Emek Demir

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Özgün BaburAssistant Professor at University of Massachusetts BostonVerified email at umb.edu
Chris SanderHarvard Medical School, Broad Institute, Dana-Farber Cancer Institute, Memorial Sloan KetteringVerified email at sanderlab.org
Ugur DogrusozProfessor of Computer Engineering, Bilkent University, Ankara, TurkeyVerified email at cs.bilkent.edu.tr
Igor RodchenkovUniversity of TorontoVerified email at utoronto.ca
Gary BaderProfessor of Molecular Genetics and Computer Science, The Donnelly Centre, University of TorontoVerified email at utoronto.ca
Augustin LunaInvestigator | Computational Biology Branch, NLM & Developmental Therapeutics Branch, NCI, NIHVerified email at mail.nih.gov
Bulent Arman AksoyObsidian TherapeuticsVerified email at aksoy.org
Nikolaus SchultzCenter for Molecular Oncology, Memorial Sloan Kettering Cancer CenterVerified email at cbio.mskcc.org
Falk SchreiberProfessor, University of Konstanz and Monash UniversityVerified email at uni-konstanz.de
Huaiyu MiPreventive Medicine, University of Southern CaliforniaVerified email at usc.edu
Ethan CeramiDirector, Knowledge Systems Group, Dana-Farber Cancer InstituteVerified email at jimmy.harvard.edu
Anatoly SorokinOkinawa Institute of Science and TechnologyVerified email at oist.jp
Hiroaki KitanoThe Systems Biology Institute, Director / Sony Computer Science Laboratories, Inc., President and CEO / Okinawa Institute of Science and Technology, ProfessorVerified email at sbi.jp
Akira FunahashiProfessor of Systems Biology, Keio UniversityVerified email at bio.keio.ac.jp
Joseph AslanAssociate Professor, Knight Cardiovascular Institute, Oregon Health & Science UniversityVerified email at ohsu.edu
Tobias CzaudernaUniversity of Applied Sciences MittweidaVerified email at hs-mittweida.de
Anil KorkutMD Anderson Cancer CenterVerified email at mdanderson.org
Mithat GönenMemorial Sloan-Kettering Cancer CenterVerified email at alumni.stanford.edu
Aaron Colak, PhDHead of AI, QualtricsVerified email at qualtrics.com
Ali ÇivrilIstanbul Atlas UniversityVerified email at atlas.edu.tr

Emek Demir

OHSU

Verified email at ohsu.edu - Homepage

Systems Biology Computational Biology Ontology Bioinformatics Gene Expression


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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	1411	2022
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	1295	2010
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	1060	2009
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	807	2010
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	496	2019
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	447	2021
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	421	2020
Automated network analysis identifies core pathways in glioblastoma E Cerami, E Demir, N Schultz, BS Taylor, C Sander PloS one 5 (2), e8918, 2010	403	2010
Proteogenomic characterization of endometrial carcinoma Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ... Cell 180 (4), 729-748. e26, 2020	358	2020
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	335	2016
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	282	2020
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	245	2021
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	228	2020
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	216	2002
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	176	2015
An expanded universe of cancer targets WC Hahn, JS Bader, TP Braun, A Califano, PA Clemons, BJ Druker, ... Cell 184 (5), 1142-1155, 2021	164	2021
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	149	2020
A layout algorithm for undirected compound graphs U Dogrusoz, E Giral, A Cetintas, A Civril, E Demir Information Sciences 179 (7), 980-994, 2009	138	2009
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	119	2015
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	106	2012

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