L, Bader G, Smolen GA, Kingsbury GA, Hart T, Kung C, Moffat J <a class="https" href="https://www.nature.com/articles/s41586-020-2746-2">Nature. 2020 Sep 23</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32968282/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nature_Sep2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Tempora: Cell trajectory inference using time-series single-cell RNA sequencing data Tran TN, Bader GD <a class="https" href="https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008205">PLoS Comput Biol. 2020 Sep 9;16(9)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32903255/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Plos_comp_bio_Sep2020.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Dynamics of the cell-free DNA methylome of metastatic prostate cancer during androgen-targeting treatment Peter MR, Bilenky M, Isserlin R, Bader GD, Shen SY, De Carvalho DD, Hansen AR, Hu P, Fleshner NE, Joshua AM, Hirst M, Bapat B <a class="https" href="https://www.futuremedicine.com/doi/abs/10.2217/epi-2020-0173">Epigenomics. 2020 Sep 1.</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32867540/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=epigenomics_Sep2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Wnt activation as a therapeutic strategy in medulloblastoma Manoranjan B, Venugopal C, Bakhshinyan D, Adile AA, Richards L, Kameda-Smith MM, Whitley O, Dvorkin-Gheva A, Subapanditha M, Savage N, Tatari N, McKenna D, Bassey-Archibong B, Winegarden N, Hallett R, Provias JP, Yarascavitch B, Ajani O, Fleming A, Bader GD, Pugh TJ, Doble BW, Singh SK <a class="https" href="https://www.nature.com/articles/s41467-020-17953-4">Nat Commun. 2020 Aug 28;11(1):4323</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32859895/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=nature_com_Aug2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Single-Cell Profiling Shows Murine Forebrain Neural Stem Cells Reacquire a Developmental State when Activated for Adult Neurogenesis Borrett MJ, Innes BT, Jeong D, Tahmasian N, Storer MA, Bader GD, Kaplan DR, Miller FD <a class="https" href="https://www.sciencedirect.com/science/article/pii/S221112472031007X">Cell Rep. 2020 Aug 11;32(6):108022</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32783944/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Cell_rep_Aug2020.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities Idicula-Thomas S, Gawde U, Bhaye S, Pokar K, Bader GD <a class="https" href="https://www.sciencedirect.com/science/article/pii/S2001037020303123">Comput Struct Biotechnol J. 2020;18:1735-1745</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32695266/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Comp_struct_bio_July2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Generation of Functional Liver Sinusoidal Endothelial Cells from Human Pluripotent Stem-Cell-Derived Venous Angioblasts Gage BK, Liu JC, Innes BT, MacParland SA, McGilvray ID, Bader GD, Keller GM <a class="https" href="https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(20)30274-5">Cell Stem Cell. 2020;S1934-5909(20)30274-5</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32640183/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=cellstem_July2020.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Distinct fibroblast functional states drive clinical outcomes in ovarian cancer and are regulated by TCF21 Hussain A, Voisin V, Poon S, Karamboulas C, Bui NHB, Meens J, Dmytryshyn J, Ho VW, Tang KH, Paterson J, Clarke BA, Bernardini MQ, Bader GD, Neel BG, Ailles LE <a class="https" href="https://rupress.org/jem/article/doi/10.1084/jem.20191094/151793/Distinct-fibroblast-functional-states-drive">J Exp Med. 2020 Aug 3;217(8)</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/32434219/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=jexm_May2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Disrupting Mitochondrial Copper Distribution Inhibits Leukemic Stem Cell Self-Renewal Singh RP, Jeyaraju DV, Voisin V, Hurren R, Xu C, Hawley JR, Barghout SH, Khan DH, Gronda M, Wang X, Jitkova Y, Sharon D, Liyanagae S, MacLean N, Seneviratene AK, Mirali S, Borenstein A, Thomas GE, Soriano J, Orouji E, Minden MD, Arruda A, Chan SM, Bader GD, Lupien M, Schimmer AD <a class="https" href="https://www.sciencedirect.com/science/article/abs/pii/S1934590920301491?via=ihub">Cell Stem Cell. 2020 May 12</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32416059">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=cellstem_May2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">BraInMap Elucidates the Macromolecular Connectivity Landscape of Mammalian Brain Pourhaghighi R, Ash PEA, Phanse S, Goebels F, Hu LZM, Chen S, Zhang Y, Wierbowski SD, Boudeau S, Moutaoufik MT, Malty RH, Malolepsza E, Tsafou K, Nathan A, Cromar G, Guo H, Abdullatif AA, Apicco DJ, Becker LA, Gitler AD, Pulst SM, Youssef A, Hekman R, Havugimana PC, White CA, Blum BC, Ratti A, Bryant CD, Parkinson J, Lage K, Babu M, Yu H, Bader GD, Wolozin B, Emili A. <a class="https" href="https://www.cell.com/cell-systems/fulltext/S2405-4712(20)30109-5">Cell Syst. 2020 Apr 22;10(4):333-350</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32325033">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellSys_April2020.pdf" title="PDF">PDF</a> PROTEIN INTERACTION </li><li class="gap">Mitochondrial carrier homolog 2 (MTCH2) is necessary for AML survival Khan DH, Mullokandov M, Wu Y, Voisin V, Gronda MV, Hurren R, Wang X, MacLean N, Jeyaraju DV, Jitkova Y, Xu GW, Laister RC, Seneviratne A, Blatman Z, Ketala T,Bader GD, Marhon SA, Carvalho DD, Minden MD, Gross A, Schimmer AD <a class="https" href="https://ashpublications.org/blood/article/doi/10.1182/blood.2019000106/454408/Mitochondrial-carrier-homolog-2-MTCH2-is-necessary">Blood. 2020 Apr 16</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32299104">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Blood_April2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Medulloblastoma Arises from the Persistence of a Rare and Transient Sox2(+) Granule Neuron Precursor Selvadurai HJ, Luis E, Desai K, Lan X, Vladoiu MC, Whitley O, Galvin C, Vanner RJ, Lee L, Whetstone H, Kushida M, Nowakowski T, Diamandis P, Hawkins C, Bader G, Kriegstein A, Taylor MD, Dirks PB <a class="https" href="https://www.cell.com/cell-reports/fulltext/S2211-1247(20)30401-0">Cell Rep. 2020 Apr 14;31(2):107511</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32294450">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellReports_April2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A reference map of the human binary protein interactome Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, Brignall R, Cafarelli T, Campos-Laborie FJ, Charloteaux B, Choi D, Coté AG, Daley M, Deimling S, Desbuleux A, Dricot A, Gebbia M, Hardy MF, Kishore N, Knapp JJ, Kovács IA, Lemmens I, Mee MW, Mellor JC, Pollis C, Pons C, Richardson AD, Schlabach S, Teeking B, Yadav A, Babor M, Balcha D, Basha O, Bowman-Colin C, Chin SF, Choi SG, Colabella C, Coppin G, D'Amata C, De Ridder D, De Rouck S, Duran-Frigola M, Ennajdaoui H, Goebels F, Goehring L, Gopal A, Haddad G, Hatchi E, Helmy M, Jacob Y, Kassa Y, Landini S, Li R, van Lieshout N, MacWilliams A, Markey D, Paulson JN, Rangarajan S, Rasla J, Rayhan A, Rolland T, San-Miguel A, Shen Y, Sheykhkarimli D, Sheynkman GM, Simonovsky E, Taşan M, Tejeda A, Tropepe V, Twizere JC, Wang Y, Weatheritt RJ, Weile J, Xia Y, Yang X, Yeger-Lotem E, Zhong Q, Aloy P, Bader GD, De Las Rivas J, Gaudet S, Hao T, Rak J, Tavernier J, Hill DE, Vidal M, Roth FP, Calderwood MA <a class="https" href="https://www.nature.com/articles/s41586-020-2188-x">Nature.2020 Apr;580(7803):402-408</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32296183">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Natuer_April2020.pdf" title="PDF">PDF</a> PROTEIN INTERACTION </li><li class="gap">The mitochondrial peptidase, neurolysin, regulates respiratory chain supercomplexformation and is necessary for AML viability Mirali S, Botham A, Voisin V, Xu C, St-Germain J, Sharon D, Hoff FW, Qiu Y, Hurren R, Gronda M, Jitkova Y, Nachmias B, MacLean N, Wang X, Arruda A, Minden MD, Horton TM, Kornblau SM, Chan SM, Bader GD, Raught B, Schimmer AD <a class="https" href="https://stm.sciencemag.org/content/12/538/eaaz8264.short">Sci Transl Med. 2020 Apr 8;12(538)</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32269163">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=SciTranslmed_April2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Nanoparticle Uptake in a Spontaneous and Immunocompetent Woodchuck Liver Cancer Model Liu LY, Ma XZ, Ouyang B, Ings DP, Marwah S, Liu J, Chen AY, Gupta R, Manuel J, Chen XC, Gage BK, Cirlan I, Khuu N, Chung S, Camat D, Cheng M, Sekhon M, Zagorovsky K, Abdou Mohamed MA, Thoeni C, Atif J, Echeverri J, Kollmann D, Fischer S, Bader GD, Chan WCW, Michalak TI, McGilvray ID, MacParland SA <a class="https" href="https://pubs.acs.org/doi/10.1021/acsnano.0c00468">ACS Nano. 2020 Apr 7</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32255624">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nano_April2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Relapse fated latent diagnosis subclones in acute B lineage leukaemia are drug tolerant and possess distinct metabolic programs Dobson SM, Garcia-Prat L, Vanner RJ, Wintersinger J, Waanders E, Gu Z, McLeod J, Gan OI, Grandal I, Payne-Turner D, Edmonson MN, Ma X, Fan Y, Voisin V, Chan-Seng-Yue M, Xie SZ, Hosseini M, Abelson S, Gupta P, Rusch M, Shao Y, Olsen SR, Neale G, Chan SM, Bader G, Easton J, Guidos CJ, Danska JS, Zhang J, Minden MD, Morris Q, Mullighan CG, Dick JE <a class="https" href="https://cancerdiscovery.aacrjournals.org/content/early/2020/02/21/2159-8290.CD-19-1059.long">Cancer Discov. 2020 Feb 21</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32086311">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerDisc_Feb2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Potential Therapeutic Targets for Lung Repair During Human Ex Vivo Lung Perfusion Wong A, Zamel R, Yeung J, Bader GD, Dos Santos CC, Bai X, Wang Y, Keshavjee S, Liu M <a class="https" href="https://erj.ersjournals.com/content/early/2020/01/16/13993003.02222-2019.long">Eur Respir J. 2020 Feb 14</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/32060066">PubMed Abstract</a> - <a class="attachment nonexistent" href="/Publications?action=AttachFile&do=upload_form&ticket=0067b6db71.0b6db5bcfc7bdb3fbe365a002b413a77f6f00035&target=EurRespir_Feb2020.pdf" title="Upload new attachment "EurRespir_Feb2020.pdf"">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A network analysis to identify mediators of germline-driven differences in breast cancer prognosis. Escala-Garcia M, Abraham J, Andrulis IL, Anton-Culver H, Arndt V, Ashworth A, Auer PL, Auvinen P, Beckmann MW, Beesley J, Behrens S, Benitez J, Bermisheva M,Blomqvist C, Blot W, Bogdanova NV, Bojesen SE, Bolla MK, Børresen-Dale AL, Brauch H, Brenner H, Brucker SY, Burwinkel B, Caldas C, Canzian F, Chang-Claude J, Chanock SJ, Chin SF, Clarke CL, Couch FJ, Cox A, Cross SS, Czene K, Daly MB, Dennis J, Devilee P, Dunn JA, Dunning AM, Dwek M, Earl HM, Eccles DM, Eliassen AH, Ellberg C, Evans DG, Fasching PA, Figueroa J, Flyger H, Gago-Dominguez M, Gapstur SM, García-Closas M, García-Sáenz JA, Gaudet MM, George A, Giles GG, Goldgar DE, González-Neira A, Grip M, Guénel P, Guo Q, Haiman CA, Håkansson N, Hamann U, Harrington PA, Hiller L, Hooning MJ, Hopper JL, Howell A, Huang CS, Huang G, Hunter DJ, Jakubowska A, John EM, Kaaks R, Kapoor PM, Keeman R, Kitahara CM, Koppert LB, Kraft P, Kristensen VN, Lambrechts D, Le Marchand L, Lejbkowicz F, Lindblom A, Lubiński J, Mannermaa A, Manoochehri M, Manoukian S, Margolin S, Martinez ME, Maurer T, Mavroudis D, Meindl A, Milne RL, Mulligan AM, Neuhausen SL, Nevanlinna H, Newman WG, Olshan AF, Olson JE, Olsson H, Orr N, Peterlongo P, Petridis C, Prentice RL, Presneau N, Punie K, Ramachandran D, Rennert G, Romero A, Sachchithananthan M, Saloustros E, Sawyer EJ, Schmutzler RK, Schwentner L, Scott C, Simard J, Sohn C, Southey MC, Swerdlow AJ, Tamimi RM, Tapper WJ, Teixeira MR, Terry MB, Thorne H, Tollenaar RAEM, Tomlinson I, Troester MA, Truong T, Turnbull C, Vachon CM, van der Kolk LE, Wang Q, Winqvist R, Wolk A, Yang XR, Ziogas A, Pharoah PDP, Hall P, Wessels LFA, Chenevix-Trench G, Bader GD, Dörk T, Easton DF, Canisius S, Schmidt MK <a class="https" href="https://www.nature.com/articles/s41467-019-14100-6">Nat Commun. 2020 Jan 16;11(1):312</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31949161">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatComm_Jan2020.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Pathway Commons 2019 Update: integration, analysis and exploration of pathway data Rodchenkov I, Babur O, Luna A, Aksoy BA, Wong JV, Fong D, Franz M, Siper MC, Cheung M, Wrana M, Mistry H, Mosier L, Dlin J, Wen Q, O'Callaghan C, Li W, Elder G, Smith PT, Dallago C, Cerami E, Gross B, Dogrusoz U, Demir E, Bader GD, Sander C <a class="https" href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz946/5606621">Nucleic Acids Res. 2020 Jan 8</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31647099">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NucAcid_Oct2019.pdf" title="PDF">PDF</a> PATHWAY DATABASE </li></ol> <h2 id="A2019">2019</h2> <ol type="1"><li>End-to-end Named Entity Recognition and Relation Extraction using Pre-trained Language Models John Giorgi, Xindi Wang, Nicola Sahar, Won Young Shin, Gary D. Bader, Bo Wang <a class="https" href="https://arxiv.org/abs/1912.13415">arXiv. 2019 Dec 20</a> <a class="https" href="https://arxiv.org/abs/1912.13415">arXiv</a> - <a class="https" href="https://arxiv.org/pdf/1912.13415">PDF</a> NATURAL LANGUAGE PROCESSING </li><li>Sphingolipid Modulation Activates Proteostasis Programs to Govern Human Hematopoietic Stem Cell Self-Renewal Xie SZ, Garcia-Prat L, Voisin V, Ferrari R, Gan OI, Wagenblast E, Kaufmann KB, Zeng AGX, Takayanagi SI, Patel I, Lee EK, Jargstorf J, Holmes G, Romm G, Pan K, Shoong M, Vedi A, Luberto C, Minden MD, Bader GD, Laurenti E, Dick JE <a class="https" href="https://www.sciencedirect.com/science/article/pii/S1934590919303935">Cell Stem Cell. 2019 Oct 11</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31631013">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=stemcell_Oct2019.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Single-cell transcriptomic profiling of the aging mouse brain Ximerakis M, Lipnick SL, Innes BT, Simmons SK, Adiconis X, Dionne D, Mayweather BA, Nguyen L, Niziolek Z, Ozek C, Butty VL, Isserlin R, Buchanan SM, Levine SS, Regev A, Bader GD, Levin JZ, Rubin LL <a class="https" href="https://www.nature.com/articles/s41593-019-0491-3">Nat Neurosci. 2019 Oct;22(10):1696-1708</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31551601">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=iNatneuro_Oct2019.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/10.1101/440032v1"><img alt="https://www.biorxiv.org/content/10.1101/440032v1" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://www.biorxiv.org/content/10.1101/440032v1" width="50" /></a> SINGLE CELL GENOMICS </li><li class="gap">Rewiring of the Human Mitochondrial Interactome during Neuronal Reprogramming Reveals Regulators of the Respirasome and Neurogenesis Moutaoufik MT, Malty R, Amin S, Zhang Q, Phanse S, Gagarinova A, Zilocchi M, Hoell L, Minic Z, Gagarinova M, Aoki H, Stockwell J, Jessulat M, Goebels F, Broderick K, Scott NE, Vlasblom J, Musso G, Prasad B, Lamantea E, Garavaglia B, Rajput A, Murayama K, Okazaki Y, Foster LJ, Bader GD, Cayabyab FS, Babu M <a class="https" href="https://www.sciencedirect.com/science/article/pii/S2589004219303360">iScience. 2019 Sep 4;19:1114-1132</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31536960">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=iScience_Sept2019.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Benchmarking to the Gold Standard: Hyaluronan-Oxime Hydrogels Recapitulate Xenograft Models with In Vitro Breast Cancer Spheroid Culture Baker AEG, Bahlmann LC, Tam RY, Liu JC, Ganesh AN, Mitrousis N, Marcellus R, Spears M, Bartlett JMS, Cescon DW, Bader GD, Shoichet MS <a class="https" href="https://onlinelibrary.wiley.com/doi/full/10.1002/adma.201901166">Adv Mater. 2019 Jul 19;31(36)</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31322299">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=AdvMater_July2019.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">EPIC: software toolkit for elution profile-based inference of protein complexes Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A <a class="https" href="https://www.nature.com/articles/s41592-019-0461-4">Nat Methods. 2019 July 15</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31308550">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureMethod_July2019.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019 Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. J <a class="https" href="https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2019-0035/jib-2019-0035.xml?format=INT">Integr Bioinform. 2019 Jul 13</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31301675">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=InteBioinfo_July2019.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap">Towards reliable named entity recognition in the biomedical domain Giorgi JM, Bader GD <a class="https" href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz504/5520946">Bioinformatics. 2019 Jun 20</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31218364">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Bioinfo_June2019.pdf" title="PDF">PDF</a> TEXT MINING </li><li class="gap">Bmi1 regulates human glioblastoma stem cells through activation of differential gene networks in CD133+ brain tumor initiating cells Vora P, Seyfrid M, Venugopal C, Qazi MA, Salim S, Isserlin R, Subapanditha M, O'Farrell E, Mahendram S, Singh M, Bakhshinyan D, Chokshi C, McFarlane N, Dvorkin-Gheva A, Brown KR, Murty N, Moffat J, Bader GD, Singh SK <a class="https" href="https://link.springer.com/article/10.1007/s11060-019-03192-1">J Neurooncol. 2019 May 21</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31115870">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=JNeruor_May2019.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">The Mitochondrial Transacylase, Tafazzin, Regulates for AML Stemness by Modulating Intracellular Levels of Phospholipids Seneviratne AK, Xu M, Henao JJA, Fajardo VA, Hao Z, Voisin V, Xu GW, Hurren R, Kim S, <a class="nonexistent" href="/MacLean">MacLean</a> N, Wang X, Gronda M, Jeyaraju D, Jitkova Y, Ketela T, Mullokandov M, Sharon D, Thomas G, Chouinard-Watkins R, Hawley JR, Schafer C, Yau HL, Khuchua Z, Aman A, Al-Awar R, Gross A, Claypool SM, Bazinet R, Lupien M, Chan S, De Carvalho DD, Minden MD, Bader GD, Stark KD, <a class="nonexistent" href="/LeBlanc">LeBlanc</a> P, Schimmer AD <a class="https" href="https://www.cell.com/cell-stem-cell/pdfExtended/S1934-5909(19)30072-4">Cell Stem Cell. 2019 Mar 19</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30930145">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=Cellstem_April2019.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Exploring targets of TET2-mediated methylation reprogramming as potential discriminators of prostate cancer progression Kamdar S, Isserlin R, Van der Kwast T, Zlotta AR, Bader GD, Fleshner NE, Bapat B <a class="https" href="https://clinicalepigeneticsjournal.biomedcentral.com/articles/10.1186/s13148-019-0651-z">Clin Epigenetics. 