Emek Demir
Title
Cited by
Cited by
Year
Pathway Commons, a web resource for biological pathway data
EG Cerami, BE Gross, E Demir, I Rodchenkov, Ö Babur, N Anwar, ...
Nucleic acids research 39 (suppl_1), D685-D690, 2010
9602010
The systems biology graphical notation
N Le Novere, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ...
Nature biotechnology 27 (8), 735-741, 2009
8442009
The BioPAX community standard for pathway data sharing
E Demir, MP Cary, S Paley, K Fukuda, C Lemer, I Vastrik, G Wu, ...
Nature biotechnology 28 (9), 935-942, 2010
6042010
Automated network analysis identifies core pathways in glioblastoma
E Cerami, E Demir, N Schultz, BS Taylor, C Sander
PloS one 5 (2), e8918, 2010
3322010
Human SRMAtlas: a resource of targeted assays to quantify the complete human proteome
U Kusebauch, DS Campbell, EW Deutsch, CS Chu, DA Spicer, ...
Cell 166 (3), 766-778, 2016
2102016
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
E Demir, O Babur, U Dogrusoz, A Gursoy, G Nisanci, R Cetin-Atalay, ...
Bioinformatics 18 (7), 996-1003, 2002
1942002
Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations
Ö Babur, M Gönen, BA Aksoy, N Schultz, G Ciriello, C Sander, E Demir
Genome biology 16 (1), 45, 2015
1172015
Software support for SBGN maps: SBGN-ML and LibSBGN
MP Van Iersel, AC Villéger, T Czauderna, SE Boyd, FT Bergmann, A Luna, ...
Bioinformatics 28 (15), 2016-2021, 2012
852012
An ontology for collaborative construction and analysis of cellular pathways
E Demir, O Babur, U Dogrusoz, A Gursoy, A Ayaz, G Gulesir, G Nisanci, ...
Bioinformatics 20 (3), 349-356, 2004
782004
A layout algorithm for undirected compound graphs
U Dogrusoz, E Giral, A Cetintas, A Civril, E Demir
Information Sciences 179 (7), 980-994, 2009
762009
Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization
U Dogrusoz, EZ Erson, E Giral, E Demir, O Babur, A Cetintas, R Colak
Bioinformatics 22 (3), 374-375, 2006
702006
Perturbation biology nominates upstream–downstream drug combinations in RAF inhibitor resistant melanoma cells
A Korkut, W Wang, E Demir, BA Aksoy, X Jing, EJ Molinelli, Ö Babur, ...
Elife 4, e04640, 2015
662015
Using biological pathway data with paxtools
E Demir, Ö Babur, I Rodchenkov, BA Aksoy, KI Fukuda, B Gross, ...
PLoS Comput Biol 9 (9), e1003194, 2013
532013
ChiBE: interactive visualization and manipulation of BioPAX pathway models
O Babur, U Dogrusoz, E Demir, C Sander
Bioinformatics 26 (3), 429-431, 2010
512010
Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative
M Hucka, DP Nickerson, GD Bader, FT Bergmann, J Cooper, E Demir, ...
Frontiers in bioengineering and biotechnology 3, 19, 2015
502015
A phase reconstruction algorithm from bispectrum (seismic reflection data)
S Alshebeili, AE Cetin
IEEE Transactions on Geoscience and Remote Sensing 28 (2), 166-170, 1990
48*1990
A compound graph layout algorithm for biological pathways
U Dogrusoz, E Giral, A Cetintas, A Civril, E Demir
International Symposium on Graph Drawing, 442-447, 2004
422004
Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites
H Nishi, E Demir, AR Panchenko
Journal of molecular biology 427 (2), 511-520, 2015
372015
Integrated proteogenomic characterization of clear cell renal cell carcinoma
DJ Clark, SM Dhanasekaran, F Petralia, J Pan, X Song, Y Hu, ...
Cell 179 (4), 964-983. e31, 2019
342019
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles
BA Aksoy, E Demir, Ö Babur, W Wang, X Jing, N Schultz, C Sander
Bioinformatics 30 (14), 2051-2059, 2014
342014
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Articles 1–20