Özgün Babur

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Emek DemirOHSUVerified email at ohsu.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
Anil KorkutMD Anderson Cancer CenterVerified email at mdanderson.org
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
Bulent Arman AksoyObsidian TherapeuticsVerified email at aksoy.org
Nikolaus SchultzCenter for Molecular Oncology, Memorial Sloan Kettering Cancer CenterVerified email at cbio.mskcc.org
Ethan CeramiDirector, Knowledge Systems Group, Dana-Farber Cancer InstituteVerified email at jimmy.harvard.edu
Jeffrey WongResearcherVerified email at utoronto.ca
Joseph AslanAssociate Professor, Knight Cardiovascular Institute, Oregon Health & Science UniversityVerified email at ohsu.edu
Larry DavidProfessor of Biochemistry and Molecular Biology, Oregon Health & Science UniversityVerified email at ohsu.edu
Selcuk Onur SumerMSKCCVerified email at mskcc.org
Mithat GönenMemorial Sloan-Kettering Cancer CenterVerified email at alumni.stanford.edu
Aaron R Colak, PhDHead of Core Machine LearningVerified email at qualtrics.com
Owen JT McCartyProfessor of Biomedical Engineering, Oregon Health & Science UniversityVerified email at ohsu.edu
Attila GursoyProfessor of Computer Science, Koc UniversityVerified email at ku.edu.tr
Rengul Cetin AtalayUniversity of ChicagoVerified email at uchicago.edu
Giovanni CirielloDepartment of Computational Biology, University of Lausanne (UNIL)Verified email at unil.ch

Özgün Babur

Assistant Professor at University of Massachusetts Boston

Verified email at umb.edu - Homepage

Computational Biology Systems Biology Pathway Informatics Biological Networks


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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	1232	2010
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	754	2010
Integrative analysis identifies four molecular and clinical subsets in uveal melanoma AG Robertson, J Shih, C Yau, EA Gibb, J Oba, KL Mungall, JM Hess, ... Cancer cell 32 (2), 204-220. e15, 2017	728	2017
Integrated analysis of TP53 gene and pathway alterations in the cancer genome atlas LA Donehower, T Soussi, A Korkut, Y Liu, A Schultz, M Cardenas, X Li, ... Cell reports 28 (5), 1370-1384. e5, 2019	417	2019
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	312	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	223	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	209	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	164	2015
A proteogenomic portrait of lung squamous cell carcinoma S Satpathy, K Krug, PMJ Beltran, SR Savage, F Petralia, C Kumar-Sinha, ... Cell 184 (16), 4348-4371. e40, 2021	133	2021
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	110	2015
Large-scale automated machine reading discovers new cancer-driving mechanisms MA Valenzuela-Escárcega, Ö Babur, G Hahn-Powell, D Bell, T Hicks, ... Database 2018, bay098, 2018	86	2018
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	80	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 Çolak Bioinformatics 22 (3), 374-375, 2006	76	2006
Using biological pathway data with paxtools E Demir, Ö Babur, I Rodchenkov, BA Aksoy, KI Fukuda, B Gross, ... PLoS computational biology 9 (9), e1003194, 2013	72	2013
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ... Molecular systems biology 17 (10), e10387, 2021	66	2021
ChiBE: interactive visualization and manipulation of BioPAX pathway models O Babur, U Dogrusoz, E Demir, C Sander Bioinformatics 26 (3), 429-431, 2010	60	2010
Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs Ö Babur, AR Melrose, JM Cunliffe, J Klimek, J Pang, ALI Sepp, ... Blood, The Journal of the American Society of Hematology 136 (20), 2346-2358, 2020	59	2020
The AML microenvironment catalyzes a stepwise evolution to gilteritinib resistance SK Joshi, T Nechiporuk, D Bottomly, PD Piehowski, JA Reisz, ... Cancer Cell 39 (7), 999-1014. e8, 2021	54	2021
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge Ö Babur, A Luna, A Korkut, F Durupinar, MC Siper, U Dogrusoz, ... Patterns 2 (6), 2021	54	2021
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data I Bahceci, U Dogrusoz, KC La, Ö Babur, J Gao, N Schultz Bioinformatics 33 (14), 2238-2240, 2017	48	2017

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