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Author Details

Ozgun Babur
Houston Methodist Research Institute
2002
40
20
PMIDPaper TitleJournal TitlePublished Year
37333072A prognostic matrix code defines functional glioblastoma phenotypes and niches.bioRxiv2023
37790408A prognostic matrix code defines functional glioblastoma phenotypes and niches.Res Sq2023
37986684A framework for considering prior information in network-based approaches to omics data analysis.Proteomics2023
37730182Protein Kinase Signaling Networks Driven by Oncogenic Gq/11 in Uveal Melanoma Identified by Phosphoproteomic and Bioinformatic Analyses.Mol Cell Proteomics2023
35105861PPM1D mutations are oncogenic drivers of de novo diffuse midline glioma formation.Nat Commun2022
33010165Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps.Bioinformatics2021
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
34569154A highly multiplexed quantitative phosphosite assay for biology and preclinical studies.Mol Syst Biol2021
34171263The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance.Cancer Cell2021
32640021Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs.Blood2020
31647099Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.Nucleic Acids Res2020
30977292Identification, Quantification, and System Analysis of Protein N-ε Lysine Methylation in Anucleate Blood Platelets.Proteomics2019
31509758Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas.Cell Rep2019
31365877Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas.Cell Rep2019
29316429Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma.Cancer Cell2018
29933164Composition and risk assessment of roasted pyrite ash from fertiliser production.Chemosphere2018
30256986Large-scale automated machine reading discovers new cancer-driving mechanisms.Database (Oxford)2018
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
28810145Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma.Cancer Cell2017
28334343PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.Bioinformatics2017
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
26030594SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.PLoS One2015
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
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
24068901Using biological pathway data with paxtools.PLoS Comput Biol2013
21071392Pathway Commons, a web resource for biological pathway data.Nucleic Acids Res2011
20007251ChiBE: interactive visualization and manipulation of BioPAX pathway models.Bioinformatics2010
20466809Discovering modulators of gene expression.Nucleic Acids Res2010
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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Collaborators

Emek Demir
Knight Cancer Institute, Oregon Health & Science University
Co-authored papers 27
Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 15
Ugur Dogrusoz
Bilkent University
Co-authored papers 13
Bülent Arman Aksoy
Co-authored papers 9
Augustin Luna
Harvard Medical School
Co-authored papers 6
Joseph E Aslan
Oregon Health & Science University
Co-authored papers 5
Nikolaus Schultz
Memorial Sloan Kettering Cancer Center
Co-authored papers 5
Selcuk Onur Sumer
Co-authored papers 4
Gary D Bader
University of Toronto
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Rehan Akbani
The University of Texas MD Anderson Cancer Center
Co-authored papers 4
Larry L David
Oregon Health and Science University
Co-authored papers 3
Benjamin M Gyori
Khoury College of Computer Sciences, Northeastern University
Co-authored papers 3
Charles Auffray
European Institute for Systems Biology and Medicine
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Benjamin E Gross
Memorial Sloan Kettering Cancer Center
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Ina Felau
National Cancer Institute
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Roel G W Verhaak
Yale School of Medicine
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Gordon B Mills
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Marc Gillespie
Ontario Institute for Cancer Research
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Aurelien Dugourd
Institute of Experimental Medicine and Systems Biology, RWTH Aachen University
Co-authored papers 2
Reinhard Schneider
Co-authored papers 2
Olivier Lichtarge
Baylor College of Medicine
Co-authored papers 2
Christopher C Benz
Buck Institute for Research on Aging
Co-authored papers 2
Alexander J Lazar
The University of Texas MD Anderson Cancer Center
Co-authored papers 2
Julian M Hess
Broad Institute of MIT and Harvard
Co-authored papers 2
Christina Yau
University of California San Francisco
Co-authored papers 2
Amy G Robertson
Present address: Dxige Research Inc.
Co-authored papers 2
Roger Stephan
Ontario Institute for Cancer Research
Co-authored papers 2
Carole Goble
University of Manchester
Co-authored papers 2
Karen Rothfels
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