Publications by authors named "Emek Demir"

37Publications

Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps.

Bioinformatics 2020 Oct 3. Epub 2020 Oct 3.

i-Vis Research Lab, Computer Engineering Department, Bilkent University, Ankara, Turkey.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btaa850DOI Listing
October 2020

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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites.

J Mol Biol 2015 Jan 9;427(2):511-20. Epub 2014 Nov 9.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jmb.2014.11.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4297578PMC
January 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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
https://dx.plos.org/10.1371/journal.pcbi.1003194
Publisher Site
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.

View Article

Download full-text PDF

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

The BioPAX Validator.

Bioinformatics 2013 Oct 5;29(20):2659-60. Epub 2013 Aug 5.

The Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada and Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt452DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789551PMC
October 2013

BioPAX support in CellDesigner.

Bioinformatics 2011 Dec 21;27(24):3437-8. Epub 2011 Oct 21.

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btr586DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3232372PMC
December 2011

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

Automated network analysis identifies core pathways in glioblastoma.

PLoS One 2010 Feb 12;5(2):e8918. Epub 2010 Feb 12.

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

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0008918PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2820542PMC
February 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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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