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Author Details

Ugur Dogrusoz
Bilkent University
2002
30
17
PMIDPaper TitleJournal TitlePublished Year
37426048A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance.Front Bioinform2023
34232882fCoSE: A Fast Compound Graph Layout Algorithm with Constraint Support.IEEE Trans Vis Comput Graph2022
36374853SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more.PLoS Comput Biol2022
33010165Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps.Bioinformatics2021
34877547Analyzing causal relationships in proteomic profiles using CausalPath.STAR Protoc2021
32568733Systems biology graphical notation markup language (SBGNML) version 0.3.J Integr Bioinform2020
31647099Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.Nucleic Acids Res2020
33146381cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.Bioinformatics2020
29688273Community-driven roadmap for integrated disease maps.Brief Bioinform2019
31199769Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.J Integr Bioinform2019
29625050Oncogenic Signaling Pathways in The Cancer Genome Atlas.Cell2018
29813080Efficient methods and readily customizable libraries for managing complexity of large networks.PLoS One2018
29872544Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.NPJ Syst Biol Appl2018
28334343PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.Bioinformatics2017
26363029An algorithm for automated layout of process description maps drawn in SBGN.Bioinformatics2016
26030594SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.PLoS One2015
25086704Integrating biological pathways and genomic profiles with ChiBE 2.BMC Genomics2014
23550210Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.Sci Signal2013
23559509CiSE: a circular spring embedder layout algorithm.IEEE Trans Vis Comput Graph2013
22581176Software support for SBGN maps: SBGN-ML and LibSBGN.Bioinformatics2012
22588877The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.Cancer Discov2012
20007251ChiBE: interactive visualization and manipulation of BioPAX pathway models.Bioinformatics2010
20466809Discovering modulators of gene expression.Nucleic Acids Res2010
20460470VISIBIOweb: visualization and layout services for BioPAX pathway models.Nucleic Acids Res2010
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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Collaborators

Emek Demir
Knight Cancer Institute, Oregon Health & Science University
Co-authored papers 15
Ozgun Babur
Houston Methodist Research Institute
Co-authored papers 13
Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 9
Augustin Luna
Harvard Medical School
Co-authored papers 7
Nikolaus Schultz
Memorial Sloan Kettering Cancer Center
Co-authored papers 5
Bülent Arman Aksoy
Co-authored papers 5
Jianjiong Gao
Memorial Sloan Kettering Cancer Center
Co-authored papers 4
Benjamin E Gross
Memorial Sloan Kettering Cancer Center
Co-authored papers 4
Nicolas Le Nov??re
Babraham Institute
Co-authored papers 4
Reinhard Schneider
Co-authored papers 3
Selcuk Onur Sumer
Co-authored papers 3
Ethan Cerami
Dana-Farber Cancer Institute
Co-authored papers 3
Charles Auffray
European Institute for Systems Biology and Medicine
Co-authored papers 3
Istemi Bahceci
Bilkent University
Co-authored papers 3
Andrei Zinovyev
INSERM U, Institut Curie, PSL Research University
Co-authored papers 3
Huaiyu Mi
University of Southern California
Co-authored papers 3
Erik Larsson
Co-authored papers 2
Leonard Dervishi
Case Western Reserve University
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Rengul Cetin-Atalay
Middle East Technical University
Co-authored papers 2
Mirit I Aladjem
National Cancer Institute, Center for Cancer Research
Co-authored papers 2
Hiroaki Kitano
Co-authored papers 2
Vasundra Tour??
Norwegian University of Science and Technology (NTNU)
Co-authored papers 2
Anders Jacobsen Skanderup
Co-authored papers 2
Konnor La
The Rockefeller University
Co-authored papers 2
Stephan Gebel
Co-authored papers 2
Emmanuel Barillot
Institut Curie, Universite PSL
Co-authored papers 2
Peter Ghazal
UK System Immunity Research Institute, Cardiff University
Co-authored papers 1
Han Liang
MD Anderson Cancer Center
Co-authored papers 1
Steven M Foltz
Washington University in St. Louis
Co-authored papers 1
Cyriac Kandoth
University of California los angeles
Co-authored papers 1
Release 1.2