2019 Mar 27;11(1):54</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30917865">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=ClinEpi_Mar2019.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">netDx: interpretable patient classification using integrated patient similarity networks Pai S, Hui S, Isserlin R, Shah MA, Kaka H, Bader GD <a class="http" href="http://msb.embopress.org/content/15/3/e8497.long">Mol Syst Biol. 2019 Mar 14;15(3):e8497</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30872331">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=MSB_Mar2019.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/10.1101/084418v4"><img alt="https://www.biorxiv.org/content/10.1101/084418v4" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://www.biorxiv.org/content/10.1101/084418v4" width="50" /></a> PRECISION MEDICINE </li><li class="gap">Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data. Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH <a class="https" href="https://f1000research.com/articles/8-296">F1000Res. 2019 Mar 15;8. pii: ISCB Comm J-296</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31508207">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=f1000_Mar2019.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Powerful gene set analysis in GWAS with the Generalized Berk-Jones statistic Sun R, Hui S, Bader GD, Lin X, Kraft P <a class="https" href="https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007530">PLoS Genet. 2019 Mar 15;15(3)</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30875371">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=PlosGenet_Mar2019.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap"> Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap Reimand J, Isserlin R, Voisin V, Kucera M, Tannus-Lopes C, Rostamianfar A, Wadi L, Meyer M, Wong J, Xu C, Merico D, Bader GD <a class="https" href="https://www.nature.com/articles/s41596-018-0103-9">Nat Protoc. 2019 Feb;14(2):482-517</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30664679">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatProt_Jan2019.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/early/2017/12/12/232835"><img alt="https://www.biorxiv.org/content/early/2017/12/12/232835" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://www.biorxiv.org/content/early/2017/12/12/232835" width="50" /></a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">ARGLU1 is a transcriptional coactivator and splicing regulator important for stress hormone signaling and development Magomedova L, Tiefenbach J, Zilberman E, Le Billan F, Voisin V, Saikali M, Boivin V, Robitaille M, Gueroussov S, Irimia M, Ray D, Patel R, Xu C, Jeyasuria P, Bader GD, Hughes TR, Morris QD, Scott MS, Krause H, Angers S, Blencowe BJ, Cummins CL <a class="https" href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkz010/5304305">Nucleic Acids Res. 2019 Jan 30</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30698747">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=NucleicAcids_Jan2019.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2018">2018</h2> <ol type="1"><li>Induction of rod versus cone photoreceptor-specific progenitors from retinal precursor cells Khalili S, Ballios BG, Belair-Hickey J, Donaldson L, Liu J, Coles BLK, Grisé KN, Baakdhah T, Bader GD, Wallace VA, Bernier G, Shoichet MS, van der Kooy D <a class="https" href="https://www.sciencedirect.com/science/article/pii/S1873506118302733">Stem Cell Res. 2018 Nov 13;33:215-227</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30453152">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=Stemcell_Nov2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">The Relative Contributions of Cell-Dependent Cortical Microcircuit Aging to Cognition and Anxiety Shukla R, Prevot TD, French L, Isserlin R, Rocco BR, Banasr M, Bader GD, Sibille E <a class="https" href="https://www.biologicalpsychiatryjournal.com/article/S0006-3223(18)31890-0/fulltext">Biol Psychiatry. 2018 Oct 5</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30446205">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=Psychiatry_Nov2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations MacParland SA, Liu, JC, Ma X, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares I, Gupta R, Cheng ML, Liu LY, Camat D, Chung SW, Seliga RK, Shao Z, Lee E, Ogawa S, Ogawa M, Wilson MD, Fish JE, Selzner M, Ghanekar A, Grant D, Greig P, Sapisochin G, Selzner N, Winegarden N, Adeyi O, Keller G, Bader GD, McGilvray ID <a class="https" href="https://www.nature.com/articles/s41467-018-06318-7">Nat Commun. 2018 Oct 22;9(1):4383</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/30348985">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureCom_Oct2018.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">scClustViz - Single-cell RNAseq cluster assessment and visualization Innes BT, Bader GD <a class="https" href="https://f1000research.com/articles/7-1522/v2">F1000Res. 2018 Sep 21;7</a> <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/31016009">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=f1000_April2019.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">The Human Cell Atlas White Paper Aviv Regev, Sarah Teichmann, Orit Rozenblatt-Rosen, Michael Stubbington, Kristin Ardlie, Ido Amit, Paola Arlotta, Gary Bader, Christophe Benoist, Moshe Biton, Bernd Bodenmiller, Benoit Bruneau, Peter Campbell, Mary Carmichael, Piero Carninci, Leslie Castelo-Soccio, Menna Clatworthy, Hans Clevers, Christian Conrad, Roland Eils, Jeremy Freeman, Lars Fugger, Berthold Goettgens, Daniel Graham, Anna Greka, Nir Hacohen, Muzlifah Haniffa, Ingo Helbig, Robert Heuckeroth, Sekar Kathiresan, Seung Kim, Allon Klein, Bartha Knoppers, Arnold Kriegstein, Eric Lander, Jane Lee, Ed Lein, Sten Linnarsson, Evan Macosko, Sonya MacParland, Robert Majovski, Partha Majumder, John Marioni, Ian McGilvray, Miriam Merad, Musa Mhlanga, Shalin Naik, Martijn Nawijn, Garry Nolan, Benedict Paten, Dana Pe'er, Anthony Philippakis, Chris Ponting, Steve Quake, Jayaraj Rajagopal, Nikolaus Rajewsky, Wolf Reik, Jennifer Rood, Kourosh Saeb-Parsy, Herbert Schiller, Steve Scott, Alex Shalek, Ehud Shapiro, Jay Shin, Kenneth Skeldon, Michael Stratton, Jenna Streicher, Henk Stunnenberg, Kai Tan, Deanne Taylor, Adrian Thorogood, Ludovic Vallier, Alexander van Oudenaarden, Fiona Watt, Wilko Weicher, Jonathan Weissman, Andrew Wells, Barbara Wold, Ramnik Xavier, Xiaowei Zhuang, Human Cell Atlas Organizing Committee <a class="https" href="https://arxiv.org/abs/1810.05192"><img alt="https://arxiv.org/abs/1810.05192" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://arxiv.org/abs/1810.05192" width="50" /></a>-<a class="attachment" href="/Publications?action=AttachFile&do=view&target=website_pdf.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS, PREPRINT </li><li class="gap">Single-Cell RNA Sequencing: A New Window into Cell Scale Dynamics Dasgupta S, Bader GD, Goyal S <a class="https" href="https://www.sciencedirect.com/science/article/pii/S0006349518307653">Biophys J. 2018 Aug 7;115(3):429-435</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/30033145">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=Biophyd_July2018.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">The Cytoscape Automation app article collection. Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. <a class="https" href="https://f1000research.com/articles/7-800/v1">F1000Res. 2018 Jun 20;7:800</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29983926">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=f1000_July2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities Casey AE, Sinha A, Singhania R, Livingstone J, Waterhouse P, Tharmapalan P,Cruickshank J, Shehata M, Drysdale E, Fang H, Kim H, Isserlin R, Bailey S, Medina T, Deblois G, Shiah YJ, Barsyte-Lovejoy D, Hofer S, Bader G, Lupien M, Arrowsmith C, Knapp S, De Carvalho D, Berman H, Boutros PC, Kislinger T, Khokha R <a class="http" href="http://jcb.rupress.org/content/early/2018/06/18/jcb.201804042">J Cell Biol. 2018 Jun 19</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29921600">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=JCB_June2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap"> GeneMANIA update 2018 Franz M, Rodriguez H, Lopes C, Zuberi K, Montojo J, Bader GD, Morris Q <a class="https" href="https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gky311/5038280">Nucleic Acids Res. 2018 Jun 15</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29912392">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=NAR_June2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Transfer learning for biomedical named entity recognition with neural networks Giorgi JM, Bader GD <a class="https" href="https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty449/5026661">Bioinformatics. 2018 Jun 1</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29868832">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=Bioinformatics_June2018.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/early/2018/02/12/262790"><img alt="https://www.biorxiv.org/content/early/2018/02/12/262790" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://www.biorxiv.org/content/early/2018/02/12/262790" width="50" /></a> </li><li class="gap">Patient Similarity Networks for Precision Medicine Pai S, Bader GD <a class="https" href="https://www.sciencedirect.com/science/article/pii/S0022283618305321">J Mol Biol. 2018 May 31</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29860027">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=JMB_June2018.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/early/2018/05/25/084418"><img alt="https://www.biorxiv.org/content/early/2018/05/25/084418" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://www.biorxiv.org/content/early/2018/05/25/084418" width="50" /></a> PRECISION MEDICINE </li><li class="gap">Identification of CDC25 as a Common Therapeutic Target for Triple-Negative Breast Cancer Liu JC, Granieri L, Shrestha M, Wang DY, Vorobieva I, Rubie EA, Jones R, Ju Y, Pellecchia G, Jiang Z, Palmerini CA, Ben-David Y, Egan SE, Woodgett JR, Bader GD, Datti A, Zacksenhaus E <a class="http" href="http://www.cell.com/cell-reports/fulltext/S2211-1247(18)30381-4?_returnURL=https://linkinghub.elsevier.com/retrieve/pii/S2211124718303814?showall=true">Cell Rep. 2018 Apr 3;23(1):112-126</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29617654">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=Cellrep_April2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017 Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D <a class="https" href="https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0013/jib-2018-0013.xml">J Integr Bioinform. 2018 Mar 29</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29596055">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=IntegrativeBio_April2018.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap">Whole transcriptome analysis reveals differential gene expression profile reflecting macrophage polarization in response to influenza A H5N1 virus infection Zhang N, Bao YJ, Tong AH, Zuyderduyn S, Bader GD, Malik Peiris JS, Lok S, Lee SM <a class="https" href="https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-018-0335-0">BMC Med Genomics. 2018 Feb 23;11(1):20</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29475453">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=BMC_medicalgenom_Feb2018.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2017">2017</h2> <ol type="1"><li>Developmental Emergence of Adult Neural Stem Cells as Revealed by Single-Cell Transcriptional Profiling Yuzwa SA, Borrett MJ, Innes BT, Voronova A, Ketela T, Kaplan DR, Bader GD, Miller FD <a class="http" href="http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31813-2">Cell Rep. 2017 Dec 26;21(13):3970-3986</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29281841">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellRe_December2017.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">A Map of Human Mitochondrial Protein Interactions Linked to Neurodegeneration Reveals New Mechanisms of Redox Homeostasis and NF-κB Signaling Malty RH, Aoki H, Kumar A, Phanse S, Amin S, Zhang Q, Minic Z, Goebels F, Musso G, Wu Z, Abou-Tok H, Meyer M, Deineko V, Kassir S, Sidhu V, Jessulat M, Scott NE, Xiong X, Vlasblom J, Prasad B, Foster LJ, Alberio T, Garavaglia B, Yu H, Bader GD, Nakamura K, Parkinson J, Babu M <a class="http" href="http://www.cell.com/cell-systems/fulltext/S2405-4712(17)30447-7">Cell Syst. 2017 Nov 7. pii:S2405-4712(17)30447-7</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29128334">PubMed Abstract</a> -<a class="attachment nonexistent" href="/Publications?action=AttachFile&do=upload_form&ticket=0067b6db71.0b6db5bcfc7bdb3fbe365a002b413a77f6f00035&target=Cell_November2017.pdf" title="Upload new attachment "Cell_November2017.pdf"">PDF</a> </li><li class="gap">Association analysis identifies 65 new breast cancer risk loci Michailidou K, Lindström S, Dennis J, Beesley J, Hui S, Kar S, Lemaçon A,Soucy P, Glubb D, Rostamianfar A, Bolla MK, Wang Q, Tyrer J, Dicks E, Lee A, Wang Z, Allen J, Keeman R, Eilber U, French JD, Qing Chen X, Fachal L, McCue K, McCart Reed AE, Ghoussaini M, Carroll JS, Jiang X, Finucane H, Adams M, Adank MA, Ahsan H, Aittomäki K, Anton-Culver H, Antonenkova NN, Arndt V, Aronson KJ, Arun B, Auer PL, Bacot F, Barrdahl M, Baynes C, Beckmann MW, Behrens S, Benitez J, Bermisheva M, Bernstein L, Blomqvist C, Bogdanova NV, Bojesen SE, Bonanni B, Børresen-Dale AL, Brand JS, Brauch H, Brennan P, Brenner H, Brinton L, Broberg P, Brock IW, Broeks A, Brooks-Wilson A, Brucker SY, Brüning T, Burwinkel B, Butterbach K, Cai Q, Cai H, Caldés T, Canzian F, Carracedo A, Carter BD, Castelao JE, Chan TL, David Cheng TY, Seng Chia K, Choi JY, Christiansen H, Clarke CL; NBCS Collaborators, Collée M, Conroy DM, Cordina-Duverger E, Cornelissen S, Cox DG, Cox A, Cross SS, Cunningham JM, Czene K, Daly MB, Devilee P, Doheny KF, Dörk T, Dos-Santos-Silva I, Dumont M, Durcan L, Dwek M, Eccles DM, Ekici AB, Eliassen AH, Ellberg C, Elvira M, Engel C, Eriksson M, Fasching PA, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Fritschi L, Gaborieau V, Gabrielson M, Gago-Dominguez M, Gao YT, Gapstur SM, García-Sáenz JA, Gaudet MM, Georgoulias V, Giles GG, Glendon G, Goldberg MS, Goldgar DE, González-Neira A, Grenaker Alnæs GI, Grip M, Gronwald J, Grundy A, Guénel P, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hamann U, Hamel N, Hankinson S, Harrington P, Hart SN, Hartikainen JM, Hartman M, Hein A, Heyworth J, Hicks B, Hillemanns P, Ho DN, Hollestelle A, Hooning MJ, Hoover RN, Hopper JL, Hou MF, Hsiung CN, Huang G, Humphreys K, Ishiguro J, Ito H, Iwasaki M, Iwata H, Jakubowska A, Janni W, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kasuga Y, Kerin MJ, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Kosma VM, Kristensen VN, Krüger U, Kwong A, Lambrechts D, Le Marchand L, Lee E, Lee MH, Lee JW, Neng Lee C, Lejbkowicz F, Li J, Lilyquist J, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Lophatananon A, Lubinski J, Luccarini C, Lux MP, Ma ESK, MacInnis RJ, Maishman T, Makalic E, Malone KE, Kostovska IM, Mannermaa A, Manoukian S, Manson JE, Margolin S, Mariapun S, Martinez ME, Matsuo K, Mavroudis D, McKay J, McLean C, Meijers-Heijboer H, Meindl A, Menéndez P, Menon U, Meyer J, Miao H, Miller N,Taib NAM, Muir K, Mulligan AM, Mulot C, Neuhausen SL, Nevanlinna H, Neven P, Nielsen SF, Noh DY, Nordestgaard BG, Norman A, Olopade OI, Olson JE, Olsson H, Olswold C, Orr N, Pankratz VS, Park SK, Park-Simon TW, Lloyd R, Perez JIA, Peterlongo P, Peto J, Phillips KA, Pinchev M, Plaseska-Karanfilska D, Prentice R, Presneau N, Prokofyeva D, Pugh E, Pylkäs K, Rack B, Radice P, Rahman N, Rennert G, Rennert HS, Rhenius V, Romero A, Romm J, Ruddy KJ, Rüdiger T, Rudolph A, Ruebner M, Rutgers EJT, Saloustros E, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schmutzler RK, Schneeweiss A, Schoemaker MJ, Schumacher F, Schürmann P, Scott RJ, Scott C, Seal S, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng G, Sherman ME, Shrubsole MJ, Shu XO, Smeets A, Sohn C, Southey MC, Spinelli JJ, Stegmaier C, Stewart-Brown S, Stone J, Stram DO, Surowy H, Swerdlow A, Tamimi R, Taylor JA, Tengström M, Teo SH, Beth Terry M, Tessier DC, Thanasitthichai S, Thöne K, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Truong T, Tseng CC, Tsugane S, Ulmer HU, Ursin G, Untch M, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van der Kolk L, van der Luijt RB, Vincent D, Vollenweider J, Waisfisz Q, Wang-Gohrke S, Weinberg CR, Wendt C, Whittemore AS, Wildiers H, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yamaji T, Yang XR, Har Yip C, Yoo KY, Yu JC, Zheng W, Zheng Y, Zhu B, Ziogas A, Ziv E; ABCTB Investigators; ConFab/AOCS Investigators, Lakhani SR, Antoniou AC, Droit A, Andrulis IL, Amos CI, Couch FJ, Pharoah PDP, Chang-Claude J, Hall P, Hunter DJ, Milne RL, García-Closas M, Schmidt MK, Chanock SJ, Dunning AM, Edwards SL, Bader GD, Chenevix-Trench G, Simard J, Kraft P, Easton DF <a class="http" href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature24284.html">Nature. 