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
Nikolaus SchultzCenter for Molecular Oncology, Memorial Sloan Kettering Cancer CenterVerified email at cbio.mskcc.org
Bulent Arman AksoyMOMA TherapeuticsVerified email at aksoy.org
Augustin LunaResearch Associate | Dept. of Data Science, Dana-Farber Cancer Institute, Harvard Medical SchoolVerified email at mail.nih.gov
Huaiyu MiPreventive Medicine, University of Southern CaliforniaVerified email at usc.edu
Falk SchreiberProfessor, University of Konstanz and Monash UniversityVerified email at uni-konstanz.de
Ethan CeramiDirector, Knowledge Systems Group, Dana-Farber Cancer InstituteVerified email at jimmy.harvard.edu
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
Anatoly SorokinInstitute of Cell Biophysics RASVerified email at icb.psn.ru
Akira FunahashiAssociate Professor of Systems Biology, Keio UniversityVerified email at bio.keio.ac.jp
Tobias CzaudernaMonash UniversityVerified email at monash.edu
Aaron R ColakPrincipal ML Scientist, R&D Leader @ QualtricsVerified email at cs.toronto.edu
Frank T. BergmannBioQUANT/COS, Heidelberg University, Heidelberg, GermanyVerified email at caltech.edu
Mithat GönenMemorial Sloan-Kettering Cancer CenterVerified email at alumni.stanford.edu
Attila GursoyProfessor of Computer Science, Koc UniversityVerified email at ku.edu.tr
Rengul Cetin AtalayUniversity of Chicago and Middle East Technical UniversityVerified email at metu.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	1021	2010
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	883	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	641	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	349	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	235	2016
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	198	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), 1-10, 2015	130	2015
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	102	2019
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	89	2012
A layout algorithm for undirected compound graphs U Dogrusoz, E Giral, A Cetintas, A Civril, E Demir Information Sciences 179 (7), 980-994, 2009	81	2009
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	77	2004
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	75	2015
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	74	2020
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	72	2006
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	64	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	63	2020
Proteogenomic characterization of endometrial carcinoma Y Dou, EA Kawaler, DC Zhou, MA Gritsenko, C Huang, L Blumenberg, ... Cell 180 (4), 729-748. e26, 2020	60	2020
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	56	2013
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	54	2015
ChiBE: interactive visualization and manipulation of BioPAX pathway models O Babur, U Dogrusoz, E Demir, C Sander Bioinformatics 26 (3), 429-431, 2010	52	2010

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