Ozgun Babur

Ozgun Babur

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Ozgun Babur

Ozgun Babur

Publications by authors named "Ozgun Babur"

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24Publications

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Identification, Quantification, and System Analysis of Protein N-ε Lysine Methylation in Anucleate Blood Platelets.

Proteomics 2019 06 9;19(11):e1900001. Epub 2019 May 9.

Department of Biomedical Engineering, Oregon Health & Science University, 97239, Portland, OR, USA.

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http://dx.doi.org/10.1002/pmic.201900001DOI Listing
June 2019

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

PaxtoolsR: pathway analysis in R using Pathway Commons.

Bioinformatics 2016 04 18;32(8):1262-4. Epub 2015 Dec 18.

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

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http://dx.doi.org/10.1093/bioinformatics/btv733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824129PMC
April 2016

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations.

Genome Biol 2015 Feb 26;16:45. Epub 2015 Feb 26.

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

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http://genomebiology.com/2015/16/1/45
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http://dx.doi.org/10.1186/s13059-015-0612-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381444PMC
February 2015

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

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.

Bioinformatics 2014 Jul 24;30(14):2051-9. Epub 2014 Mar 24.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 and Tri-Institutional Training Program in Computational Biology & Medicine, New York, NY 10065, USA.

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http://dx.doi.org/10.1093/bioinformatics/btu164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080742PMC
July 2014

Using biological pathway data with paxtools.

PLoS Comput Biol 2013 19;9(9):e1003194. Epub 2013 Sep 19.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

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https://dx.plos.org/10.1371/journal.pcbi.1003194
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http://dx.doi.org/10.1371/journal.pcbi.1003194DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3777916PMC
April 2014

Pattern search in BioPAX models.

Bioinformatics 2014 Jan 16;30(1):139-40. Epub 2013 Sep 16.

Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA, Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY 10065, USA and Banting and Best Department of Medical Research, The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada.

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http://dx.doi.org/10.1093/bioinformatics/btt539DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3866551PMC
January 2014

Pathway Commons, a web resource for biological pathway data.

Nucleic Acids Res 2011 Jan 10;39(Database issue):D685-90. Epub 2010 Nov 10.

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/10.1093/nar/gkq1039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013659PMC
January 2011

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

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