Ugur Dogrusoz

Ugur Dogrusoz

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Ugur Dogrusoz

Ugur Dogrusoz

Publications by authors named "Ugur Dogrusoz"

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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

Authors:
Adrien Rougny Vasundra Touré Stuart Moodie Irina Balaur Tobias Czauderna Hanna Borlinghaus Ugur Dogrusoz Alexander Mazein Andreas Dräger Michael L Blinov Alice Villéger Robin Haw Emek Demir Huaiyu Mi Anatoly Sorokin Falk Schreiber Augustin Luna

J Integr Bioinform 2019 Jun 13;16(2). Epub 2019 Jun 13.

cBio Center, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

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http://dx.doi.org/10.1515/jib-2019-0022DOI Listing
June 2019

Community-driven roadmap for integrated disease maps.

Authors:
Marek Ostaszewski Stephan Gebel Inna Kuperstein Alexander Mazein Andrei Zinovyev Ugur Dogrusoz Jan Hasenauer Ronan M T Fleming Nicolas Le Novère Piotr Gawron Thomas Ligon Anna Niarakis David Nickerson Daniel Weindl Rudi Balling Emmanuel Barillot Charles Auffray Reinhard Schneider

Brief Bioinform 2019 03;20(2):659-670

Luxembourg Centre for Systems Biomedicine, Universite du Luxembourg, 7 Avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.

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https://academic.oup.com/bib/advance-article/doi/10.1093/bib
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http://dx.doi.org/10.1093/bib/bby024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556900PMC
March 2019

Efficient methods and readily customizable libraries for managing complexity of large networks.

Authors:
Ugur Dogrusoz Alper Karacelik Ilkin Safarli Hasan Balci Leonard Dervishi Metin Can Siper

PLoS One 2018 29;13(5):e0197238. Epub 2018 May 29.

Computer Engineering Dept., Bilkent University, Ankara 06800, Turkey.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0197238PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5973603PMC
December 2018

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

Authors:
Alexander Mazein Marek Ostaszewski Inna Kuperstein Steven Watterson Nicolas Le Novère Diane Lefaudeux Bertrand De Meulder Johann Pellet Irina Balaur Mansoor Saqi Maria Manuela Nogueira Feng He Andrew Parton Nathanaël Lemonnier Piotr Gawron Stephan Gebel Pierre Hainaut Markus Ollert Ugur Dogrusoz Emmanuel Barillot Andrei Zinovyev Reinhard Schneider Rudi Balling Charles Auffray

NPJ Syst Biol Appl 2018 2;4:21. Epub 2018 Jun 2.

1European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Avenue Tony Garnier, 69007 Lyon, France.

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http://dx.doi.org/10.1038/s41540-018-0059-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984630PMC
June 2018

Oncogenic Signaling Pathways in The Cancer Genome Atlas.

Authors:
Francisco Sanchez-Vega Marco Mina Joshua Armenia Walid K Chatila Augustin Luna Konnor C La Sofia Dimitriadoy David L Liu Havish S Kantheti Sadegh Saghafinia Debyani Chakravarty Foysal Daian Qingsong Gao Matthew H Bailey Wen-Wei Liang Steven M Foltz Ilya Shmulevich Li Ding Zachary Heins Angelica Ochoa Benjamin Gross Jianjiong Gao Hongxin Zhang Ritika Kundra Cyriac Kandoth Istemi Bahceci Leonard Dervishi Ugur Dogrusoz Wanding Zhou Hui Shen Peter W Laird Gregory P Way Casey S Greene Han Liang Yonghong Xiao Chen Wang Antonio Iavarone Alice H Berger Trever G Bivona Alexander J Lazar Gary D Hammer Thomas Giordano Lawrence N Kwong Grant McArthur Chenfei Huang Aaron D Tward Mitchell J Frederick Frank McCormick Matthew Meyerson Eliezer M Van Allen Andrew D Cherniack Giovanni Ciriello Chris Sander Nikolaus Schultz

Cell 2018 04;173(2):321-337.e10

Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Departments of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.03.035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6070353PMC
April 2018

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data.

Authors:
Istemi Bahceci Ugur Dogrusoz Konnor C La Özgün Babur Jianjiong Gao Nikolaus Schultz

Bioinformatics 2017 Jul;33(14):2238-2240

Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx149DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859976PMC
July 2017

SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps.