2017 Oct 23</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29059683">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nature_October2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer Milne RL, Kuchenbaecker KB, Michailidou K, Beesley J, Kar S, Lindström S, Hui S, Lemaçon A, Soucy P, Dennis J, Jiang X, Rostamianfar A, Finucane H, Bolla MK, McGuffog L, Wang Q, Aalfs CM; ABCTB Investigators, Adams M, Adlard J, Agata S, Ahmed S, Ahsan H, Aittomäki K, Al-Ejeh F, Allen J, Ambrosone CB, Amos CI, Andrulis IL, Anton-Culver H, Antonenkova NN, Arndt V, Arnold N, Aronson KJ, Auber B, Auer PL, Ausems MGEM, Azzollini J, Bacot F, Balmaña J, Barile M, Barjhoux L, Barkardottir RB, Barrdahl M, Barnes D, Barrowdale D, Baynes C, Beckmann MW, Benitez J, Bermisheva M, Bernstein L, Bignon YJ, Blazer KR, Blok MJ, Blomqvist C, Blot W, Bobolis K, Boeckx B, Bogdanova NV, Bojesen A, Bojesen SE, Bonanni B, Børresen-Dale AL, Bozsik A, Bradbury AR, Brand JS, Brauch H, Brenner H, Bressac-de Paillerets B, Brewer C, Brinton L, Broberg P, Brooks-Wilson A, Brunet J, Brüning T, Burwinkel B, Buys SS, Byun J, Cai Q, Caldés T, Caligo MA, Campbell I, Canzian F, Caron O, Carracedo A, Carter BD, Castelao JE, Castera L, Caux-Moncoutier V, Chan SB, Chang-Claude J, Chanock SJ, Chen X, Cheng TD, Chiquette J, Christiansen H, Claes KBM, Clarke CL, Conner T, Conroy DM, Cook J, Cordina-Duverger E, Cornelissen S, Coupier I, Cox A, Cox DG, Cross SS, Cuk K, Cunningham JM, Czene K, Daly MB, Damiola F, Darabi H, Davidson R, De Leeneer K, Devilee P, Dicks E, Diez O, Ding YC, Ditsch N, Doheny KF, Domchek SM, Dorfling CM, Dörk T, Dos-Santos-Silva I, Dubois S, Dugué PA, Dumont M, Dunning AM, Durcan L, Dwek M, Dworniczak B, Eccles D, Eeles R, Ehrencrona H, Eilber U, Ejlertsen B, Ekici AB, Eliassen AH; EMBRACE, Engel C, Eriksson M, Fachal L, Faivre L, Fasching PA, Faust U, Figueroa J, Flesch-Janys D, Fletcher O, Flyger H, Foulkes WD, Friedman E, Fritschi L, Frost D, Gabrielson M, Gaddam P, Gammon MD, Ganz PA, Gapstur SM, Garber J, Garcia-Barberan V, García-Sáenz JA, Gaudet MM, Gauthier-Villars M, Gehrig A; GEMO Study Collaborators, Georgoulias V, Gerdes AM, Giles GG, Glendon G, Godwin AK, Goldberg MS, Goldgar DE, González-Neira A, Goodfellow P, Greene MH, Alnæs GIG, Grip M, Gronwald J, Grundy A, Gschwantler-Kaulich D, Guénel P, Guo Q, Haeberle L, Hahnen E, Haiman CA, Håkansson N, Hallberg E, Hamann U, Hamel N, Hankinson S, Hansen TVO, Harrington P, Hart SN, Hartikainen JM, Healey CS; HEBON, Hein A, Helbig S, Henderson A, Heyworth J, Hicks B, Hillemanns P, Hodgson S, Hogervorst FB, Hollestelle A, Hooning MJ, Hoover B, Hopper JL, Hu C, Huang G, Hulick PJ, Humphreys K, Hunter DJ, Imyanitov EN, Isaacs C, Iwasaki M, Izatt L, Jakubowska A, James P, Janavicius R, Janni W, Jensen UB, John EM, Johnson N, Jones K, Jones M, Jukkola-Vuorinen A, Kaaks R, Kabisch M, Kaczmarek K, Kang D, Kast K; kConFab/AOCS Investigators, Keeman R, Kerin MJ, Kets CM, Keupers M, Khan S, Khusnutdinova E, Kiiski JI, Kim SW, Knight JA, Konstantopoulou I, Kosma VM, Kristensen VN, Kruse TA, Kwong A, Lænkholm AV, Laitman Y, Lalloo F, Lambrechts D, Landsman K, Lasset C, Lazaro C, Le Marchand L, Lecarpentier J, Lee A, Lee E, Lee JW, Lee MH, Lejbkowicz F, Lesueur F, Li J, Lilyquist J, Lincoln A, Lindblom A, Lissowska J, Lo WY, Loibl S, Long J, Loud JT, Lubinski J, Luccarini C, Lush M, MacInnis RJ, Maishman T, Makalic E, Kostovska IM, Malone KE, Manoukian S, Manson JE, Margolin S, Martens JWM, Martinez ME, Matsuo K, Mavroudis D, Mazoyer S, McLean C, Meijers-Heijboer H, Menéndez P, Meyer J, Miao H, Miller A, Miller N, Mitchell G, Montagna M, Muir K, Mulligan AM, Mulot C, Nadesan S, Nathanson KL; NBSC Collaborators, Neuhausen SL, Nevanlinna H, Nevelsteen I, Niederacher D, Nielsen SF, Nordestgaard BG, Norman A, Nussbaum RL, Olah E, Olopade OI, Olson JE, Olswold C, Ong KR, Oosterwijk JC, Orr N, Osorio A, Pankratz VS, Papi L, Park-Simon TW, Paulsson-Karlsson Y, Lloyd R,Pedersen IS, Peissel B, Peixoto A, Perez JIA, Peterlongo P, Peto J, Pfeiler G,Phelan CM, Pinchev M, Plaseska-Karanfilska D, Poppe B, Porteous ME, Prentice R, Presneau N, Prokofieva D, Pugh E, Pujana MA, Pylkäs K, Rack B, Radice P, Rahman N, Rantala J, Rappaport-Fuerhauser C, Rennert G, Rennert HS, Rhenius V, Rhiem K, Richardson A, Rodriguez GC, Romero A, Romm J, Rookus MA, Rudolph A, Ruediger T,Saloustros E, Sanders J, Sandler DP, Sangrajrang S, Sawyer EJ, Schmidt DF, Schoemaker MJ, Schumacher F, Schürmann P, Schwentner L, Scott C, Scott RJ, Seal S, Senter L, Seynaeve C, Shah M, Sharma P, Shen CY, Sheng X, Shimelis H,Shrubsole MJ, Shu XO, Side LE, Singer CF, Sohn C, Southey MC, Spinelli JJ, Spurdle AB, Stegmaier C, Stoppa-Lyonnet D, Sukiennicki G, Surowy H, Sutter C, Swerdlow A, Szabo CI, Tamimi RM, Tan YY, Taylor JA, Tejada MI, Tengström M, Teo SH, Terry MB, Tessier DC, Teulé A, Thöne K, Thull DL, Tibiletti MG, Tihomirova L, Tischkowitz M, Toland AE, Tollenaar RAEM, Tomlinson I, Tong L, Torres D, Tranchant M, Truong T, Tucker K, Tung N, Tyrer J, Ulmer HU, Vachon C, van Asperen CJ, Van Den Berg D, van den Ouweland AMW, van Rensburg EJ, Varesco L, Varon-Mateeva R, Vega A, Viel A, Vijai J, Vincent D, Vollenweider J, Walker L, Wang Z, Wang-Gohrke S, Wappenschmidt B, Weinberg CR, Weitzel JN, Wendt C, Wesseling J, Whittemore AS, Wijnen JT, Willett W, Winqvist R, Wolk A, Wu AH, Xia L, Yang XR, Yannoukakos D, Zaffaroni D, Zheng W, Zhu B, Ziogas A, Ziv E, Zorn KK, Gago-Dominguez M, Mannermaa A, Olsson H, Teixeira MR, Stone J, Offit K, Ottini L, Park SK, Thomassen M, Hall P, Meindl A, Schmutzler RK, Droit A, Bader GD, Pharoah PDP, Couch FJ, Easton DF, Kraft P, Chenevix-Trench G, García-Closas M, Schmidt MK, Antoniou AC, Simard J <a class="https" href="https://www.nature.com/articles/ng.3785">Nat Genet. 2017 Oct 23</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/29058716">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureGenetics_Octoboer2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Comprehensive Analysis of the Human SH3 Domain Family Reveals a Wide Variety of Non-canonical Specificities Teyra J, Huang H, Jain S, Guan X, Dong A, Liu Y, Tempel W, Min J, Tong Y, Kim PM, Bader GD, Sidhu SS <a class="http" href="http://www.cell.com/structure/abstract/S0969-2126(17)30251-4">Structure. 2017 Aug 28. S0969-2126(17)30251-4</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28890361">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Structure_September2017.pdf" title="PDF">PDF</a> PROTEIN INTERACTION </li><li class="gap">microRNA-143/145 loss induces Ras signaling to promote aggressive Pten-deficient basal-like breast cancer Wang S, Liu JC, Ju Y, Pellecchia G, Voisin V, Wang DY, Leha L R, Ben-David Y, Bader GD, Zacksenhaus E <a class="https" href="https://insight.jci.org/articles/view/93313">JCI Insight. 2017 Aug 3;2(15)</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28768903">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=JCI_August2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">ASCL1 Reorganizes Chromatin to Direct Neuronal Fate and Suppress Tumorigenicity of Glioblastoma Stem Cells Park NI, Guilhamon P, Desai K, <a class="nonexistent" href="/McAdam">McAdam</a> RF, Langille E, O'Connor M, Lan X,Whetstone H, Coutinho FJ, Vanner RJ, Ling E, Prinos P, Lee L, Selvadurai H, Atwal G, Kushida M, Clarke ID, Voisin V, Cusimano MD, Bernstein M, Das S, Bader G, Arrowsmith CH, Angers S, Huang X, Lupien M, Dirks PB <a class="http" href="http://www.cell.com/cell-stem-cell/fulltext/S1934-5909(17)30230-8">Cell Stem Cell. 2017 Aug 3;21(2):209-224</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28712938">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Cell_July2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Tracing the origins of relapse in acute myeloid leukaemia to stem cells Shlush LI, Mitchell A, Heisler L, Abelson S, Ng SWK, Trotman-Grant A, Medeiros JJF, Rao-Bhatia A, Jaciw-Zurakowsky I, Marke R, <a class="nonexistent" href="/McLeod">McLeod</a> JL, Doedens M, Bader G, Voisin V, Xu C, <a class="nonexistent" href="/McPherson">McPherson</a> JD, Hudson TJ, Wang JCY, Minden MD, Dick JE <a class="https" href="https://www.nature.com/nature/journal/v547/n7661/full/nature22993.html">Nature. 2017 Jul 6;547(7661):104-108</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28658204">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nature_July2017.pdf" title="PDF">PDF</a> </li><li class="gap">Intertumoral Heterogeneity within Medulloblastoma Subgroups Cavalli FMG, Remke M, Rampasek L, Peacock J, Shih DJH, Luu B, Garzia L,Torchia J, Nor C, Morrissy AS, Agnihotri S, Thompson YY, Kuzan-Fischer CM, Farooq H, Isaev K, Daniels C, Cho BK, Kim SK, Wang KC, Lee JY, Grajkowska WA, Perek-Polnik M, Vasiljevic A, Faure-Conter C, Jouvet A, Giannini C, Nageswara Rao AA, Li KKW, Ng HK, Eberhart CG, Pollack IF, Hamilton RL, Gillespie GY, Olson JM, Leary S, Weiss WA, Lach B, Chambless LB, Thompson RC, Cooper MK, Vibhakar R, Hauser P, van Veelen MC, Kros JM, French PJ, Ra YS, Kumabe T, López-Aguilar E, Zitterbart K, Sterba J, Finocchiaro G, Massimino M, Van Meir EG, Osuka S, Shofuda T, Klekner A, Zollo M, Leonard JR, Rubin JB, Jabado N, Albrecht S, Mora J, Van Meter TE, Jung S, Moore AS, Hallahan AR, Chan JA, Tirapelli DPC, Carlotti CG, Fouladi M, Pimentel J, Faria CC, Saad AG, Massimi L, Liau LM, Wheeler H, Nakamura H, Elbabaa SK, Perezpeña-Diazconti M, Chico Ponce de León F, Robinson S, Zapotocky M, Lassaletta A, Huang A, Hawkins CE, Tabori U, Bouffet E, Bartels U, Dirks PB, Rutka JT, Bader GD, Reimand J, Goldenberg A, Ramaswamy V, Taylor MD <a class="http" href="http://www.cell.com/cancer-cell/abstract/S1535-6108(17)30201-5">Cancer Cell. 2017 Jun 12;31(6):737-754</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28609654">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerCell_June2017.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Spatial heterogeneity in medulloblastoma Morrissy AS, Cavalli FM, Remke M, Ramaswamy V, Shih DJ, Holgado BL, Farooq H, Donovan LK, Garzia L, Agnihotri S, Kiehna EN, Mercier E, Mayoh C, Papillon-Cavanagh S, Nikbakht H, Gayden T, Torchia J, Picard D, Merino DM, Vladoiu M, Luu B, Wu X, Daniels C, Horswell S, Thompson YY, Hovestadt V, Northcott PA, Jones DT, Peacock J, Wang X, Mack SC, Reimand J, Albrecht S, Fontebasso AM, Thiessen N, Li Y, Schein JE, Lee D, Carlsen R, Mayo M, Tse K, Tam A, Dhalla N, Ally A, Chuah E, Cheng Y, Plettner P, Li HI, Corbett RD, Wong T, Long W, Loukides J, Buczkowicz P, Hawkins CE, Tabori U, Rood BR, Myseros JS, Packer RJ, Korshunov A, Lichter P, Kool M, Pfister SM, Schüller U, Dirks P, Huang A, Bouffet E, Rutka JT, Bader GD, Swanton C, Ma Y, Moore RA, Mungall AJ, Majewski J, Jones SJ, Das S, Malkin D, Jabado N, Marra MA, Taylor MD <a class="http" href="http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3838.html">Nat Genet. 2017 Apr 10</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28394352">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureGenetics_April2017.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Integrative cancer pharmacogenomics to infer large-scale drug taxonomy El-Hachem N, Gendoo DM, Soltan Ghoraie L, Safikhani Z, Smirnov P, Chung C, Deng K, Fang A, Birkwood E, Ho C, Isserlin R, Bader G, Goldenberg A, Haibe-Kains B <a class="http" href="http://cancerres.aacrjournals.org/content/early/2017/03/17/0008-5472.CAN-17-0096.long">Cancer Res. 2017 Mar 17</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28314784">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerResearch_March2017.pdf" title="PDF">PDF</a> <a class="https" href="https://www.biorxiv.org/content/early/2017/01/05/046219"><img alt="https://www.biorxiv.org/content/early/2017/01/05/046219" class="attachment" src="/Publications?action=AttachFile&do=get&target=bioarxiv.png" title="https://www.biorxiv.org/content/early/2017/01/05/046219" width="50" /></a> NETWORK ANALYSIS </li><li class="gap">Leveraging increased cytoplasmic nucleoside kinase activity to target mtDNA and oxidative phosphorylation in AML Liyanage SU, Hurren R, Voisin V, Bridon G, Wang X, Xu C, MacLean N, Siriwardena TP, Gronda M, Yehudai D, Sriskanthadevan S, Avizonis D, Shamas-Din A, Minden MD, Bader GD, Laposa R, Schimmer AD <a class="http" href="http://www.bloodjournal.org/content/early/2017/03/10/blood-2016-10-741207.long?sso-checked=true">Blood. 2017 Mar 10</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28283480">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Blood_March2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Integrated analysis of proteome, phosphotyrosine-proteome, tyrosine-kinome and tyrosine-phosphatome in acute myeloid leukemia Tong J, Helmy M, Cavalli FM, Jin L, St-Germain J, Karisch R, Taylor P, Minden MD, Taylor MD, Neel BG, Bader GD, Moran MF <a class="http" href="http://onlinelibrary.wiley.com/doi/10.1002/pmic.201600361/full">Proteomics. 2017 Feb 7.</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28176486">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=proteomics_Feb2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2016">2016</h2> <ol type="1"><li>Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016 Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Le Novère N, Myers C, Nickerson D, Sommer B, Walthemath D <a class="http" href="http://journal.imbio.de/article.php?aid=289">J Integr Bioinform. 2016 Dec 18;13(3):289</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28187405">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=integerbioinfo_Feb2017.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap">Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DM, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, <a class="nonexistent" href="/McGlade">McGlade</a> CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N,Huang A <a class="http" href="http://www.cell.com/cancer-cell/fulltext/S1535-6108(16)30509-8">Cancer Cell. 2016 Dec 12;30(6):891-908</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27960086">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=cancercell_Dec2016.pdf" title="PDF">PDF</a> </li><li class="gap">Global neuroscience and mental health research: a bibliometrics case study Buchan AMJ, Jurczyk E, Isserlin R, Bader GD <a class="https" href="https://link.springer.com/article/10.1007/s11192-016-2094-z">Scientometrics 109 (1), 515-531</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Scientometrics_Oct2016.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">AutoAnnotate: A Cytoscape app for summarizing networks with semantic annotations Kucera M, Isserlin R, Arkhangorodsky A, Bader GD <a class="https" href="https://f1000research.com/articles/5-1717/v1">F1000Res. 2016 Jul 15;5:1717</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27830058">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=F1000Nov2016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Ten Simple Rules for Developing Public Biological Databases Helmy M, Crits-Christoph A, Bader GD <a class="http" href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005128">PLoS Comput Biol. 2016 Nov 10;12(11)</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27832061">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=CompBioNov2016.pdf" title="PDF">PDF</a> </li><li class="gap">RB1 deficiency in triple-negative breast cancer induces mitochondrial protein translation Jones RA, Robinson TJ, Liu JC, Shrestha M, Voisin V, Ju Y, Chung PE, Pellecchia G, Fell VL, Bae S, Muthuswamy L, Datti A, Egan SE, Jiang Z, Leone G, Bader GD, Schimmer A, Zacksenhaus E <a class="https" href="https://www.jci.org/articles/view/81568">J Clin Invest. 2016 Aug 29</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27571409">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=ClinInvestAug20162016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Ectopic miR-125a Expression Induces Long-Term Repopulating Stem Cell Capacity in Mouse and Human Hematopoietic Progenitors Wojtowicz EE, Lechman ER, Hermans KG, Schoof EM, Wienholds E, Isserlin R, van Veelen PA, Broekhuis MJ, Janssen GM, Trotman-Grant A, Dobson SM, Krivdova G, Elzinga J, Kennedy J, Gan OI, Sinha A, Ignatchenko V, Kislinger T, Dethmers-Ausema B, Weersing E, Alemdehy MF, de Looper HW, Bader GD, Ritsema M, Erkeland SJ, Bystrykh LV, Dick JE, de Haan G <a class="http" href="http://www.cell.com/cell-stem-cell/abstract/S1934-5909(16)30158-8">Cell Stem Cell. 2016 Jul 12. pii: S1934-5909(16)30158-8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27424784">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=StemCellJuly2016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Transcriptomic analysis reveals abnormal muscle repair and remodeling in survivors of critical illness with sustained weakness Walsh CJ, Batt J, Herridge MS, Mathur S, Bader GD, Hu P, Dos Santos CC <a class="http" href="http://www.nature.com/articles/srep29334">Sci Rep. 2016 Jul 14;6:29334</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27411715">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=ScirepJuly2016.pdf" title="PDF">PDF</a> </li><li class="gap">Inhibition of Dopamine Receptor D4 Impedes Autophagic Flux, Proliferation, and Survival of Glioblastoma Stem Cells Dolma S, Selvadurai HJ, Lan X, Lee L, Kushida M, Voisin V, Whetstone H, So M, Aviv T, Park N, Zhu X, Xu C, Head R, Rowland KJ, Bernstein M, Clarke ID, Bader G, Harrington L, Brumell JH, Tyers M, Dirks PB <a class="http" href="http://www.sciencedirect.com/science/article/pii/S1535610816302070">Cancer Cell. 2016 Jun 13;29(6):859-73</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27300435">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerCellJune2016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancer Narayan S, Bader GD, Reimand J <a class="http" href="http://genomemedicine.biomedcentral.com/articles/10.1186/s13073-016-0311-2">Genome Med. 2016 May 12;8(1):55</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27175787">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=GenomeMedMay2016.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Musashi-2 attenuates AHR signalling to expand human haematopoietic stem cells Rentas S, Holzapfel NT, Belew MS, Pratt GA, Voisin V, Wilhelm BT, Bader GD, Yeo GW, Hope KJ <a class="http" href="http://www.nature.com/nature/journal/v532/n7600/full/nature17665.html">Nature. 2016 Apr 28;532(7600):508-11</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27121842">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureApril2016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">HOX gene complement and expression in the planarian Schmidtea mediterranea Currie KW, Brown DD, Zhu S, Xu C, Voisin V, Bader GD, Pearson BJ <a class="http" href="http://evodevojournal.biomedcentral.com/articles/10.1186/s13227-016-0044-8">Evodevo. 2016 Mar 30;7:7</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/27034770">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=EvodevoMarch2016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Social Network: a Cytoscape app for visualizing co-authorship networks Kofia V, Isserlin R, Buchan AM, Bader GD <a class="http" href="http://f1000research.com/articles/10.12688/f1000research.6804.3/doi">F1000Res. 2015 Aug 5;4:481</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26949516">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=f1000March2016.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast Jain S, Bader GD <a class="http" href="http://bioinformatics.oxfordjournals.org/content/early/2016/02/09/bioinformatics.btw045.abstract">Bioinformatics. 2016 Feb 9</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26861823">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BioinfoFeb2016.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">miR-126 Regulates Distinct Self-Renewal Outcomes in Normal and Malignant Hematopoietic Stem Cells Lechman ER, Gentner B, Ng SW, Schoof EM, van Galen P, Kennedy JA, Nucera S, Ciceri F, Kaufmann KB, Takayama N, Dobson SM, Trotman-Grant A, Krivdova G, Elzinga J, Mitchell A, Nilsson B, Hermans KG, Eppert K, Marke R, Isserlin R, Voisin V, Bader GD, Zandstra PW, Golub TR, Ebert BL, Lu J, Minden M, Wang JC, Naldini L, Dick JE <a class="http" href="http://www.cell.com/cancer-cell/abstract/S1535-6108(15)00475-4">Cancer Cell. 2016 Apr 11;29(4):602-606</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26832662">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerCellFeb2016.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance Marcotte R, Sayad A, Brown KR, Sanchez-Garcia F, Reimand J, Haider M, Virtanen C, Bradner JE, Bader GD, Mills GB, Pe'er D, Moffat J, Neel BG <a class="http" href="http://www.cell.com/cell/abstract/S0092-8674(15)01624-4">Cell. 2016 Jan 14;164(1-2):293-309</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26771497">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CellJan2016.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Divergent clonal selection dominates medulloblastoma at recurrence Morrissy AS, Garzia L, Shih DJ, Zuyderduyn S, Huang X, Skowron P, Remke M, Cavalli FM, Ramaswamy V, Lindsay PE, Jelveh S, Donovan LK, Wang X, Luu B, Zayne K, Li Y, Mayoh C, Thiessen N, Mercier E, Mungall KL, Ma Y, Tse K, Zeng T, Shumansky K, Roth AJ, Shah S, Farooq H, Kijima N, Holgado BL, Lee JJ, Matan-Lithwick S, Liu J, Mack SC, Manno A, Michealraj KA, Nor C, Peacock J, Qin L, Reimand J, Rolider A, Thompson YY, Wu X, Pugh T, Ally A, Bilenky M, Butterfield YS, Carlsen R, Cheng Y, Chuah E, Corbett RD, Dhalla N, He A, Lee D, Li HI, Long W, Mayo M, Plettner P, Qian JQ, Schein JE, Tam A, Wong T, Birol I, Zhao Y, Faria CC, Pimentel J, Nunes S, Shalaby T, Grotzer M, Pollack IF, Hamilton RL, Li XN, Bendel AE, Fults DW, Walter AW, Kumabe T, Tominaga T, Collins VP, Cho YJ, Hoffman C, Lyden D, Wisoff JH, Garvin JH, Stearns DS, Massimi L, Schüller U, Sterba J, Zitterbart K, Puget S, Ayrault O, Dunn SE, Tirapelli DP, Carlotti CG, Wheeler H, Hallahan AR, Ingram W, <a class="nonexistent" href="/MacDonald">MacDonald</a> TJ, Olson JJ, Van Meir EG, Lee JY, Wang KC, Kim SK, Cho BK, Pietsch T, Fleischhack G, Tippelt S, Ra YS, Bailey S, Lindsey JC, Clifford SC, Eberhart CG, Cooper MK, Packer RJ, Massimino M, Garre ML, Bartels U, Tabori U, Hawkins CE, Dirks P, Bouffet E, Rutka JT, Wechsler-Reya RJ, Weiss WA, Collier LS, Dupuy AJ, Korshunov A, Jones DT, Kool M, Northcott PA, Pfister SM, Largaespada DA, Mungall AJ, Moore RA, Jabado N, Bader GD, Jones SJ, Malkin D, Marra MA, Taylor MD <a class="http" href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16478.html">Nature. 