Ugur Dogrusoz

Ugur Dogrusoz

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Ugur Dogrusoz

Ugur Dogrusoz

Publications by authors named "Ugur Dogrusoz"

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20Publications

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

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.

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

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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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.

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.

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.

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.

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

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