Publications by authors named "Ugur Dogrusoz"

25Publications

Systems biology graphical notation markup language (SBGNML) version 0.3.

J Integr Bioinform 2020 Jun 22;17(2-3). Epub 2020 Jun 22.

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

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June 2020

cd2sbgnml: bidirectional conversion between CellDesigner and SBGN formats.

Bioinformatics 2020 04;36(8):2620-2622

Institut National de la Santé et de la Recherche Médicale (INSERM), U900, F-75005 Paris, France.

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April 2020

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

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

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

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December 2018

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

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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July 2017

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

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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January 2016

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

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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April 2016

Integrating biological pathways and genomic profiles with ChiBE 2.

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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August 2014

CiSE: a circular spring embedder layout algorithm.

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

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

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June 2013

The BioPAX community standard for pathway data sharing.

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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September 2010

Discovering modulators of gene expression.

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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September 2010

VISIBIOweb: visualization and layout services for BioPAX pathway models.

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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July 2010

ChiBE: interactive visualization and manipulation of BioPAX pathway models.

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

Center for Bioinformatics, Bilkent University, Ankara, Turkey.

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February 2010

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

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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November 2009

PATIKAmad: putting microarray data into pathway context.

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

Center for Bioinformatics, Bilkent University, Ankara, Turkey.

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June 2008