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Emek Demir
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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
11762010
The systems biology graphical notation
NL Novère, M Hucka, H Mi, S Moodie, F Schreiber, A Sorokin, E Demir, ...
Nature biotechnology 27 (8), 735-741, 2009
9892009
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
7412010
Automated network analysis identifies core pathways in glioblastoma
E Cerami, E Demir, N Schultz, BS Taylor, C Sander
PloS one 5 (2), e8918, 2010
3812010
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
2902019
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
2832016
The reactome pathway knowledgebase 2022
M Gillespie, B Jassal, R Stephan, M Milacic, K Rothfels, A Senff-Ribeiro, ...
Nucleic acids research 50 (D1), D687-D692, 2022
2702022
The human tumor atlas network: charting tumor transitions across space and time at single-cell resolution
O Rozenblatt-Rosen, A Regev, P Oberdoerffer, T Nawy, A Hupalowska, ...
Cell 181 (2), 236-249, 2020
2432020
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
2062002
Proteogenomic characterization of endometrial carcinoma
Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ...
Cell 180 (4), 729-748. e26, 2020
2042020
Proteogenomic and metabolomic characterization of human glioblastoma
LB Wang, A Karpova, MA Gritsenko, JE Kyle, S Cao, Y Li, D Rykunov, ...
Cancer cell 39 (4), 509-528. e20, 2021
1932021
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data
I Rodchenkov, O Babur, A Luna, BA Aksoy, JV Wong, D Fong, M Franz, ...
Nucleic acids research 48 (D1), D489-D497, 2020
1712020
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, 1-10, 2015
1592015
Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
C Huang, L Chen, SR Savage, RV Eguez, Y Dou, Y Li, ...
Cancer cell 39 (3), 361-379. e16, 2021
1272021
SBML Level 3: an extensible format for the exchange and reuse of biological models
SM Keating, D Waltemath, M König, F Zhang, A Dräger, C Chaouiya, ...
Molecular systems biology 16 (8), e9110, 2020
1272020
COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
M Ostaszewski, A Mazein, ME Gillespie, I Kuperstein, A Niarakis, ...
Scientific data 7 (1), 136, 2020
1262020
A layout algorithm for undirected compound graphs
U Dogrusoz, E Giral, A Cetintas, A Civril, E Demir
Information Sciences 179 (7), 980-994, 2009
1192009
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
1052012
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
1012015
An expanded universe of cancer targets
WC Hahn, JS Bader, TP Braun, A Califano, PA Clemons, BJ Druker, ...
Cell 184 (5), 1142-1155, 2021
1002021
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