2016 Jan 13. doi: 10.1038/nature16478</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26760213">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureJan2016.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li></ol> <h2 id="A2015">2015</h2> <ol type="1"><li>NetMatchStar: an enhanced Cytoscape network querying app Rinnone F, Micale G, Bonnici V, Bader GD, Shasha D, Ferro A, Pulvirenti A,Giugno R <a class="http" href="http://f1000research.com/articles/4-479/v2">F1000Res.2015 Aug 5;4:479</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26594341">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=f10000Nov2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Specifications of Standards in Systems and Synthetic Biology Schreiber F, Bader GD, Golebiewski M, Hucka M, Kormeier B, Le Novère N, Myers C, Nickerson D, Sommer B, Waltemath D, Weise S <a class="http" href="http://journal.imbio.de/article.php?aid=258">J Integr Bioinform. 2015 Sep 4;12(2):258</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26528556">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=IntbioNov2015.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap">Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma Wei Q, Tang YJ, Voisin V, Sato S, Hirata M, Whetstone H, Han I, Ailles L, Bader GD, Wunder J, Alman BA <a class="http" href="http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path[]=5375&pubmed-linkout=1">Oncotarget. 2015 Oct 26.</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26517673">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=OncotargetOct2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Antitumor activity of the novel multi-kinase inhibitor EC-70124 in triple negative breast cancer Cuenca-López MD, Serrano-Heras G, Montero JC, Corrales-Sánchez V, Gomez-Juarez M, Gascón-Escribano MJ, Morales JC, Voisin V, Núñez LE, Morís F, Bader GD, Pandiella A, Ocaña A <a class="http" href="http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path[]=4736&pubmed-linkout=1">Oncotarget. 2015 Sep 29;6(29):27923-37</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26314846">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=OncotargetSept2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Systematic analysis of somatic mutations impacting gene expression in 12 tumour types Ding J, McConechy MK, Horlings HM, Ha G, Chun Chan F, Funnell T, Mullaly SC, Reimand J, Bashashati A, Bader GD, Huntsman D, Aparicio S, Condon A, Shah SP <a class="http" href="http://www.nature.com/ncomms/2015/151005/ncomms9554/full/ncomms9554.html">Nat Commun. 2015 Oct 5;6:8554</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26436532">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatCommun2015.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Cytoscape.js: a graph theory library for visualisation and analysis Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD <a class="http" href="http://bioinformatics.oxfordjournals.org/content/early/2015/09/28/bioinformatics.btv557.abstract">Bioinformatics 2015 Sep 28</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26415722">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=bioinfoSept2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">EAG2 potassium channel with evolutionarily conserved function as a brain tumor target Huang X, He Y, Dubuc AM, Hashizume R, Zhang W, Reimand J, Yang H, Wang TA,Stehbens SJ, Younger S, Barshow S, Zhu S, Cooper MK, Peacock J, Ramaswamy V, Garzia L, Wu X, Remke M, Forester CM, Kim CC, Weiss WA, James CD, Shuman MA, Bader GD, Mueller S, Taylor MD, Jan YN, Jan LY <a class="http" href="http://www.nature.com/neuro/journal/vaop/ncurrent/full/nn.4088.html">Nat Neurosci 2015 Aug 10</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26258683">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatNeuro2015.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks Law B, Bader GD <a class="http" href="http://www.nature.com/articles/srep12074">Sci Rep 2015 Jul 13;5:12074</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26165520">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=SciRepJuly2015.pdf" title="PDF">PDF</a> PROTEIN INTERACTIONS </li><li class="gap">Inferring interaction type in gene regulatory networks using co-expression data Khosravi P, Gazestani VH, Pirhaji L, Law B, Sadeghi M, Bader GD,Goliaei B <a class="http" href="http://www.almob.org/content/10/1/23">Algorithms Mol Biol 2015 Jul 8;10:23</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26157474">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Algorithm2015.pdf" title="PDF">PDF</a> GENE REGULATORY INTERACTIONS </li><li class="gap">Canadian Open Genetics Repository (COGR): a unified clinical genomics database as a community resource for standardising and sharing genetic interpretations Lerner-Ellis J, Wang M, White S, Lebo MS; Canadian Open Genetics Repository Group <a class="http" href="http://jmg.bmj.com/cgi/pmidlookup?view=long&pmid=25904639">J Med Genet 2015 Jul;52(7):438-45</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25904639">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=JMedGen2015.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Pathway and network analysis of cancer genomes Mutation Consequences and Pathway Analysis working group of the International Cancer Genome Consortium <a class="http" href="http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3440.html">Nat Methods 2015 Jun 30;12(7):615-21</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26125594">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatMethods2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Cardioprotective Signature of Short-Term Caloric Restriction Noyan H, El-Mounayri O, Isserlin R, Arab S, Momen A, Cheng HS, Wu J, Afroze T,Li RK, Fish JE, Bader GD, Husain M <a class="http" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0130658">PLoS One 2015 Jun 22;10(6)</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26098549">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=PlosOneJune2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Inhibition of the Mitochondrial Protease ClpP as a Therapeutic Strategy for Human Acute Myeloid Leukemia Cole A, Wang Z, Coyaud E, Voisin V, Gronda M, Jitkova Y, Mattson R, Hurren R, Babovic S, Maclean N, Restall I, Wang X, Jeyaraju DV, Sukhai MA, Prabha S, Bashir S, Ramakrishnan A, Leung E, Qia YH, Zhang N, Combes KR, Ketela T, Lin F, Houry WA, Aman A, Al-Awar R, Zheng W, Wienholds E, Xu CJ, Dick J, Wang JC, Moffat J, Minden MD, Eaves CJ, Bader GD, Hao Z, Kornblau SM, Raught B, Schimmer AD <a class="http" href="http://www.cell.com/cancer-cell/abstract/S1535-6108(15)00180-4">Cancer Cell 2015 Jun 8;27(6):864-76</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/26058080">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerCellJune2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">MIMP: predicting the impact of mutations on kinase-substrate phosphorylation Wagih O, Reimand J, Bader GD <a class="http" href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3396.html">Nat Methods 2015 Jun;12(6):531-3</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25938373">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureMethosMay2015.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups Pajtler KW, Witt H, Sill M, Jones DT, Hovestadt V, Kratochwil F, Wani K, Tatevossian R, Punchihewa C, Johann P, Reimand J, Warnatz HJ, Ryzhova M, Mack S, Ramaswamy V, Capper D, Schweizer L, Sieber L, Wittmann A, Huang Z, van Sluis P, Volckmann R, Koster J, Versteeg R, Fults D, Toledano H, Avigad S, Hoffman LM, Donson AM, Foreman N, Hewer E, Zitterbart K, Gilbert M, Armstrong TS, Gupta N, Allen JC, Karajannis MA, Zagzag D, Hasselblatt M, Kulozik AE, Witt O, Collins VP, von Hoff K, Rutkowski S, Pietsch T, Bader G, Yaspo ML, von Deimling A, Lichter P, Taylor MD, Gilbertson R, Ellison DW, Aldape K, Korshunov A, Kool M, Pfister SM <a class="http" href="http://www.sciencedirect.com/science/article/pii/S153561081500135X">Cancer Cell 2015 May 11;27(5):728-43</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25965575">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CancerCell2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Metabolomic profiling in liver of adiponectin knockout mice uncovers lysophospholipid metabolism as an important target of adiponectin action Liu Y, Sen S, Wannaiampikul S, Palanivel R, Hoo RL, Isserlin R, Bader GD, Tungtrongchitr R, Deshaies Y, Xu A, Sweeney G <a class="http" href="http://www.biochemj.org/content/469/1/71.long">Biochem J 2015 Jul 1;469(1):71-82</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25915851">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BiochemApr2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes Ammar R, Paton TA, Torti D, Shlien A, Bader GD <a class="http" href="http://f1000research.com/articles/4-17/v1">F1000Res 2015 Jan 21;4:17</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25901276">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=F1000Apr2015.pdf" title="PDF">PDF</a> DNA SEQUENCING </li><li class="gap">Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis Torchia J, Picard D, Lafay-Cousin L, Hawkins CE, Kim SK, Letourneau L, Ra YS, Ho KC, Chan TS, Sin-Chan P, Dunham CP, Yip S, Ng HK, Lu JQ, Albrecht S, Pimentel J, Chan JA, Somers GR, Zielenska M, Faria CC, Roque L, Baskin B, Birks D, Foreman N, Strother D, Klekner A, Garami M, Hauser P, Hortobágyi T, Bognár L, Wilson B, Hukin J, Carret AS, Van Meter TE, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheineman K, Johnston D, Michaud J, Zelcer S,Hammond R, Ramsay DA, Fleming AJ, Lulla RR, Fangusaro JR, Sirachainan N, Larbcharoensub N, Hongeng S, Barakzai MA, Montpetit A, Stephens D, Grundy RG, Schüller U, Nicolaides T, Tihan T, Phillips J, Taylor MD, Rutka JT, Dirks P, Bader GD, Warmuth-Metz M, Rutkowski S, Pietsch T, Judkins AR, Jabado N, Bouffet E, Huang A <a class="http" href="http://www.thelancet.com/journals/lanonc/article/PIIS1470-2045(15)70114-2/abstract">Lancet Oncol 2015 May;16(5):569-82</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25882982">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=LancetApr2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative Hucka M, Nickerson DP, Bader GD, Bergmann FT, Cooper J, Demir E, Garny A, Golebiewski M, Myers CJ, Schreiber F, Waltemath D, Le Novère N <a class="http" href="http://journal.frontiersin.org/article/10.3389/fbioe.2015.00019/abstract">Front Bioeng Biotechnol 2015 Feb 24;3:19</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25759811">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CombineMar2015.pdf" title="PDF">PDF</a> DATA STANDARDS </li><li class="gap"> IL-7 coordinates proliferation, differentiation and Tcra recombination during thymocyte β-selection Boudil A, Matei IR, Shih HY, Bogdanoski G, Yuan JS, Chang SG, Montpellier B,Kowalski PE, Voisin V, Bashir S, Bader GD, Krangel MS, Guidos CJ <a class="http" href="http://www.nature.com/ni/journal/vaop/ncurrent/full/ni.3122.html">Nat Immunol 2015 Apr;16(4):397-405</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25729925">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NatureImmunolotyMar2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A Progesterone-CXCR4 Axis Controls Mammary Progenitor Cell Fate in the Adult Gland. Shiah YJ, Tharmapalan P, Casey AE, Joshi PA, McKee TD, Jackson HW, Beristain AG, Chan-Seng-Yue MA, Bader GD, Lydon JP, Waterhouse PD, Boutros PC, Khokha R <a class="http" href="http://www.sciencedirect.com/science/article/pii/S2213671115000326">Stem Cell Reports. 2015 Mar 10;4(3):313-322</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/28447939">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Nstemcellreports_April2017.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes Reimand J, Wagih O, Bader GD <a class="http" href="http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004919">PLoS Genet 2015 Jan 22;11(1)</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25611800">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=plosgeneticsJan2015_Reimand.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity Meyer M, Reimand J, Lan X, Head R, Zhu X, Kushida M, Bayani J, Pressey JC, Lionel AC, Clarke ID, Cusimano M, Squire JA, Scherer SW, Bernstein M, Woodin MA, Bader GD, Dirks PB <a class="http" href="http://www.pnas.org/content/early/2015/01/02/1320611111.abstract">Proc Natl Acad Sci U S A 2015 Jan 20;112(3):851-6</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25561528">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=PNASJan2015.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2014">2014</h2> <ol type="1"><li>Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy Isserlin R, Merico D, Wang D, Vuckovic D, Bousette N, Gramolini AO, Bader GD, Emili A <a class="http" href="http://pubs.rsc.org/en/Content/ArticleLanding/2015/MB/C4MB00265B">Mol Biosyst 2015 Jan;11(1):239-51</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25361207">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=mbs2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Combined deletion of Pten and p53 in mammary epithelium accelerates triple-negative breast cancer with dependency on eEF2K Liu JC, Voisin V, Wang S, Wang DY, Jones RA, Datti A, Uehling D, Al-Awar R, Egan SE, Bader GD, Tsao M, Mak TW, Zacksenhaus E <a class="http" href="http://onlinelibrary.wiley.com/doi/10.15252/emmm.201404402/abstract">EMBO Mol Med 2014 Oct 20;6(12):1542-60</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25330770">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=embo2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap"> Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo, Bahram Samanfar, Luke Chang, Sadhna Phanse, Ashkan Golshani, Jack F. Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris, Gary Bader, Mohan Babu <a class="http" href="http://bioinformatics.oxfordjournals.org/content/early/2014/10/13/bioinformatics.btu671.abstract">Bioinformatics 2015 Feb 1;31(3):306-10</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25316676">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=genemania_ecoli.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">The Cytoscape app article collection Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C,Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. <a class="http" href="http://f1000research.com/articles/3-138/v1">F1000Res 2014 Jul 1;3:138.</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25580224">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=pico_f10002014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap"> GeneMANIA: Fast gene network construction and function prediction for Cytoscape Jason Montojo,Khalid Zuberi, Harold Rodriguez, Gary D. Bader, Quaid Morris <a class="http" href="http://f1000research.com/articles/3-153/v1">F1000Res 2014 Jul 1;3:153</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25254104">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Montojo_f10002014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results Isserlin R, Merico D, Voisin V, Bader GD <a class="http" href="http://f1000research.com/articles/3-141/v1">F1000Res 2014 Jul 1;3:141</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25075306">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Isserlin_f10002014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Intercellular network structure and regulatory motifs in the human hematopoietic system Qiao W, Wang W, Laurenti E, Turinsky AL, Wodak SJ, Bader GD, Dick JE, Zandstra PW <a class="http" href="http://msb.embopress.org/content/10/7/741.long">Mol Syst Biol 2014 Jul 15;10(7):741</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25028490">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Qiao_MSB2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma Northcott PA, Lee C, Zichner T, Stütz AM, Erkek S, Kawauchi D, Shih DJ, Hovestadt V, Zapatka M, Sturm D, Jones DT, Kool M, Remke M, Cavalli FM, Zuyderduyn S, Bader GD, <a class="nonexistent" href="/VandenBerg">VandenBerg</a> S, Esparza LA, Ryzhova M, Wang W, Wittmann A, Stark S, Sieber L, Seker-Cin H, Linke L, Kratochwil F, Jäger N, Buchhalter I, Imbusch CD, Zipprich G, Raeder B, Schmidt S, Diessl N, Wolf S, Wiemann S, Brors B, Lawerenz C, Eils J, Warnatz HJ, Risch T, Yaspo ML, Weber UD, Bartholomae CC, von Kalle C, Turányi E, Hauser P, Sanden E, Darabi A, Siesjö P, Sterba J, Zitterbart K, Sumerauer D, van Sluis P, Versteeg R, Volckmann R, Koster J, Schuhmann MU, Ebinger M, Grimes HL, Robinson GW, Gajjar A, Mynarek M, von Hoff K, Rutkowski S, Pietsch T, Scheurlen W, Felsberg J, Reifenberger G, Kulozik AE, von Deimling A, Witt O, Eils R, Gilbertson RJ, Korshunov A, Taylor MD, Lichter P, Korbel JO, Wechsler-Reya RJ, Pfister SM <a class="http" href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13379.html">Nature 2014 Jul 24;511(7510):428-34</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25043047">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Northcott_Nature2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma Vanner RJ, Remke M, Gallo M, Selvadurai HJ, Coutinho F, Lee L, Kushida M, Head R, Morrissy S, Zhu X, Aviv T, Voisin V, Clarke ID, Li Y, Mungall AJ, Moore RA, Ma Y, Jones SJ, Marra MA, Malkin D, Northcott PA, Kool M, Pfister SM, Bader G, Hochedlinger K, Korshunov A, Taylor MD, Dirks PB <a class="http" href="http://www.cell.com/cancer-cell/abstract/S1535-6108(14)00220-7">Cancer Cell 2014 Jul 14;26(1):33-47</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24954133">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=vanner_dirks_2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Network Assessor: an automated method for quantitative assessment of a network's potential for gene function prediction Montojo J, Zuberi K, Shao Q, Bader GD, Morris Q <a class="http" href="http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00123/abstract">Front Genet 2014 May 16;5:123</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24904632">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=montojoFrontgenet_2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A draft map of the human proteome Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A <a class="http" href="http://www.nature.com/nature/journal/v509/n7502/full/nature13302.html">Nature 2014 May 29;509(7502):575-81</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24870542">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=pandeymay2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Mapping the cellular response to small molecules using chemogenomic fitness signatures Lee AY, St Onge RP, Proctor MJ, Wallace IM, Nile AH, Spagnuolo PA, Jitkova Y, Gronda M, Wu Y, Kim MK, Cheung-Ong