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Author Details

Emek Demir
Knight Cancer Institute, Oregon Health & Science University
2002
48
25
PMIDPaper TitleJournal TitlePublished Year
36526735Asxl1 deletion disrupts MYC and RNA polymerase II function in granulocyte progenitors.Leukemia2023
36976323Disruption of the MYC Superenhancer Complex by Dual Targeting of FLT3 and LSD1 in Acute Myeloid Leukemia.Mol Cancer Res2023
34788843The reactome pathway knowledgebase 2022.Nucleic Acids Res2022
33010165Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps.Bioinformatics2021
337539822D MXenes with antiviral and immunomodulatory properties: A pilot study against SARS-CoV-2.Nano Today2021
34860157Author-sourced capture of pathway knowledge in computable form using Biofactoid.Elife2021
34939300COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Mol Syst Biol2021
34877547Analyzing causal relationships in proteomic profiles using CausalPath.STAR Protoc2021
34664389COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Mol Syst Biol2021
33957863Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes.BMC Bioinformatics2021
34171263The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance.Cancer Cell2021
32371892COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.Sci Data2020
31647099Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.Nucleic Acids Res2020
32678106Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.Sci Data2020
32640021Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs.Blood2020
31417090Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis.Nat Commun2019
31199769Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.J Integr Bioinform2019
29412690Platelet procoagulant phenotype is modulated by a p38-MK2 axis that regulates RTN4/Nogo proximal to the endoplasmic reticulum: utility of pathway analysis.Am J Physiol Cell Physiol2018
30256986Large-scale automated machine reading discovers new cancer-driving mechanisms.Database (Oxford)2018
28148498Assessment of roles for the Rho-specific guanine nucleotide dissociation inhibitor Ly-GDI in platelet function: a spatial systems approach.Am J Physiol Cell Physiol2017
26685306PaxtoolsR: pathway analysis in R using Pathway Commons.Bioinformatics2016
27453469Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.Cell2016
25451034Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites.J Mol Biol2015
26528563Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.J Integr Bioinform2015
26528562Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.J Integr Bioinform2015
26528561Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.J Integr Bioinform2015
26284497Perturbation biology nominates upstream-downstream drug combinations in RAF inhibitor resistant melanoma cells.Elife2015
25887147Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.Genome Biol2015
26030594SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.PLoS One2015
25759811Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative.Front Bioeng Biotechnol2015
24045775Pattern search in BioPAX models.Bioinformatics2014
25086704Integrating biological pathways and genomic profiles with ChiBE 2.BMC Genomics2014
24665131Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.Bioinformatics2014
23918249The BioPAX Validator.Bioinformatics2013
24068901Using biological pathway data with paxtools.PLoS Comput Biol2013
22581176Software support for SBGN maps: SBGN-ML and LibSBGN.Bioinformatics2012
21071392Pathway Commons, a web resource for biological pathway data.Nucleic Acids Res2011
22021903BioPAX support in CellDesigner.Bioinformatics2011
22180826Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE).Stand Genomic Sci2011
20007251ChiBE: interactive visualization and manipulation of BioPAX pathway models.Bioinformatics2010
20466809Discovering modulators of gene expression.Nucleic Acids Res2010
20169195Automated network analysis identifies core pathways in glioblastoma.PLoS One2010
19668183The Systems Biology Graphical Notation.Nat Biotechnol2009
19917102Algorithms for effective querying of compound graph-based pathway databases.BMC Bioinformatics2009
18452226PATIKAmad: putting microarray data into pathway context.Proteomics2008
16287939PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.Bioinformatics2006
14960461An ontology for collaborative construction and analysis of cellular pathways.Bioinformatics2004
12117798PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.Bioinformatics2002
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Houston Methodist Research Institute
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Co-authored papers 21
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Co-authored papers 15
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Joseph E Aslan
Oregon Health & Science University
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Brian J Druker
Oregon Health & Science University
Co-authored papers 3
Marija Milacic
Co-authored papers 3
Tom C Freeman
The Roslin Institute, University of Edinburgh
Co-authored papers 3
Laurence Calzone
Institut Curie, Universite PSL
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Lisa Matthews
NYU Grossman School of Medicine
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Guanming Wu
Oregon Health and Science University
Co-authored papers 3
Cristoffer Sevilla
Co-authored papers 3
Roger Stephan
Ontario Institute for Cancer Research
Co-authored papers 3
Karen Rothfels
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Release 1.2