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Özgün Babur
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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
12642010
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
7892017
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
7722010
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
4842019
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
3572020
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
2492020
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
2092002
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
1752021
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
1702015
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
1122015
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
912018
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
802004
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
762021
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
762006
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
732013
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
652021
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
622020
ChiBE: interactive visualization and manipulation of BioPAX pathway models
O Babur, U Dogrusoz, E Demir, C Sander
Bioinformatics 26 (3), 429-431, 2010
612010
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
572021
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
502017
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