K, Torres NP, Spear ED, Han MK, Schlecht U, Suresh S, Duby G, Heisler LE, Surendra A, Fung E, Urbanus ML, Gebbia M, Lissina E, Miranda M, Chiang JH, Aparicio AM, Zeghouf M, Davis RW, Cherfils J, Boutry M, Kaiser CA, Cummins CL, Trimble WS, Brown GW, Schimmer AD, Bankaitis VA, Nislow C, Bader GD, Giaever G <a class="http" href="http://www.sciencemag.org/content/344/6180/208.long">Science 2014 Apr 11;344(6180):208-11</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24723613">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Lee_Science.pdf" title="PDF">PDF</a> CHEMICAL GENOMICS </li><li class="gap">Prediction and Experimental Characterization of nsSNPs Altering Human PDZ-Binding Motifs Gfeller D, Ernst A, Jarvik N, Sidhu SS, Bader GD <a class="http" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094507">PLoS One 2014 Apr 10;9(4):e94507</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24722214">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=gfeller_plosone2014.pdf" title="PDF">PDF</a> FUNCTIONAL MUTATION ANALYSIS </li><li class="gap">HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery Leung A, Bader GD, Reimand J <a class="http" href="http://bioinformatics.oxfordjournals.org/content/early/2014/03/28/bioinformatics.btu172.long">Bioinformatics 2014 Apr 8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24713437">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=leung_Bioinformatics2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition Kool M, Jones DT, Jäger N, Northcott PA, Pugh TJ, Hovestadt V, Piro RM, Esparza LA, Markant SL, Remke M, Milde T, Bourdeaut F, Ryzhova M, Sturm D, Pfaff E, Stark S, Hutter S, Seker-Cin H, Johann P, Bender S, Schmidt C, Rausch T, Shih D, Reimand J, Sieber L, Wittmann A, Linke L, Witt H, Weber UD, Zapatka M, König R, Beroukhim R, Bergthold G, van Sluis P, Volckmann R, Koster J, Versteeg R, Schmidt S, Wolf S, Lawerenz C, Bartholomae CC, von Kalle C, Unterberg A, Herold-Mende C, Hofer S, Kulozik AE, von Deimling A, Scheurlen W, Felsberg J, Reifenberger G, Hasselblatt M, Crawford JR, Grant GA, Jabado N, Perry A, Cowdrey C, Croul S, Zadeh G, Korbel JO, Doz F, Delattre O, Bader GD, <a class="nonexistent" href="/McCabe">McCabe</a> MG, Collins VP, Kieran MW, Cho YJ, Pomeroy SL, Witt O, Brors B, Taylor MD, Schüller U, Korshunov A, Eils R, Wechsler-Reya RJ, Lichter P, Pfister SM, ICGC <a class="nonexistent" href="/PedBrain">PedBrain</a> Tumor Project <a class="http" href="http://www.sciencedirect.com/science/article/pii/S1535610814000737">Cancer Cell 2014 Mar 17;25(3):393-405</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24651015">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Kool_CancerCell2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Highlights of B/D-HPP and HPP Resource Pillar Workshops at Yokohama 12th Annual HUPO World Congress of Proteomics Aebersold R, Bader GD, Edwards AM, van Eyk J, Kussman M, Qin J, Omenn GS <a class="http" href="http://onlinelibrary.wiley.com/doi/10.1002/pmic.201400041/abstract">Proteomics 2014 May;14(9):975-88</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24596128">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=abersold_prot.pdf" title="PDF">PDF</a> PROTEOMICS </li><li class="gap">Epigenomic alterations define lethal CIMP-positive ependymomas of infancy Mack SC, Witt H, Piro RM, Gu L, Zuyderduyn S, Stütz AM, Wang X, Gallo M, Garzia L, Zayne K, Zhang X, Ramaswamy V, Jäger N, Jones DT, Sill M, Pugh TJ, Ryzhova M, Wani KM, Shih DJ, Head R, Remke M, Bailey SD, Zichner T, Faria CC, Barszczyk M, Stark S, Seker-Cin H, Hutter S, Johann P, Bender S, Hovestadt V, Tzaridis T, Dubuc AM, Northcott PA, Peacock J, Bertrand KC, Agnihotri S, Cavalli FM, Clarke I, Nethery-Brokx K, Creasy CL, Verma SK, Koster J, Wu X, Yao Y, Milde T, Sin-Chan P, Zuccaro J, Lau L, Pereira S, Castelo-Branco P, Hirst M, Marra MA, Roberts SS, Fults D, Massimi L, Cho YJ, Van Meter T, Grajkowska W, Lach B, Kulozik AE, von Deimling A, Witt O, Scherer SW, Fan X, Muraszko KM, Kool M, Pomeroy SL, Gupta N, Phillips J, Huang A, Tabori U, Hawkins C, Malkin D, Kongkham PN, Weiss WA, Jabado N, Rutka JT, Bouffet E, Korbel JO, Lupien M, Aldape KD, Bader GD, Eils R, Lichter P, Dirks PB, Pfister SM, Korshunov A, Taylor MD <a class="http" href="http://www.nature.com/nature/journal/v506/n7489/full/nature13108.html">Nature 2014 Feb 27;506(7489):445-50</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24553142">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Mack_Nature2014.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2013">2013</h2> <ol type="1"><li>TCGA pan-cancer project, thread 2: Network models Reimand J, Bader GD, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton <a class="http" href="http://www.nature.com/ng/2013/131017/full/ng.2787.html">Nature Genetics (2013) doi:10.1038/ng.2787</a> CANCER MUTATIONS, NETWORKS </li><li class="gap">Coordinate microRNA-mediated regulation of protein complexes in prostate cancer Alshalalfa M, Bader GD, Bismar TA, Alhajj R <a class="http" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0084261">PLoS One 2013 Dec 31;8(12):e84261</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24391925">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Alshalalfa_PLOSONE.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Comprehensive identification of mutational cancer driver genes across 12 tumor types Tamborero D, Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Kandoth C, Reimand J, Lawrence MS, Getz G, Bader GD, Ding L, Lopez-Bigas N <a class="http" href="http://www.nature.com/srep/2013/131002/srep02650/full/srep02650.html">Sci Rep 2013 Oct 2;3:2650</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24084849">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Tamborero_SciRep_TCGA-pancancer.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap">The mutational landscape of phosphorylation signaling in cancer Reimand J, Wagih O, Bader GD <a class="http" href="http://www.nature.com/srep/2013/131002/srep02651/full/srep02651.html">Sci Rep 2013 Oct 2;3:2651</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24089029">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Reimand_SciRep_TCGA-pancancer.pdf" title="PDF">PDF</a> CANCER MUTATIONS, NETWORKS </li><li class="gap">Using biological pathway data with paxtools Demir E, Babur O, Rodchenkov I, Aksoy BA, Fukuda KI, Gross B, Sümer OS, Bader GD, Sander C. <a class="http" href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003194">PLoS Comput Biol 2013;9(9):e1003194</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/24068901">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Demir_paxtools_ploone.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">The BioPAX Validator Rodchenkov I, Demir E, Sander C, Bader GD <a class="http" href="http://bioinformatics.oxfordjournals.org/content/29/20/2659.long">Bioinformatics 2013 Oct 15;29(20):2659-60</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23918249">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Rodchenkov_valid_bioinfo.pdf" title="PDF">PDF</a> DATA STANDARD </li><li class="gap">Computational approaches to identify functional genetic variants in cancer genomes Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group <a class="http" href="http://www.nature.com/nmeth/journal/v10/n8/full/nmeth.2562.html">Nature Methods 2013 Aug;10(8):723-9</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23900255">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=GonzalezPerez_cancer_mutations_NatMeth.pdf" title="PDF">PDF</a> CANCER MUTATIONS </li><li class="gap"> GeneMANIA prediction server 2013 update Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q <a class="http" href="http://nar.oxfordjournals.org/content/41/W1/W115.long">Nucleic Acids Res 2013 Jul;41(Web Server issue):W115-22</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23794635">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Zuberi_genemanis_NAR.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Cytoscape App Store Lotia S, Montojo J, Dong Y, Bader GD, Pico AR <a class="http" href="http://bioinformatics.oxfordjournals.org/content/29/10/1350.long">Bioinformatics 2013 May 15;29(10):1350-1</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23595664">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Pico_Bioinformatics.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">SH3 interactome conserves general function over specific form Xin X, Gfeller D, Cheng J, Tonikian R, Sun L, Guo A, Lopez L, Pavlenco A, Akintobi A, Zhang Y, Rual JF, Currell B, Seshagiri S, Hao T, Yang X, Shen YA, Salehi-Ashtiani K, Li J, Cheng AT, Bouamalay D, Lugari A, Hill DE, Grimes ML, Drubin DG, Grant BD, Vidal M, Boone C, Sidhu SS, Bader GD <a class="http" href="http://www.nature.com/msb/journal/v9/n1/full/msb20139.html">Mol Syst Biol 2013 Apr 2;9:652</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23549480">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Xin_SH3inter_MSB.pdf" title="PDF">PDF</a> <a class="http" href="http://www.ebi.ac.uk/intact/search/do/search?searchString=pubid:23549480">Interactions in Intact Database</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">Metabolic adaptation to chronic inhibition of mitochondrial protein synthesis in acute myeloid leukemia cells Jhas B, Sriskanthadevan S, Skrtic M, Sukhai MA, Voisin V, Jitkova Y, Gronda M, Hurren R, Laister RC, Bader GD, Minden MD, Schimmer AD. <a class="http" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0058367">PLoS One 2013;8(3):e58367</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23520503">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Jhas_leuk_plosone.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers Reimand J, Bader GD <a class="http" href="http://www.nature.com/msb/journal/v9/n1/full/msb201268.html">Mol Syst Biol 2013;9:637</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23340843">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Reimand_MSB_phosphomutations.pdf" title="PDF">PDF</a> <a class="http" href="http://genomemedicine.com/content/5/2/19/abstract">Research Highlight in Genome Medicine (2013)</a> CANCER MUTATIONS, SIGNALING NETWORKS </li><li class="gap">Predicting PDZ domain mediated protein interactions from structure Hui S, Xing X, Bader GD <a class="http" href="http://www.biomedcentral.com/1471-2105/14/27/abstract">BMC Bioinformatics 2013 Jan 21;14:27</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23336252">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=pdz-struct-2013.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">Integrative pathway dissection of molecular mechanisms of moxLDL-induced vascular smooth muscle phenotype transformation Karagiannis GS, Weile J, Bader GD, Minta J. <a class="http" href="http://www.biomedcentral.com/1471-2261/13/4">BMC Cardiovasc Disord 2013 Jan 16;13:4</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23324130">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=WeileBMC.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">GESTODIFFERENT: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi and Giancarlo Mauri <a class="http" href="http://bioinformatics.oxfordjournals.org/content/early/2013/01/03/bioinformatics.bts726.abstract">Bioinformatics 2013 Feb 15;29(4):513-4</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23292740">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=GESTODIFFERENT.pdf" title="PDF">PDF</a> NETWORK SIMULATION </li></ol> <h2 id="A2012">2012</h2> <ol type="1"><li>The Biology/Disease-driven Human Proteome Project (B/D-HPP): Enabling Protein Research for the Life Sciences Community Aebersold R, Bader GD, Edwards AM, van Eyk JE, Kussmann M, Qin J, Omenn GS <a class="http" href="http://pubs.acs.org/doi/abs/10.1021/pr301151m">J Proteome Res 2013 Jan 4;12(1):23-7</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23259511">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=hupo-bdhpp.pdf" title="PDF">PDF</a> PROTEOMICS </li><li class="gap">Chromatin is an ancient innovation conserved between Archaea and Eukarya Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C <a class="http" href="http://elife.elifesciences.org/content/1/e00078">Elife 2012 Dec 13;1:e00078</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23240084">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=e00078.full+%281%29.pdf" title="PDF">PDF</a> ANALYSIS OF ARCHAEAL CHROMATIN </li><li class="gap">Attenuation of miR-126 Activity Expands HSC In Vivo without Exhaustion Lechman ER, Gentner B, van Galen P, Giustacchini A, Saini M, Boccalatte FE, Hiramatsu H, Restuccia U, Bachi A, Voisin V, Bader GD, Dick JE, Naldini L <a class="http" href="http://www.sciencedirect.com/science/article/pii/S1934590912005371">Cell Stem Cell 2012 Nov 7</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23142521">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2012_mir126andHSC.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A travel guide to Cytoscape plugins Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T <a class="http" href="http://www.nature.com/nmeth/journal/v9/n11/full/nmeth.2212.html">Nat Methods 2012 Nov;9(11):1069-76</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23132118">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2012_CytoscapePluginTravelGuide.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Detecting microRNAs of high influence on protein functional interaction networks: a prostate cancer case study Alshalalfa M, Bader GD, Goldenberg A, Morris Q, Alhajj R <a class="http" href="http://www.biomedcentral.com/1752-0509/6/112">BMC Syst Biol 2012 Aug 28;6:112</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22929553">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2012_microRNAinfluence.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice Xiong X, Chorzalska A, Dubielecka PM, White JR, Vedvyas Y, Hedvat CV, Haimovitz-Friedman A, Koutcher JA, Reimand J, Bader GD, Sawicki JA, Kotula L <a class="http" href="http://www.nature.com/oncsis/journal/v1/n9/full/oncsis201228a.html">Oncogenesis 2012 Sep 3;1:e26</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/23552839">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2012_Xiong_ABI1_Oncogenesis.pdf" title="PDF">PDF</a> CANCER GENOMICS </li><li class="gap">Subgroup-specific structural variation across 1,000 medulloblastoma genomes Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD <a class="http" href="http://www.nature.com/nature/journal/v488/n7409/full/nature11327.html">Nature 2012 Aug 2;488(7409):49-56</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22832581">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Northcott_Nature2012.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals Labbé RM, Irimia M, Currie KW, Lin A, Zhu SJ, Brown DD, Ross EJ, Voisin V, Bader GD, Blencowe BJ, Pearson BJ <a class="http" href="http://onlinelibrary.wiley.com/doi/10.1002/stem.1144/abstract">Stem Cells 2012 Jun 13</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22696458">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=PlanariaStemCells.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Multiple Genetic Interaction Experiments Provide Complementary Information Useful for Gene Function Prediction Michaut M, Bader GD <a class="http" href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002559">PLoS Comput Biol 8(6): e1002559</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22737063">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=MultipleGeneticInteractions.pdf" title="PDF">PDF</a> GENETIC INTERACTIONS </li><li class="gap">Domain-mediated protein interaction prediction: From genome to network Reimand J, Hui S, Jain S, Law B, Bader GD <a class="http" href="http://www.sciencedirect.com/science/article/pii/S001457931200316X">FEBS Lett 2012 May 3</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22561014">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Genome2NetworkReview.pdf" title="PDF">PDF</a> PROTEIN INTERACTIONS </li><li class="gap">Seventeen-gene signature from enriched Her2/Neu mammary tumor-initiating cells predicts clinical outcome for human HER2+:ERα- breast cancer Liu JC, Voisin V, Bader GD, Deng T, Pusztai L, Symmans WF, Esteva FJ, Egan SE, Zacksenhaus E <a class="http" href="http://www.pnas.org/content/early/2012/03/27/1201105109.abstract">Proc Natl Acad Sci U S A 2012 Mar 28</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22460789">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=breastcancer-2012.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Phosphorylation sites of higher stoichiometry are more conserved Tan CS, Bader GD <a class="http" href="http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1941.html">Nat Methods 2012 Mar 27;9(4):317</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22453906">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=phospholetter-2012.pdf" title="PDF">PDF</a> PHOSPHOPROTEOMICS </li><li class="gap">Mapping the Hsp90 Genetic Interaction Network in Candida albicans Reveals Environmental Contingency and Rewired Circuitry Diezmann S, Michaut M, Shapiro RS, Bader GD, Cowen LE <a class="http" href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002562">PLoS Genet 2012 Mar;8(3):e1002562</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22438817">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=candida2012.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li></ol> <h2 id="A2011">2011</h2> <ol type="1"><li>MUSI: an integrated system for identifying multiple specificity from very large peptide or nucleic acid data sets Kim T, Tyndel MS, Huang H, Sidhu SS, Bader GD, Gfeller D, Kim PM <a class="http" href="http://nar.oxfordjournals.org/content/early/2011/12/30/nar.gkr1294.long">Nucleic Acids Res 2011 Dec 30</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22210894">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=musi-2011.pdf" title="PDF">PDF</a> DOMAIN SPECIFICITY SOFTWARE </li><li class="gap">Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE) Le Novère N, Hucka M, Anwar N, Bader GD, Demir E, Moodie S, Sorokin A <a class="http" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235518/?tool=pubmed">Stand Genomic Sci 2011 Nov 30;5(2):230-42</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22180826">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=combine-report-2011.pdf" title="PDF">PDF</a> DATA STANDARD </li><li class="gap">clusterMaker: a multi-algorithm clustering plugin for Cytoscape Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE <a class="http" href="http://www.biomedcentral.com/1471-2105/12/436">BMC Bioinformatics 2011 Nov 9;12(1):436</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22070249">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=clustermaker.