Authors:
Mecit Sari Istemi Bahceci Ugur Dogrusoz Selcuk Onur Sumer Bülent Arman Aksoy Özgün Babur Emek Demir

PLoS One 2015 1;10(6):e0128985. Epub 2015 Jun 1.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0128985PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4451519PMC
April 2016

An algorithm for automated layout of process description maps drawn in SBGN.

Authors:
Begum Genc Ugur Dogrusoz

Bioinformatics 2016 Jan 10;32(1):77-84. Epub 2015 Sep 10.

Computer Engineering Department, Faculty of Engineering, Bilkent University, Ankara 06800, Turkey and Sander Lab, Memorial Sloan-Kettering Cancer Center, 417 E68th St., New York, NY 10065, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2015/
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http://bioinformatics.oxfordjournals.org/lookup/doi/10.1093/
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http://dx.doi.org/10.1093/bioinformatics/btv516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681988PMC
January 2016

Integrating biological pathways and genomic profiles with ChiBE 2.

Authors:
Özgün Babur Ugur Dogrusoz Merve Çakır Bülent Arman Aksoy Nikolaus Schultz Chris Sander Emek Demir

BMC Genomics 2014 Aug 3;15:642. Epub 2014 Aug 3.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, Box 460, New York, NY 10065, USA.

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http://dx.doi.org/10.1186/1471-2164-15-642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4131037PMC
August 2014

CiSE: a circular spring embedder layout algorithm.

Authors:
Ugur Dogrusoz Mehmet E Belviranli Alptug Dilek

IEEE Trans Vis Comput Graph 2013 Jun;19(6):953-66

Department of Computer Engineering, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1109/TVCG.2012.178DOI Listing
June 2013

Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

Authors:
Jianjiong Gao Bülent Arman Aksoy Ugur Dogrusoz Gideon Dresdner Benjamin Gross S Onur Sumer Yichao Sun Anders Jacobsen Rileen Sinha Erik Larsson Ethan Cerami Chris Sander Nikolaus Schultz

Sci Signal 2013 Apr 2;6(269):pl1. Epub 2013 Apr 2.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

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http://dx.doi.org/10.1126/scisignal.2004088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4160307PMC
April 2013

Software support for SBGN maps: SBGN-ML and LibSBGN.

Authors:
Martijn P van Iersel Alice C Villéger Tobias Czauderna Sarah E Boyd Frank T Bergmann Augustin Luna Emek Demir Anatoly Sorokin Ugur Dogrusoz Yukiko Matsuoka Akira Funahashi Mirit I Aladjem Huaiyu Mi Stuart L Moodie Hiroaki Kitano Nicolas Le Novère Falk Schreiber

Bioinformatics 2012 Aug 10;28(15):2016-21. Epub 2012 May 10.

EMBL European Bioinformatics Institute, Hinxton, UK.

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http://bioinformatics.oxfordjournals.org/content/28/15/2016.
Web Search
http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/bts270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400951PMC
August 2012

The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data.

Authors:
Ethan Cerami Jianjiong Gao Ugur Dogrusoz Benjamin E Gross Selcuk Onur Sumer Bülent Arman Aksoy Anders Jacobsen Caitlin J Byrne Michael L Heuer Erik Larsson Yevgeniy Antipin Boris Reva Arthur P Goldberg Chris Sander Nikolaus Schultz

Cancer Discov 2012 May;2(5):401-4

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.

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http://cancerdiscovery.aacrjournals.org/lookup/doi/10.1158/2
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http://dx.doi.org/10.1158/2159-8290.CD-12-0095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3956037PMC
May 2012

Discovering modulators of gene expression.

Authors:
Ozgün Babur Emek Demir Mithat Gönen Chris Sander Ugur Dogrusoz

Nucleic Acids Res 2010 Sep 13;38(17):5648-56. Epub 2010 May 13.

Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/nar/gkq287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943625PMC
September 2010

The BioPAX community standard for pathway data sharing.

