Emek Demir

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Özgün BaburAssistant Professor at University of Massachusetts BostonVerified email at umb.edu
Chris SanderDana-Farber Cancer Institute, Harvard Medical School, Broad 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 LunaResearch Associate | Dept. of Data Science, Dana-Farber Cancer Institute, Harvard Medical SchoolVerified email at mail.nih.gov
Nikolaus SchultzCenter for Molecular Oncology, Memorial Sloan Kettering Cancer CenterVerified email at cbio.mskcc.org
Bulent Arman AksoyMOMA TherapeuticsVerified email at aksoy.org
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
Falk SchreiberProfessor, University of Konstanz and Monash UniversityVerified email at uni-konstanz.de
Anatoly SorokinInstitute of Cell Biophysics RASVerified email at icb.psn.ru
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 AslanAssistant Professor, Knight Cardiovascular Institute, Oregon Health & Science UniversityVerified email at ohsu.edu
Tobias CzaudernaUniversity of Applied Sciences MittweidaVerified email at hs-mittweida.de
Aaron R ColakPrincipal ML Scientist, R&D Leader @ QualtricsVerified email at cs.toronto.edu
Mithat GönenMemorial Sloan-Kettering Cancer CenterVerified email at alumni.stanford.edu
Anil KorkutMD Anderson Cancer CenterVerified email at mdanderson.org
Attila GursoyProfessor of Computer Science, Koc UniversityVerified email at ku.edu.tr

Emek Demir

OHSU

Verified email at ohsu.edu - Homepage

Systems Biology Computational Biology Ontology Bioinformatics Gene Expression


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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	1133	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	956	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	700	2010
Automated network analysis identifies core pathways in glioblastoma E Cerami, E Demir, N Schultz, BS Taylor, C Sander PloS one 5 (2), e8918, 2010	370	2010
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	268	2016
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	205	2019
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	205	2002
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	183	2020
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), 1-10, 2015	152	2015
Proteogenomic characterization of endometrial carcinoma Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ... Cell 180 (4), 729-748. e26, 2020	143	2020
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	127	2020
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), 1-4, 2020	110	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	106	2009
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	100	2012
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	96	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	86	2020
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	85	2015
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	79	2004
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	74	2006
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	65	2021

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