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Compound Prioritization Methods Increase Rates of Chemical Probe Discovery in Model Organisms Iain M. Wallace, Malene L. Urbanus, Genna M. Luciani,Andrew R. Burns,Mitchell K.L. Han, Hao Wang, Kriti Arora, Lawrence E. Heisler, Michael Proctor, Robert P. St. Onge, Terry Roemer, Peter J. Roy,Carolyn L. Cummins, Gary D. Bader, Corey Nislow, Guri Giaever <a class="http" href="http://www.cell.com/chemistry-biology/abstract/S1074-5521(11)00276-6">Cell Chemistry & Biology 2011 18, 1273–1283</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/22035796">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=yactives.pdf" title="PDF">PDF</a> <a class="http" href="http://www.cell.com/chemistry-biology/abstract/S1074-5521(11)00364-4">Chemistry & Biology 2011 18:10, 1204-1205</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=commentary_yactives.pdf" title="Commentary on paper">Commentary on paper</a> CHEMICAL GENOMICS </li><li class="gap">NetSlim: high-confidence curated signaling maps Raju R, Nanjappa V, Balakrishnan L, Radhakrishnan A, Thomas JK, Sharma J, Tian M, Palapetta SM, Subbannayya T, Sekhar NR, Muthusamy B, Goel R, Subbannayya Y, Telikicherla D, Bhattacharjee M, Pinto SM, Syed N, Srikanth MS, Sathe GJ, Ahmad S, Chavan SN, Sameer Kumar GS, Marimuthu A, Prasad TS, Harsha HC, Rahiman BA, Ohara O, Bader GD, Sujatha Mohan S, Schiemann WP, Pandey A <a class="http" href="http://database.oxfordjournals.org/content/2011/bar032.long">Database (Oxford) 2011 Sep 29;2011(0):bar032</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21959865">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=netslim.pdf" title="PDF">PDF</a> PATHWAY DATABASE </li><li class="gap">Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma Witt H, Mack SC, Ryzhova M, Bender S, Sill M, Isserlin R, Benner A, Hielscher T, Milde T, Remke M, Jones DTW, Northcott PA, Garzia L, Bertrand KC, Wittmann A, Yao Y, Roberts SS, Massimi L, Van Meter T, Weiss WA, Gupta N, Grajkowska W, Lach B, Cho YJ, von Deimling A, Kulozik AE, Witt O, Bader GD, Hawkins CE, Tabori U, Guha A, Rutka JT, Lichter P, Korshunov A, Taylor MD, Pfister SM <a class="http" href="http://www.sciencedirect.com/science/article/pii/S1535610811002625">Cancer Cell, Volume 20, Issue 2, 143-157, 16 August 2011</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21840481">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=ependymoma.pdf" title="PDF">PDF</a> PATHWAY ANALYSIS </li><li class="gap">A comprehensive manually curated reaction map of RANKL/RANK-signaling pathway Raju R, Balakrishnan L, Nanjappa V, Bhattacharjee M, Getnet D, Muthusamy B, Kurian Thomas J, Sharma J, Rahiman BA, Harsha HC, Shankar S, Prasad TS, Mohan SS, Bader GD, Wani MR, Pandey A <a class="http" href="http://database.oxfordjournals.org/content/2011/bar021.long">Database (Oxford) 2011 Jul 8;2011</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21742767">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=2011_Raju-RANKL_Database.pdf" title="PDF">PDF</a> PATHWAY DATABASE </li><li class="gap">PSICQUIC and PSISCORE: accessing and scoring molecular interactions Aranda B, Blankenburg H, Kerrien S, Brinkman FS, Ceol A, Chautard E, Dana JM, De Las Rivas J, Dumousseau M, Galeota E, Gaulton A, Goll J, Hancock RE, Isserlin R, Jimenez RC, Kerssemakers J, Khadake J, Lynn DJ, Michaut M, O'Kelly G, Ono K, Orchard S, Prieto C, Razick S, Rigina O, Salwinski L, Simonovic M, Velankar S, Winter A, Wu G, Bader GD, Cesareni G, Donaldson IM, Eisenberg D, Kleywegt GJ, Overington J, Ricard-Blum S, Tyers M, Albrecht M, Hermjakob H <a class="http" href="http://www.nature.com/nmeth/journal/v8/n7/full/nmeth.1637.html">Nature Methods 2011 Jun 29;8(7):528-9</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21716279">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=psicquic.pdf" title="PDF">PDF</a> PROTEIN INTERACTIONS </li><li class="gap">Response to Comment on Positive Selection of Tyrosine Loss in Metazoan Evolution, Tan CS, Schoof EM, Creixell P, Pasculescu A, Lim WA, Pawson T, Bader GD and Linding R <a class="http" href="http://www.sciencemag.org/content/332/6032/917.2.full">Science 332(6032):917, 20 May 2011</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Science-2011-tan-917.pdf" title="PDF">PDF</a> NETWORK EVOLUTION </li><li class="gap">The multiple-specificity landscape of modular peptide recognition domains Gfeller D, Butty F, Wierzbicka M, Verschueren E, Vanhee P, Huang H, Ernst A, Dar N, Stagljar I, Serrano L, Sidhu SS, Bader GD, Kim PM <a class="http" href="http://www.nature.com/msb/journal/v7/n1/full/msb201118.html">Molecular Systems Biology 7:484, 26 April 2011</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21525870">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2011_Gfeller.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">WordCloud: a Cytoscape plugin to create a visual semantic summary of networks Oesper L, Merico D, Isserlin R, Bader GD <a class="http" href="http://www.scfbm.org/content/6/1/7/abstract">Source Code for Biology and Medicine 2011, 6:7, 7 April 2011</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21473782">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=wordcloud.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Protein Complexes are Central in the Yeast Genetic Landscape Michaut M, Baryshnikova A, Costanzo M, Myers CL, Andrews BJ, Boone C, Bader GD <a class="http" href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1001092">PLoS Computational Biology 7(2): e1001092 Feb 24 2011</a> <a class="http" href="http://www.ploscompbiol.org/article/browseIssue.action?issue=info:doi/10.1371/issue.pcbi.v07.i02">February 2011 Issue Cover</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21390331">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2011_Michaut_Mono.pdf" title="PDF">PDF</a> GENETIC INTERACTION NETWORK ANALYSIS </li><li class="gap">Bringing order to protein disorder through comparative genomics and genetic interactions Bellay J*, Han S*, Michaut M*, Kim T, Costanzo M, Andrews BJ, Boone C, Bader GD, Myers CL, Kim PM <a class="http" href="http://genomebiology.com/2011/12/2/R14/abstract">Genome Biology 12(2):R14 Feb 15 2011</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21324131">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2011_Michaut_Diso.pdf" title="PDF">PDF</a> PROTEIN DISORDER AND COMPARATIVE GENOMICS </li><li class="gap">Too Many Roads Not Taken Edwards AM, Isserlin R, Bader GD, Frye SV, Willson TM, Yu FH <a class="http" href="http://www.nature.com/nature/journal/v470/n7333/full/470163a.html">Nature. (470) 163-165 Feb 9 2011</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21307913">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=nature_comment_Feb2011.pdf" title="PDF">PDF</a> <a class="http" href="http://arxiv.org/abs/1102.0448">Full Paper on arxiv.org</a> BIBLIOMETRIC ANALYSIS </li><li class="gap">The Biomolecular Interaction Network Database in PSI-MI 2.5 Isserlin R, El-Badrawi RA, Bader GD <a class="http" href="http://database.oxfordjournals.org/cgi/content/abstract/baq037?ijkey=5ex1hxBFa242Q8L&keytype=ref">Database 2011 Jan 12;2011:baq037</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21233089">PubMed Abstract</a> - <a class="http" href="http://database.oxfordjournals.org/content/2011/baq037.full.pdf?keytype=ref&ijkey=5ex1hxBFa242Q8L">PDF</a> PROTEIN INTERACTION DATABASE </li></ol> <h2 id="A2010">2010</h2> <ol type="1"><li>A regression framework incorporating quantitative and negative interaction data improves prediction of quantitative PDZ domain-peptide interaction from primary sequence Shao X, Tan CS, Voss C, Li SS, Deng N, Bader GD <a class="http" href="http://bioinformatics.oxfordjournals.org/content/early/2010/12/02/bioinformatics.btq657.abstract">Bioinformatics 2010 Dec 2</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21127034">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_ShaoTanBader-PDZAffinity_Bioinformatics.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation Merico D, Isserlin R, Stueker O, Emili A, Bader GD <a class="http" href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013984">PLoS One 2010 Nov 15;5(11):e13984</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21085593">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_MericoIsserlinStuekerBader-EnrichmentMap_PLoSOne.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology Jain S, Bader GD <a class="http" href="http://www.biomedcentral.com/1471-2105/11/562">BMC Bioinformatics 2010 Nov 15;11(1):562</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21078182">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_JainBader-SemanticSimilarityGO_BMCBioinformatics.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">Quantitative analysis of fitness and genetic interactions in yeast on a genome scale Baryshnikova A, Costanzo M, Kim Y, Ding H, Koh J, Toufighi K, Youn JY, Ou J, San Luis BJ, Bandyopadhyay S, Hibbs M, Hess D, Gingras AC, Bader GD, Troyanskaya OG, Brown GW, Andrews B, Boone C, Myers CL <a class="http" href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1534.html">Nat Methods 2010 Nov 14</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21076421">PubMed Abstract</a> -<a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_BaryshnikovaMyers-SGAScore_NatMethods.pdf" title="PDF">PDF</a> GENETIC INTERACTION NETWORK ANALYSIS </li><li class="gap">Pathway Commons, a web resource for biological pathway data Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, Schultz N, Bader GD, Sander C <a class="http" href="http://nar.oxfordjournals.org/content/early/2010/11/10/nar.gkq1039.long">Nucleic Acids Res 2010 Nov 10</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21071392">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_CeramiBaderSander-PathwayCommons_NAR.pdf" title="PDF">PDF</a> PATHWAY DATABASE </li><li class="gap">Proteome scanning to predict PDZ domain interactions using support vector machines Hui S, Bader GD <a class="http" href="http://www.biomedcentral.com/1471-2105/11/507">BMC Bioinformatics 2010 Oct 12;11(1):50</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20939902">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_HuiBader-ProteomeScanningPDZ_BMCBioinformatics.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap"> GeneMANIA Cytoscape Plugin: Fast gene function predictions on the desktop Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD <a class="http" href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btq562">Bioinformatics 2010 Nov 15;26(22):2927-8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20926419">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_GeneMANIA_Cytoscape_Plugin_Montojo_Bioinformatics_Oct.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Dynamic interaction networks in a hierarchically organized tissue Kirouac DC, Ito C, Csaszar E, Roch A, Yu M, Sykes EA, Bader GD, Zandstra PW <a class="http" href="http://www.nature.com/msb/journal/v6/n1/full/msb201071.html">Mol Syst Biol 2010 Oct 5;6:417</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20924352">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_KirouacZandstra_DynamicCellCellInteractionNetworks_MSB_Oct.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Functional complex between YAP2 and ZO-2 is PDZ domain dependent, regulates YAP2 nuclear localization and signaling Oka T, Remue E, Meerschaert K, Vanloo B, Boucherie C, Gfeller D, Bader GD, Sidhu S, Vandekerckhove J, Gettemans J, Sudol M <a class="http" href="http://www.biochemj.org/bj/imps/abs/BJ20100870.htm">Biochem J 2010 Sep 24</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20868367">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_OkaSudol_YAP2_ZO2_BJ_Oct.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">The BioPAX community standard for pathway data sharing Demir E, Cary MP, Paley S, Fukuda K, Lemer C, Vastrik I, Wu G, D'Eustachio P, Schaefer C, Luciano J, Schacherer F, Martinez-Flores I, Hu Z, Jimenez-Jacinto V, Joshi-Tope G, Kandasamy K, Lopez-Fuentes AC, Mi H, Pichler E, Rodchenkov I, Splendiani A, Tkachev S, Zucker J, Gopinath G, Rajasimha H, Ramakrishnan R, Shah I, Syed M, Anwar N, Babur O, Blinov M, Brauner E, Corwin D, Donaldson S, Gibbons F, Goldberg R, Hornbeck P, Luna A, Murray-Rust P, Neumann E, Reubenacker O, Samwald M, van Iersel M, Wimalaratne S, Allen K, Braun B, Whirl-Carrillo M, Cheung KH, Dahlquist K, Finney A, Gillespie M, Glass E, Gong L, Haw R, Honig M, Hubaut O, Kane D, Krupa S, Kutmon M, Leonard J, Marks D, Merberg D, Petri V, Pico A, Ravenscroft D, Ren L, Shah N, Sunshine M, Tang R, Whaley R, Letovksy S, Buetow KH, Rzhetsky A, Schachter V, Sobral BS, Dogrusoz U, McWeeney S, Aladjem M, Birney E, Collado-Vides J, Goto S, Hucka M, Novère NL, Maltsev N, Pandey A, Thomas P, Wingender E, Karp PD, Sander C, Bader GD <a class="http" href="http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html">Nat Biotechnol 2010 Sep;28(9):935-42</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20829833">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_Demir_BioPAX_NatBiotech_Sep.pdf" title="PDF">PDF</a> DATA STANDARD </li><li class="gap">Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing Ernst A, Gfeller D, Kan Z, Seshagiri S, Kim PM, Bader GD, Sidhu SS <a class="http" href="http://pubs.rsc.org/en/Content/ArticleLanding/2010/MB/C0MB00061B">Mol. BioSyst., 2010, Advance Article</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20714644">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_ErnstSidhu_PDZSpecificityEvolution_MBS_Aug.pdf" title="PDF">PDF</a> PROTEIN INTERACTION NETWORK EVOLUTION </li><li class="gap">Cytoscape Web: an interactive web-based network browser Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD <a class="http" href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btq430v1">Bioinformatics 2010 Jul 23</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20656902">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_CytoscapeWeb_Lopes_Bioinformatics_Jul.pdf" title="PDF">PDF</a> NETWORK VISUALIZATION </li><li class="gap"> The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q <a class="http" href="http://nar.oxfordjournals.org/cgi/content/abstract/38/suppl_2/W214">Nucleic Acids Res 2010 Jul 1;38 Suppl:W214-20</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20576703">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_GeneMANIA_Warde-Farley_NAR_Jun.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">Functional impact of global rare copy number variation in autism spectrum disorders Pinto D, Pagnamenta AT, Klei L, Anney R, Merico D, Regan R, Conroy J, Magalhaes TR, Correia C, Abrahams BS, Almeida J, Bacchelli E, Bader GD, Bailey AJ, Baird G, Battaglia A, Berney T, Bolshakova N, Bölte S, Bolton PF, Bourgeron T, Brennan S, Brian J, Bryson SE, Carson AR, Casallo G, Casey J, Chung BH, Cochrane L, Corsello C, Crawford EL, Crossett A, Cytrynbaum C, Dawson G, de Jonge M, Delorme R, Drmic I, Duketis E, Duque F, Estes A, Farrar P, Fernandez BA, Folstein SE, Fombonne E, Freitag CM, Gilbert J, Gillberg C, Glessner JT, Goldberg J, Green A, Green J, Guter SJ, Hakonarson H, Heron EA, Hill M, Holt R, Howe JL, Hughes G, Hus V, Igliozzi R, Kim C, Klauck SM, Kolevzon A, Korvatska O, Kustanovich V, Lajonchere CM, Lamb JA, Laskawiec M, Leboyer M, Le Couteur A, Leventhal BL, Lionel AC, Liu XQ, Lord C, Lotspeich L, Lund SC, Maestrini E, Mahoney W, Mantoulan C, Marshall CR, <a class="nonexistent" href="/McConachie">McConachie</a> H, <a class="nonexistent" href="/McDougle">McDougle</a> CJ, <a class="nonexistent" href="/McGrath">McGrath</a> J, <a class="nonexistent" href="/McMahon">McMahon</a> WM, Merikangas A, Migita O, Minshew NJ, Mirza GK, Munson J, Nelson SF, Noakes C, Noor A, Nygren G, Oliveira G, Papanikolaou K, Parr JR, Parrini B, Paton T, Pickles A, Pilorge M, Piven J, Ponting CP, Posey DJ, Poustka A, Poustka F, Prasad A, Ragoussis J, Renshaw K, Rickaby J, Roberts W, Roeder K, Roge B, Rutter ML, Bierut LJ, Rice JP, Salt J, Sansom K, Sato D, Segurado R, Sequeira AF, Senman L, Shah N, Sheffield VC, Soorya L, Sousa I, Stein O, Sykes N, Stoppioni V, Strawbridge C, Tancredi R, Tansey K, Thiruvahindrapduram B, Thompson AP, Thomson S, Tryfon A, Tsiantis J, Van Engeland H, Vincent JB, Volkmar F, Wallace S, Wang K, Wang Z, Wassink TH, Webber C, Weksberg R, Wing K, Wittemeyer K, Wood S, Wu J, Yaspan BL, Zurawiecki D, Zwaigenbaum L, Buxbaum JD, Cantor RM, Cook EH, Coon H, Cuccaro ML, Devlin B, Ennis S, Gallagher L, Geschwind DH, Gill M, Haines JL, Hallmayer J, Miller J, Monaco AP, Nurnberger Jr JI, Paterson AD, Pericak-Vance MA, Schellenberg GD, Szatmari P, Vicente AM, Vieland VJ, Wijsman EM, Scherer SW, Sutcliffe JS, Betancur C <a class="http" href="http://www.nature.com/nature/journal/vaop/ncurrent/abs/nature09146.html">Nature 2010 Jul 15;466(7304):368-72</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20531469">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_AutismNature.pdf" title="PDF">PDF</a> <a class="http" href="http://blogs.nature.com/news/thegreatbeyond/2010/06/rare_genetic_variants_linked_t.html">Nature Blogs</a> - <a class="http" href="http://www.theglobeandmail.com/news/national/autism-caused-by-wide-array-of-rare-gene-changes-study/article1597861/">In the news (The Globe and Mail)</a> PATHWAY AND NETWORK ANALYSIS </li><li class="gap">A predictive model for drug bioaccumulation and bioactivity in Caenorhabditis elegans Burns AR, Wallace IM, Wildenhain J, Tyers M, Giaever G, Bader GD, Nislow C, Cutler SR, Roy PJ <a class="http" href="http://www.nature.com/nchembio/journal/vaop/ncurrent/abs/nchembio.380.html">Nat Chem Biol 2010 May 30</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20512140">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_BurnsWallace_bioaccumulationWorms_May.pdf" title="PDF">PDF</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=NCB_News%26Views.pdf" title="">NCB_News&Views.pdf</a> CHEMICAL GENOMICS </li><li class="gap">International network of cancer genome projects International Cancer Genome Consortium <a class="http" href="http://www.nature.com/nature/journal/v464/n7291/full/nature08987.html">Nature 2010 Apr 15;464(7291):993-8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20393554">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_ICGC.pdf" title="PDF">PDF</a> CANCER GENOMICS </li><li class="gap">Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps Isserlin R, Merico D, Alikhani-Koupaei R, Gramolini A, Bader GD, Emili A <a class="http" href="http://www3.interscience.wiley.com/journal/123269335/abstract">Proteomics 2010, March 10(6):1316-27</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20127684">Pubmed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_EM_proteomics.pdf" title="PDF">PDF</a> PATHWAY ANALYSIS </li><li class="gap">The Genetic Landscape of a Cell Costanzo M, Baryshnikova A, Bellay J, Kim Y, Spear ED, Sevier CS, Ding H, Koh JL, Toufighi K, Mostafavi S, Prinz J, St Onge RP, VanderSluis B, Makhnevych T, Vizeacoumar FJ, Alizadeh S, Bahr S, Brost RL, Chen Y, Cokol M, Deshpande R, Li Z, Lin ZY, Liang W, Marback M, Paw J, San Luis BJ, Shuteriqi E, Tong AH, van Dyk N, Wallace IM, Whitney JA, Weirauch MT, Zhong G, Zhu H, Houry WA, Brudno M, Ragibizadeh S, Papp B, Pál C, Roth FP, Giaever G, Nislow C, Troyanskaya OG, Bussey H, Bader GD, Gingras AC, Morris QD, Kim PM, Kaiser CA, Myers CL, Andrews BJ, Boone C <a class="http" href="http://www.sciencemag.org/cgi/content/short/327/5964/425">Science 2010 Jan 22;327(5964):425-31</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20093466">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_CostanzoBaryshnikova_GeneticLandscapeOfTheCell_Science_Jan.pdf" title="PDF">PDF</a> GENETIC INTERACTION NETWORK ANALYSIS </li><li class="gap">NetPath: a public resource of curated signal transduction pathways Kandasamy K, Mohan S, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro DJ, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman A, Keshava Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu S, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A <a class="http" href="http://genomebiology.com/2010/11/1/R3">Genome Biology 2010 Jan 