Authors:
Emek Demir Michael P Cary Suzanne Paley Ken Fukuda Christian Lemer Imre Vastrik Guanming Wu Peter D'Eustachio Carl Schaefer Joanne Luciano Frank Schacherer Irma Martinez-Flores Zhenjun Hu Veronica Jimenez-Jacinto Geeta Joshi-Tope Kumaran Kandasamy Alejandra C Lopez-Fuentes Huaiyu Mi Elgar Pichler Igor Rodchenkov Andrea Splendiani Sasha Tkachev Jeremy Zucker Gopal Gopinath Harsha Rajasimha Ranjani Ramakrishnan Imran Shah Mustafa Syed Nadia Anwar Ozgün Babur Michael Blinov Erik Brauner Dan Corwin Sylva Donaldson Frank Gibbons Robert Goldberg Peter Hornbeck Augustin Luna Peter Murray-Rust Eric Neumann Oliver Ruebenacker Oliver Reubenacker Matthias Samwald Martijn van Iersel Sarala Wimalaratne Keith Allen Burk Braun Michelle Whirl-Carrillo Kei-Hoi Cheung Kam Dahlquist Andrew Finney Marc Gillespie Elizabeth Glass Li Gong Robin Haw Michael Honig Olivier Hubaut David Kane Shiva Krupa Martina Kutmon Julie Leonard Debbie Marks David Merberg Victoria Petri Alex Pico Dean Ravenscroft Liya Ren Nigam Shah Margot Sunshine Rebecca Tang Ryan Whaley Stan Letovksy Kenneth H Buetow Andrey Rzhetsky Vincent Schachter Bruno S Sobral Ugur Dogrusoz Shannon McWeeney Mirit Aladjem Ewan Birney Julio Collado-Vides Susumu Goto Michael Hucka Nicolas Le Novère Natalia Maltsev Akhilesh Pandey Paul Thomas Edgar Wingender Peter D Karp Chris Sander Gary D Bader

Nat Biotechnol 2010 Sep 9;28(9):935-42. Epub 2010 Sep 9.

Computational Biology, Memorial Sloan-Kettering Cancer Center, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.1666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3001121PMC
September 2010

VISIBIOweb: visualization and layout services for BioPAX pathway models.

Authors:
Alptug Dilek Mehmet E Belviranli Ugur Dogrusoz

Nucleic Acids Res 2010 Jul 11;38(Web Server issue):W150-4. Epub 2010 May 11.

Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara 06800, Turkey.

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http://dx.doi.org/10.1093/nar/gkq352DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896092PMC
July 2010

ChiBE: interactive visualization and manipulation of BioPAX pathway models.

Authors:
Ozgun Babur Ugur Dogrusoz Emek Demir Chris Sander

Bioinformatics 2010 Feb 9;26(3):429-31. Epub 2009 Dec 9.

Center for Bioinformatics, Bilkent University, Ankara, Turkey.

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http://dx.doi.org/10.1093/bioinformatics/btp665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2815657PMC
February 2010

Algorithms for effective querying of compound graph-based pathway databases.

Authors:
Ugur Dogrusoz Ahmet Cetintas Emek Demir Ozgun Babur

BMC Bioinformatics 2009 Nov 16;10:376. Epub 2009 Nov 16.

Computer Engineering Dept, Bilkent University, Center for Bioinformatics, Ankara, Turkey.

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http://dx.doi.org/10.1186/1471-2105-10-376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2784781PMC
November 2009

The Systems Biology Graphical Notation.

Authors:
Nicolas Le Novère Michael Hucka Huaiyu Mi Stuart Moodie Falk Schreiber Anatoly Sorokin Emek Demir Katja Wegner Mirit I Aladjem Sarala M Wimalaratne Frank T Bergman Ralph Gauges Peter Ghazal Hideya Kawaji Lu Li Yukiko Matsuoka Alice Villéger Sarah E Boyd Laurence Calzone Melanie Courtot Ugur Dogrusoz Tom C Freeman Akira Funahashi Samik Ghosh Akiya Jouraku Sohyoung Kim Fedor Kolpakov Augustin Luna Sven Sahle Esther Schmidt Steven Watterson Guanming Wu Igor Goryanin Douglas B Kell Chris Sander Herbert Sauro Jacky L Snoep Kurt Kohn Hiroaki Kitano

Nat Biotechnol 2009 Aug 7;27(8):735-41. Epub 2009 Aug 7.

EMBL European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/nbt.1558DOI Listing
August 2009

PATIKAmad: putting microarray data into pathway context.

Authors:
Ozgun Babur Recep Colak Emek Demir Ugur Dogrusoz

Proteomics 2008 Jun;8(11):2196-8

Center for Bioinformatics, Bilkent University, Ankara, Turkey.

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http://dx.doi.org/10.1002/pmic.200700769DOI Listing
June 2008