12;11(1):R3</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/20067622">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2010_Kandasamy_NetPath_GenomeBiol_Jan.pdf" title="PDF">PDF</a> PATHWAY DATABASE </li><li class="gap">DRYGIN: a database of quantitative genetic interaction networks in yeast Koh JL, Ding H, Costanzo M, Baryshnikova A, Toufighi K, Bader GD, Myers CL, Andrews BJ, Boone C <a class="http" href="http://nar.oxfordjournals.org/cgi/content/full/38/suppl_1/D502">Nucleic Acids Res 2010 Jan;38(Database issue):D502-7</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/19880385">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2009_Koh_Drygin_NAR_Oct.pdf" title="PDF">PDF</a> GENETIC INTERACTION NETWORK DATABASE </li></ol> <h2 id="A2009">2009</h2> <ol type="1"><li>Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of uncharacterized endocytosis proteins Tonikian R, Xin X, Toret CP, Gfeller D, Landgraf C, Panni S, Paoluzi S, Castagnoli L, Yu H, Winsor B, Vidal M, Davidson AR, Gerstein MB, Bader GD, Volkmer R, Cesareni G, Drubin DG, Kim PM, Sidhu SS, Boone C <a class="http" href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1000218">PLoS Biology 2009 Oct Vol. 7, No. 10, e1000218</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/19841731">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2009_Tonikian_YeastSH3_PLoSBiology_Oct.pdf" title="PDF">PDF</a> PROTEIN-PROTEIN INTERACTION ANALYSIS </li><li class="gap"> How to visually interpret biological data using networks Merico D, Gfeller D, Bader GD <a class="http" href="http://www.nature.com/nbt/journal/v27/n10/abs/nbt.1567.html">Nature Biotechnology 2009 Oct 27, 921-924</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/19816451">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2009_Merico_Primer_NatBiotech_Oct.pdf" title="PDF">PDF</a> Data: <a class="http" href="http://www.baderlab.org/NetworkPrimerNBT">http://www.baderlab.org/NetworkPrimerNBT</a> NETWORK PRIMER </li><li class="gap">Rapid evolution of functional complexity in a domain family Ernst A, Sazinsky SL, Hui S, Currell B, Dharsee M, Seshagiri S, Bader GD, Sidhu SS <a class="http" href="http://stke.sciencemag.org/cgi/content/full/sigtrans;2/87/ra50">Science Signaling 2009 Sep 8;2(87):ra50</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/19738200">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2009_Ernst_PDZEvolution_ScienceSignaling_Sep.pdf" title="PDF">PDF</a> PROTEIN INTERACTION NETWORK EVOLUTION </li><li class="gap">Positive Selection of Tyrosine Loss in Metazoan Evolution Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R <a class="http" href="http://www.sciencemag.org/cgi/content/abstract/1174301v2">Science. Sep 25;325(5948):1686-8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/19589966">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2009_Tan_TyrosineLoss_Science.pdf" title="PDF">PDF</a> PROTEIN INTERACTION NETWORK EVOLUTION </li><li class="gap">Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R <a class="http" href="http://stke.sciencemag.org/cgi/content/abstract/sigtrans;2/81/ra39">Science Signaling 2(81):r39 (2009)</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/19638616">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2009_Tan_ComparativePhosphoProteomics_ScienceSignaling_Jul.pdf" title="PDF">PDF</a> PROTEIN INTERACTION NETWORK EVOLUTION </li></ol> <h2 id="A2008">2008</h2> <ol type="1"><li>A Specificity Map for the PDZ Domain Family Tonikian R, Zhang Y, Sazinsky SL, Currell B, Yeh JH, Reva B, Held HA, Appleton BA, Evangelista M, Wu Y, Xin X, Chan AC, Seshagiri S, Lasky LA, Sander C, Boone C, Bader GD, Sidhu SS <a class="http" href="http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0060239">PLoS Biology Vol. 6, No. 9, e239</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/18828675">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2008_Tonikian_PDZSpecificityMap_PlosBiology.pdf" title="PDF">PDF</a> PROTEIN-PROTEIN INTERACTION ANALYSIS </li><li class="gap">Cytoscape ESP: simple search of complex biological networks Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ <a class="http" href="http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btn208v1">Bioinformatics 2008 Jun 15;24(12):1465-6</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/18445605">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2008_Ashkenazi_CytoscapeESP_Bioinformatics.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Computational prediction of protein-protein interactions Skrabanek L, Saini HK, Bader GD, Enright AJ <a class="http" href="http://humanapress.com/index.php?option=com_journalshome&task=articledetails&category=journals&article_code=MB:38:1:1">Molecular Biotechnology 2008 Jan;38(1):1-17</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/18095187">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2008_Skrabanek_MolBiotech_PPI.pdf" title="PDF">PDF</a> REVIEW </li></ol> <h2 id="A2007">2007</h2> <ol type="1"><li>Integration of biological networks and gene expression data using Cytoscape Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD <a class="http" href="http://www.nature.com/nprot/journal/v2/n10/abs/nprot.2007.324.html">Nature Protocols 2007;2(10):2366-82</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17947979">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_Cytoscape_Cline_NatureProtocols_Oct.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Broadening the Horizon - Level 2.5 of the HUPO-PSI Format for Molecular Interactions Kerrien S, Orchard S, Montecchi-Palazzi L, Aranda B, Quinn AF, Vinod N, Bader GD, Xenarios I, Wojcik J, Sherman D, Tyers M, Salama JJ, Moore S, Ceol A, Chatr-Aryamontri A, Oesterheld M, Stumpflen V, Salwinski L, Nerothin J, Cerami E, Cusick ME, Vidal M, Gilson M, Armstrong J, Woollard P, Hogue C, Eisenberg D, Cesareni G, Apweiler R, Hermjakob H <a class="http" href="http://www.biomedcentral.com/1741-7007/5/44/abstract">BMC Biology 2007 Oct 9;5(1):44</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17925023">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_Kerrien_PSIMI_BMCBiology.pdf" title="PDF">PDF</a> DATA STANDARD </li><li class="gap">The minimum information required for reporting a molecular interaction experiment (MIMIx) Orchard S, Salwinski L, Kerrien S, Montecchi-Palazzi L, Oesterheld M, Stumpflen V, Ceol A, Chatr-Aryamontri A, Armstrong J, Woollard P, Salama JJ, Moore S, Wojcik J, Bader GD, Vidal M, Cusick ME, Gerstein M, Gavin AC, Superti-Furga G, Greenblatt J, Bader J, Uetz P, Tyers M, Legrain P, Fields S, Mulder N, Gilson M, Niepmann M, Burgoon L, Rivas Jde L, Prieto C, Perreau VM, Hogue C, Mewes HW, Apweiler R, Xenarios I, Eisenberg D, Cesareni G, Hermjakob H <a class="http" href="http://www.nature.com/nbt/journal/v25/n8/abs/nbt1324.html">Nat Biotechnol 2007 Aug;25(8):894-8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17687370">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_MIMIx_OrchardEtAl_NatBiotech_August.pdf" title="PDF">PDF</a> DATA STANDARD </li><li class="gap">Germ-line DNA copy number variation frequencies in a large North American population Zogopoulos G, Ha KC, Naqib F, Moore S, Kim H, Montpetit A, Robidoux F, Laflamme P, Cotterchio M, Greenwood C, Scherer SW, Zanke B, Hudson TJ, Bader GD, Gallinger S <a class="http" href="http://www.springerlink.com/content/f57t61764r0t21mv/">Hum Genet 2007 Nov;122(3-4):345-53</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&TermToSearch=17638019">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_Germ-lineDNACopyNumberVariationFrequenciesInALargeNorthAmericanPopulation_Zogopoulos_Bader_Gallinder_HumanGenetics.pdf" title="PDF">PDF</a> GENOMICS </li><li class="gap">From bytes to bedside: data integration and computational biology for translational cancer research Mathew JP, Taylor BS, Bader GD, Pyarajan S, Antoniotti M, Chinnaiyan AM, Sander C, Burakoff SJ, Mishra B <a class="http" href="http://compbiol.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pcbi.0030012">PLoS Comput Biol 2007 Feb 23;3(2):e12</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17319736">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_MatthewTaylorBader_TranslationalReview_PLoSCompBio_Feb.pdf" title="PDF">PDF</a> CANCER REVIEW </li><li class="gap">NetMatch: a Cytoscape Plugin for Searching Biological Networks Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D <a class="http" href="http://bioinformatics.oxfordjournals.org/cgi/reprint/btm032v1">Bioinformatics 2007 Apr 1;23(7):910-2</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17277332">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_NetMatch-ACytoscapePluginForSearchingBiologicalNetworks_Ferro_Guigno_Bader_Shasha_Apr.pdf" title="PDF">PDF</a> <a href="/Software/NetMatch">Download software</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Computational prediction of cancer-gene function Hu P, Bader G, Wigle DA, Emili A <a class="http" href="http://www.nature.com/nrc/journal/v7/n1/abs/nrc2036.html">Nature Reviews Cancer 2007 Jan;7(1):23-34</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17167517">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2007_ComputationalPredictionOfCancerGeneFunction_Hu_Bader_Wigle_Emili_NatRevCancer_Jan.pdf" title="PDF">PDF</a> CANCER REVIEW </li></ol> <h2 id="A2006">2006</h2> <ol type="1"><li>cPath: open source software for collecting, storing, and querying biological pathways Cerami EG, Bader GD, Gross BE, Sander C <a class="http" href="http://www.biomedcentral.com/1471-2105/7/497/abstract">BMC Bioinformatics 2006, 7:497</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17101041">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2006_cPathOpenSourceSoftwareForCollectingStoringAndQueryingBiologicalPathways_Cerami_Bader_Gross_Sander_BMCBioinfo_Nov.pdf" title="PDF">PDF</a> PATHWAY SOFTWARE </li><li class="gap">Pathguide: a Pathway Resource List Bader GD, Cary MP, Sander C <a class="http" href="http://nar.oxfordjournals.org/cgi/content/full/34/suppl_1/D504">Nucleic Acids Research 2006 Jan 1;34(Database issue):D504-6</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16381921&query_hl=14&itool=pubmed_docsum">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2006_Pathguide_Bader_Cary_Sander_NAR_Jan.pdf" title="PDF">PDF</a> PATHWAY WEBSITE </li></ol> <h2 id="A2005">2005</h2> <ol type="1"><li>Pathway information for systems biology Cary MP, Bader GD, Sander C <a class="http" href="http://www.febsletters.org/retrieve/pii/S0014579305001705">FEBS Lett 2005 Mar 21;579(8):1815-20</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=15763557&query_hl=14&itool=pubmed_docsum">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2005_PathwayInformationForSystemsBiology_Cary_Bader_Sander_FEBSLetters_Mar.pdf" title="PDF">PDF</a> PATHWAY REVIEW </li></ol> <h2 id="A2004">2004</h2> <ol type="1"><li>Global Mapping of the Yeast Genetic Interaction Network Tong AH, Lesage G, Bader GD, Ding H, Xu H, Xin X, Young J, Berriz GF, Brost RL, Chang M, Chen Y, Cheng X, Chua G, Friesen H, Goldberg DS, Haynes J, Humphries C, He G, Hussein S, Ke L, Krogan N, Li Z, Levinson JN, Lu H, Menard P, Munyana C, Parsons AB, Ryan O, Tonikian R, Roberts T, Sdicu AM, Shapiro J, Sheikh B, Suter B, Wong SL, Zhang LV, Zhu H, Burd CG, Munro S, Sander C, Rine J, Greenblatt J, Peter M, Bretscher A, Bell G, Roth FP, Brown GW, Andrews B, Bussey H, Boone C <a class="http" href="http://www.sciencemag.org/cgi/content/full/303/5659/808">Science 2004 Feb 6;303(5659):808-813</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14764870">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2004_GlobalMappingoftheYeastGeneticInteractionNetwork_TongEtAl_Science_Feb.pdf" title="PDF">PDF</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2004_SGA_Hartwell_comment.pdf" title="Science Perspective PDF">Science Perspective PDF</a> GENETIC INTERACTION NETWORK ANALYSIS </li><li class="gap">The HUPO PSI Molecular Interaction Format - a community standard for the representation of protein interaction data Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, Von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, Apweiler R <a class="http" href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n2/abs/nbt926.html&dynoptions=doi1079900147">Nature Biotechnology 2004 Feb;22(2):177-83</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/14755292">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2004_TheHUPOPSIsMolecularInteractionFormat_HermjakobMontecchiBaderEtAl_NatBiotech_Feb.pdf" title="PDF">PDF</a> DATA STANDARD </li></ol> <h2 id="A2003">2003</h2> <ol type="1"><li>Playing tag with the yeast proteome Andrews BJ, Bader GD, Boone C <a class="http" href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v21/n11/full/nbt1103-1297.html">Nature Biotechnology Nov;21(11):1297-1299</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=14595360">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2003_OsheaWeissmanReview_NatureBiotech.pdf" title="PDF">PDF</a> REVIEW </li><li class="gap">Functional Genomics and Proteomics: Charting a Multidimensional Map of the Cell Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C <a class="http" href="http://linkinghub.elsevier.com/retrieve/pii/S0962892403001272">Trends in Cell Biology Jul, 2003 13(7):344-56</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12837605&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2003_BaderHeilbutAndrewsTyersHughesBooneFunctionalGenomicsProteomicsReview.pdf" title="PDF">PDF</a> REVIEW </li><li class="gap">PreBIND and Textomy - mining the biomedical literature for protein-protein interactions using a support vector machine Donaldson I, Martin J, De Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, Hogue CW <a class="http" href="http://www.biomedcentral.com/1471-2105/4/11">BMC Bioinformatics Mar 27, 2003 4(1):11</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12689350&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=PreBIND_BMC2003.pdf" title="PDF">PDF</a> TEXT MINING SOFTWARE </li><li class="gap">Functional genomics of intracellular peptide recognition domains with combinatorial biology methods Sidhu SS, Bader GD, Boone C <a class="http" href="http://linkinghub.elsevier.com/retrieve/pii/S136759310200011X">Current Opinion in Chemical Biology 2003 Feb;7(1):97-102</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12547433&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2003_FunctionalGenomicsOfIntracellularPeptideRecognitionDomainsWithCombinatorialBiologyMethods_Sidhu_Bader_Boone_CurrOpinChemBiol_Feb.pdf" title="PDF">PDF</a> REVIEW </li><li class="gap">An automated method for finding molecular complexes in large protein interaction networks Bader GD, Hogue CWV <a class="http" href="http://www.biomedcentral.com/1471-2105/4/2">BMC Bioinformatics 2003 Jan 13;4(1):2</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12525261&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2003_BaderHogue_MCODE.pdf" title="PDF">PDF</a> ALGORITHM </li><li class="gap">BIND-The Biomolecular Interaction Network Database Bader GD, Betel D, Hogue CWV <a class="http" href="http://nar.oupjournals.org/cgi/content/abstract/31/1/248">Nucleic Acids Research Jan 1, 2003 31(1):248-250</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519993&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2003_BIND-theBiomolecularInteractionNetwork_Bader_Betel_Hogue_NAR_Jan.pdf" title="PDF">PDF</a> INTERACTION DATABASE </li></ol> <h2 id="A2002">2002</h2> <ol type="1"><li>SeqHound: biological sequence and structure database as a platform for bioinformatics research Michalickova K, Bader GD, Dumontier M, Lieu H, Betel D, Isserlin R, Hogue CW <a class="http" href="http://www.biomedcentral.com/1471-2105/3/32">BMC Bioinformatics 2002, 3:32 (25 October 2002)</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12401134&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2002_SeqHound_BMCBioinfo.pdf" title="PDF">PDF</a> PROTEIN DATABASE </li><li class="gap">Analyzing yeast protein–protein interaction data obtained from different sources Bader GD, Hogue CW <a class="http" href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nbt/journal/v20/n10/abs/nbt1002-991.html&dynoptions=doi1040752166">Nature Biotechnology 2002 Oct;20(10):991-997</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12355115&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BaderHogueNBT2002.pdf" title="PDF">PDF</a> META-ANALYSIS </li><li class="gap">A Combined Experimental and Computational Strategy to Define Protein Interaction Networks for Peptide Recognition Modules Tong AH, Drees B, Nardelli G, Bader GD, Brannetti B, Castagnoli L, Evangelista M, Ferracuti S, Nelson B, Paoluzi S, Quondam M, Zucconi A, Hogue CW, Fields S, Boone C, Cesareni G <a class="http" href="http://www.sciencemag.org/cgi/content/abstract/295/5553/321">Science 2002 Jan 11;295(5553):321-324</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743162&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=SH3ScienceJan11_2002.pdf" title="PDF">PDF</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Perspective_ScienceJan11_2002.pdf" title="Science Perspective PDF">Science Perspective PDF</a> PROTEIN INTERACTION PREDICTION </li><li class="gap">Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M <a class="http" href="http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v415/n6868/abs/415180a_fs.html">Nature 2002 Jan 10;415(6868): 180-183</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11805837&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=HMS-PCI-Nature-Jan10_2002.pdf" title="PDF">PDF</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=HMS-PCINewsAndViews-NatureJan10_2002.pdf" title="Nature News and Views PDF">Nature News and Views PDF</a> PROTEIN INTERACTION NETWORK ANALYSIS </li></ol> <h2 id="A2001">2001</h2> <ol type="1"><li>Systematic Genetic Analysis with Ordered Arrays of Yeast Deletion Mutants Tong AH, Evangelista M, Parsons AB, Xu H, Bader GD, Page N, Robinson M, Raghibizadeh S, Hogue CW, Bussey H, Andrews B, Tyers M, Boone C <a class="http" href="http://www.sciencemag.org/cgi/content/abstract/294/5550/2364">Science 2001 Dec 14;294(5550):2364-8</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11743205&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=SGA_ScienceVol294-2001.pdf" title="PDF">PDF</a> GENETIC INTERACTION NETWORK ANALYSIS </li><li class="gap">BIND - The Biomolecular Interaction Network Database Bader GD, Donaldson I, Wolting C, Ouellette BF, Pawson T, Hogue CW <a class="http" href="http://nar.oupjournals.org/cgi/content/abstract/29/1/242">Nucleic Acids Research Jan 1, 2001 29(1):242-245</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=11125103&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BIND_NAR_2001.pdf" title="PDF">PDF</a> INTERACTION DATABASE </li></ol> <h2 id="A2000">2000</h2> <ol type="1"><li>BIND - A data specification for storing and describing biomolecular interactions, molecular complexes and pathways Bader GD, Hogue CW <a class="http" href="http://bioinformatics.oupjournals.org/cgi/content/abstract/16/5/465">Bioinformatics 2000 May;16(5):465-77</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10871269&dopt=Abstract">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BIND_Spec_2000.pdf" title="PDF">PDF</a> INTERACTION DATABASE </li></ol> <h1 id="Preprints">Preprints</h1> <h2 id="A2024-1">2024</h2> <ol type="1"><li>Interpretable single-cell factor decomposition using sciRED Pouyabahar D, Andrews T, Bader GD <a class="https" href="https://www.biorxiv.org/content/10.1101/2024.08.01.605536v1">bioRxiv [Preprint]. 2024 Aug 6:2024.08.01.605536</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/39149356/">PubMed Abstract</a>-<a class="attachment" href="/Publications?action=AttachFile&do=view&target=preprintbioarxiv_August2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Direct lineage conversion of postnatal mouse cortical astrocytes to oligodendrocyte lineage cells Bajohr J, Scott EY, Olfat A, Sadria M, Lee K, Fahim M, Taha HT, Casasbuenas DL, Derham A, Yuzwa SA, Bader GD, Maryam Faiz <a class="https" href="https://www.biorxiv.org/content/10.1101/2024.05.28.596294v1.abstract">bioRxiv [Preprint]. May 2024 - 2024.05.28.596294</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=preprint_May2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Deep Lineage: Single-Cell Lineage Tracing and Fate Inference Using Deep Learning Sadria M, Zhang A, Bader GD <a class="https" href="https://www.biorxiv.org/content/10.1101/2024.04.25.591126v1.abstract">bioRxiv [Preprint]. April 2024 - 2024.04.25.591126</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=preprint_April2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Single-cell analysis of an engineered organoid-based model of pancreatic cancer identifies hypoxia as a contributing factor in the determination of transcriptional subtypes Natalie Landon-Brace N, Innes BT, Latour S, Cadavid JL, Co IL, Tan CM, Nowlan F, Drissler S, Notta F, Jackson HW, Bader GD, McGuigan AP <a class="https" href="https://www.biorxiv.org/content/10.1101/2024.03.05.583412v1.abstract">bioRxiv [Preprint]. March 2024 - 2024.03.14.584861</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=preprint_March2024.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">PRMT5 is required for full-length HTT expression by repressing multiple proximal intronic polyadenylation sites AlQazzaz MA, Ciamponi FE, Ho JC, Maron MI, Yadav M, Sababi AM, MacLeod G, Ahmadi M, Bullivant G, Tano V, Langley SR, Sánchez-Osuna M, Sachamitr P, Kushida M, Richards L, Bardile CF, Pouladi MA, Pugh T, Tyers M, Angers S, Dirks PB, Bader GD, Massirer KB, Barsyte-Lovejoy D, Shechter D, Harding RJ, Arrowsmith CH, Prinos P <a class="https" href="https://www.biorxiv.org/content/10.1101/2024.03.14.584861v1.article-info">bioRxiv [Preprint]. March 2024 - 2024.03.05.583412</a> <a class="attachment" href="/Publications?action=AttachFile&do=view&target=preprint_March2024_2.pdf" title="PDF">PDF</a> SINGLE CELL GENOMICS </li><li class="gap">Metformin reduces the clonal fitness of Dnmt3aR878H hematopoietic stem and progenitor cells by reversing their aberrant metabolic and epigenetic state Hosseini M, Voisin V, Chegini A, Varesi A, Cathelin S, Ayyathan DM, Liu ACH, Yang Y, Wang V, Maher A, Grignano E, Reisz JA, D'Alessandro A, Young K, Wu Y, Fiumara M, Ferrari S, Naldini L, Gaiti F, Pai S, Schimmer AD, Bader GD, Dick JE, Xie SZ, Trowbridge JJ, Chan SM <a class="https" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10889081/">Preprint 2024 Feb 6</a> <a class="https" href="https://pubmed.ncbi.nlm.nih.gov/38405837/">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=preprint_Feb2024.pdf" title="PDF">PDF</a> PATHWAY AND NETWORK ANALYSIS, SINGLE CELL GENOMICS </li></ol> <h2 id="A2023-1">2023</h2> <ol type="1"><li>Cell networks in the mouse liver during partial hepatectomy Li B, Rodrigo-Torres D, Pelz C, Innes B, Canaday P, Chai S, Zandstra P, Bader GD, Grompe M <a class="https" href="https://www.biorxiv.org/content/10.1101/2023.07.16.549116v1">bioRxiv [Preprint]. 2023 Jul</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/37503083">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Mouseliver_BioarxivJuly2023.pdf" title="PDF">PDF</a> </li><li class="gap">Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Oubounyt M, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Pržulj N, Sadegh S, Saez-Rodriguez J, Sakar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang R, Zolotareva O, Baumbach J <a class="https" href="https://arxiv.org/abs/2305.15453">ArXiv [Preprint]. 2023 May 24</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/37332567">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=drugstone_BioarxivJune202023.pdf" title="PDF">PDF</a> </li></ol> <h2 id="A2022-1">2022</h2> <ol type="1"><li> A single-nucleus and spatial transcriptomic atlas of the COVID-19 liver reveals topological, functional, and regenerative organ disruption in patients Pita-Juarez Y, Karagkouni D, Kalavros N, Melms JC, Niezen S, Delorey TM, Essene AL, Brook OR, Pant D, Skelton-Badlani D, Naderi P, Huang P, Pan L, Hether T, Andrews TS, Ziegler CGK, Reeves J, Myloserdnyy A, Chen R, Nam A, Phelan S, Liang Y, Amin AD, Biermann J, Hibshoosh H, Veregge M, Kramer Z, Jacobs C, Yalcin Y, Phillips D, Slyper M, Subramanian A, Ashenberg O, Bloom-Ackermann Z, Tran VM, Gomez J, Sturm A, Zhang S, Fleming SJ, Warren S, Beechem J, Hung D, Babadi M, Padera RF, MacParland SA, Bader GD, Imad N, Solomon IH, Miller E, Riedel S, Porter CBM, Villani AC, Tsai LT, Hide W, Szabo G, Hecht J, Rozenblatt-Rosen O, Shalek AK, Izar B, Regev A, Popov Y, Jiang ZG, Vlachos IS <a class="https" href="https://www.biorxiv.org/content/10.1101/2022.10.27.514070v1">bioRxiv Preprint. 2022 Oct 28</a> <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/36324805">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=BioarxivOct282022.pdf" title="PDF">PDF</a> COVID-19 </li></ol> <h1 id="Textbook_Chapters">Textbook Chapters</h1> <h2 id="A2020-1">2020</h2> <ol type="1"><li>Biological Networks and Pathways Bader GD. in <a class="https" href="https://www.wiley.com/en-us/Bioinformatics,+4th+Edition-p-9781119335580">Bioinformatics 4th Eds. Andreas D. Baxevanis, Gary D. Bader, and David Wishart. John Wiley and Sons, New Jersey</a> NETWORK ANALYSIS </li></ol> <h2 id="A2018-1">2018</h2> <ol type="1"><li>Automated Computational Inference of Multi-protein Assemblies from Biochemical Co-purification Data Goebels F., Hu L., Bader G., Emili A. <a class="https" href="https://link.springer.com/protocol/10.1007/978-1-4939-7759-8_25">Methods Mol Bio 2018;1764:391-399</a> - <a class="https" href="https://www.ncbi.nlm.nih.gov/pubmed/29605929">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=automatedcopm.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li></ol> <h2 id="A2014-1">2014</h2> <ol type="1"><li>Biological network exploration with Cytoscape 3 Su G, Morris JH, Demchak B, Bader GD <a class="http" href="http://dx.doi.org/10.1002/0471250953.bi0813s47">Curr Protoc Bioinformatics 2014 Sep 8;47:8.13.1-8.13.24</a> - <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/25199793">PubMed Abstract</a> - <a class="attachment nonexistent" href="/Publications?action=AttachFile&do=upload_form&ticket=0067b6db71.0b6db5bcfc7bdb3fbe365a002b413a77f6f00035&target=CurrProtocols2014.pdf" title="Upload new attachment "CurrProtocols2014.pdf"">PDF</a> NETWORK ANALYSIS SOFTWARE </li></ol> <h2 id="A2011-1">2011</h2> <ol type="1"><li>Displaying chemical information on a biological network using cytoscape Wallace IM, Bader GD, Giaever G, Nislow C <a class="http" href="http://www.springerlink.com/content/q321h06847668r94/#section=953422&page=1">Methods Mol Biol 2011;781:363-76</a> - <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21877291">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=ChemicalInformationCytoscape_Wallace2011.pdf" title="PDF">PDF</a> <a class="http" href="http://baderlab.org/VisualizingChemicalInformation">Supplemental Website</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map Merico D, Isserlin R, Bader GD <a class="http" href="http://www.springerlink.com/content/hq415338j6u8k124/#section=953415&page=1">Methods Mol Biol 2011;781:257-77</a> - <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/21877285">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=EnrichmentMapsCytoscape_MericoIsserlin2011.pdf" title="PDF">PDF</a> NETWORK ANALYSIS SOFTWARE </li></ol> <h2 id="A2008-1">2008</h2> <ol type="1"><li>Exploring Biological Networks with Cytoscape Software Natalie Yeung, Melissa S. Cline, Allan Kuchinsky, Michael E. Smoot, and Gary D. Bader <a class="http" href="http://mrw.interscience.wiley.com/emrw/9780471250951/cp/cpbi/article/bi0813/current/abstract">Current Protocols in Bioinformatics</a> - <a class="http" href="http://www.ncbi.nlm.nih.gov/pubmed/18819078">PubMed Abstract</a> - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=CytoscapeCurrProtocolsProof-YeungBader_Sep2008.pdf" title="PDF">PDF</a> John Wiley & Sons, Inc. NETWORK ANALYSIS SOFTWARE </li></ol> <h2 id="A2006-1">2006</h2> <ol type="1"><li>BioPAX - Biological Pathway Data Exchange Format Gary D. Bader, Michael Cary, Chris Sander <a class="http" href="http://www.mrw.interscience.wiley.com/ggpb/articles/g408117/frame.html">Encyclopedia of Genomics, Proteomics and Bioinformatics</a> Humana Press, New Jersey DATA STANDARD </li></ol> <h2 id="A2005-1">2005</h2> <ol type="1"><li>Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Rowan Christmas, Iliana Avila-Campillo, Hamid Bolouri, Benno Schwikowski, Mark Anderson, Ryan Kelley, Nerius Landys, Chris Workman, Trey Ideker, Ethan Cerami, Rob Sheridan, Gary D. Bader, and Chris Sander <a class="http" href="http://educationbook.aacrjournals.org/cgi/content/full/2005/1/12">Am Assoc Cancer Res Educ Book 2005: 12-16</a> NETWORK ANALYSIS SOFTWARE </li><li class="gap">Exploiting Synthetic Genetic Interactions to Predict Pathways and Complexes Gary D. Bader, Amy Tong, Lan V. Zhang, Frederick P. Roth, Brenda Andrews and Charles Boone in <a class="http" href="http://www.amazon.com/gp/product/0879697237/qid=1147320880/sr=1-1/ref=sr_1_1/102-2952413-6681722?s=books&v=glance&n=283155">Protein-Protein Interactions: A Molecular Cloning Manual, 2nd Edition</a> Ed. Erica Golemis, Cold Spring Harbor Laboratory Press, New York, USA GENETIC INTERACTION NETWORK ANALYSIS </li></ol> <h2 id="A2004-1">2004</h2> <ol type="1"><li>Interaction Databases, in Genomics and Bioinformatics, 2nd Edition Gary D. Bader, Christopher W.V. Hogue in <a class="http" href="http://www.wiley-vch.de/books/biotech/con_v05b.html">Volume 5B of the Series: Biotechnology, 2nd Edition</a> Eds Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany INTERACTION DATABASE </li><li class="gap">Intermolecular Interactions and Biological Pathways Gary D. Bader, Anton J. Enright in <a class="http" href="http://jws-edcv.wiley.com/college/bcs/redesign/student/0,,_0471478784_BKS_2102____,00.html">Bioinformatics 3E Eds. Andreas D. Baxevanis and B.F.Francis Ouellette. John Wiley and Sons, New Jersey</a> INTERACTION DATABASE </li><li class="gap">Computational Prediction of Protein-Protein Interactions Anton J. Enright, Lucy Skrabanek, Gary D. Bader in <a class="http" href="http://www.humanapress.com/ProductDetail.pasp?txtCatalog=HumanaBooks&txtProductID=1-58829-593-1">The Proteomics Handbook Ed. John Walker. (Humana Press, New Jersey)</a> PROTEIN INTERACTION PREDICTION </li></ol> <h2 id="A2003-1">2003</h2> <ol type="1"><li>Peptide Recognition Module Networks: Combining Phage Display with Two-hybrid Analysis to Define Protein-Protein Interactions Gary D. Bader, Amy Hin Yan Tong, Gianni Cesareni, Christopher W.V. Hogue, Stanley Fields, Charles Boone in <a class="http" href="http://books.elsevier.com/us//apcatalog/us/subindex.asp?maintarget=&isbn=0121245462">Handbook of Cell Signaling</a> Eds. Ralph Bradshaw and Edward Dennis. (San Diego: Academic/Elsevier Press) <a class="attachment" href="/Publications?action=AttachFile&do=view&target=2003_PeptideRecognitionModuleNetworks.pdf" title="PDF">PDF</a> PROTEIN INTERACTION PREDICTION </li></ol> <h2 id="A2002-1">2002</h2> <ol type="1"><li>Interaction Databases Gary D. Bader, Christopher W.V. Hogue Chapter 18, in <a class="http" href="http://www.wiley-vch.de/books/biotech/vol_05b.html">Genomics and Bioinformatics (Volume 5B of the Series: Biotechnology, 2nd Edition.)</a> Eds. Rehm, H.-J., Reed, G., Pühler, A., Stadler, P. Wiley-VCH, Germany INTERACTION DATABASE </li></ol> <h1 id="Theses">Theses</h1> <ol type="1"><li>2023 Duncan Forster - BIONIC: Biological Network Integration using Convolutions - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Forster_Duncan_Terell_202311_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2023 Brendan Innes - Intercellular Signaling Networks of a Tissue from Single-Cell Transcriptomics - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Innes_Brendan_T_202406_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2022 Owen Whitley - Transcriptional and Multi -Omic Heterogeneity in Glioblastoma Stem Cells - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Whitley_Owen_Kenneth+Nora_202211_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2021 Gurnit Atwal - Automatic tumour typing based on patterns of somatic passenger mutations - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Atwal_Gurnit_202106_PhD_Thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2021 Stuart Matan-Lithwick - Identifying Novel Genes and Pathways Correlated with Group 3 and Group 4 Medulloblastoma Metastasis to the Spine - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Lithwick__Stuart_Aaron+%28Matan-Lithwick%29_202106_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2020 Patryk Skowron - Deciphering Genetic Drivers in Primary and Metastatic Medulloblastoma - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Skowron_Patryk_+_202006_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Laboratory Medicine and Pathobiology </li><li>2020 Lucas Hu - Biochemical Profile-Based Computational Inference of Protein Complexes - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Hu_Zhongming_+_202006_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2019 Brian Law - Protein-Protein Interaction Network Alignment and Evolution - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Law_Brian_201911_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Computer Science </li><li>2019 Thinh Ngoc Tran - Pathway-based Lineage Analysis of Time-course Single-Cell RNA Sequencing Data - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Tran_Thinh_N_201911_MSc_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Molecular Genetics </li><li>2018 Catherine Ross - Detecting Signals of Coevolution within Immune Response Pathways in the African-American Ancestral Population - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Ross_Catherine_201806_MSc_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Molecular Genetics </li><li>2018 Shobhit Jain - Computational Models For Domain-Peptide Mediated Protein-Protein Interactions - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Jain_Shobhit_201806_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Computer Science </li><li>2015 David Shih - Molecular Classification and Clinical Genomics of Medulloblastoma - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Shih_J._H._David_201511_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Laboratory Medicine and Pathobiology </li><li>2015 Marina Olhovsky - Using Text Mining of <a class="nonexistent" href="/PubMed">PubMed</a> Abstracts as an Evidence Source in Computational Predictions of WW Domain-Mediated Protein-Protein Interactions - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Olhovsky_Marina_2015_Masters.pdf" title="PDF">PDF</a>, York University, Graduate Program in Biology </li><li>2013 Omar Wagih - Assessing the impact of single nucleotide variants on kinase–substrate phosphorylation - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=omarwagih_thesis_msc.pdf" title="PDF">PDF</a>, University of Toronto, Department of Computer Science </li><li>2013 Shirley Hui - Computational Prediction of PDZ Mediated Protein-Protein Interactions - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Hui_Shirley_201311_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2013 Ron Ammar - Understanding Genome Structure and Response to Perturbation - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Ammar_Ron_201311_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2013 Anastasia Baryshnikova - Mapping Genetic Interaction Networks in Yeast - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Baryshnikova_Anastasia_201303_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2012 Chris Tan - Characterizing the Evolutionary Dynamics of Protein Phosphorylation Sites for Functional Phospho-proteomics - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=Tan_SoonHeng_20126_PhD_thesis.pdf" title="PDF">PDF</a>, University of Toronto, Department of Molecular Genetics </li><li>2011 Xiaojian Shao - Prediction of Protein-Nucleic Acids and Protein-Protein Interactions Using Kernel Methods - <a class="attachment" href="/Publications?action=AttachFile&do=view&target=PhDThesis%28XiaojianShao%29.pdf" title="PDF">PDF</a> (in Mandarin), China Agricultural University and the University of Toronto </li></ol></div>  <div class="clearfix"></div> </div>   </div>  </div>   <div id="pageinfo-container"> <div class="container"> Publications (last edited 2024-12-09 17:34:14 by <a href="/RuthIsserlin" title="RuthIsserlin @ server2.baderlab.med.utoronto.ca[192.168.81.22]">RuthIsserlin</a>) </div> </div>   <div id="footer"> <div class="container text-right text-muted"> <ul id="credits"> <li><a href="http://moinmo.in/" title="This site uses the MoinMoin Wiki software.">MoinMoin Powered</a></li><li><a href="http://moinmo.in/Python" title="MoinMoin is written in Python.">Python Powered</a></li><li><a href="http://moinmo.in/GPL" title="MoinMoin is GPL licensed.">GPL licensed</a></li><li><a href="http://validator.w3.org/check?uri=referer" title="Click here to validate this page.">Valid HTML 4.01</a></li> </ul> <center><a href='http://host-tracker.com/' onMouseOver='this.href='http://host-tracker.com/website-uptime-statistics/474337/lvuc/';'><img width=80 height=15 border=0 alt='website tracker' src='http://ext.host-tracker.com/uptime-img/?s=15&t=474337&m=00.0&p=Total&src=lvuc'></a><noscript><a href='http://host-tracker.com/' >remote server monitor</a></noscript></center><script src='http://www.google-analytics.com/urchin.js' type='text/javascript'></script><script type='text/javascript'> _uacct = 'UA-387720-1';urchinTracker();</script> </div>  </div>     <script src="/moin_static198/memodump/js/jquery.min.js"></script>  <script src="/moin_static198/memodump/js/bootstrap.min.js"></script>  <script src="/moin_static198/memodump/js/toggle.js"></script>  <script> +function ($) { // Toggle minified navbar under mobile landscape view $('.navbar-collapse').on('show.bs.collapse', function () { $('.navbar-mobile-toggle').togglejs('show'); }); $('.navbar-collapse').on('hidden.bs.collapse', function () { $('.navbar-mobile-toggle').togglejs('hide'); }); //Scroll position fix for hash anchors var mdAnchorFix = { escapeRe: /[ !"#$%&'()*+,.\/:;<=>?@\[\\\]^`{|}~]/g, escape: function (str) { return str.replace(mdAnchorFix.escapeRe, '\\$&'); }, rgbRe: /^rgba$([ \t]*\d{1,3},){3}([ \t]*\d{1,3})$$/i, isTransparent: function (rgbstr) { if (rgbstr === 'transparent') { return true; } rgbMatch = rgbstr.match(mdAnchorFix.rgbRe); if (rgbMatch) { return (Number(rgbMatch[2]) ? false : true); } return false; }, navbarHeight: function () { var height = 0; var $navbar = $('.navbar'); if ( !mdAnchorFix.isTransparent($navbar.css('background-color')) && ($navbar.css('display') !== 'none') && ($navbar.css('visibility') !== 'hidden') ) { height = $navbar.height(); } return height; }, jump: function () { origin = $('#' + mdAnchorFix.escape(location.hash.substr(1))).offset().top; offset = mdAnchorFix.navbarHeight() + 15; setTimeout(function () { window.scrollTo(0, origin - 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