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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
11332010
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
7002010
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
5492017
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
2462019
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
2052002
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
1842020
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
1522015
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
1282020
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
852015
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
792004
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
742006
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
652013
Large-scale automated machine reading discovers new cancer-driving mechanisms
MA Valenzuela-Escárcega, Ö Babur, G Hahn-Powell, D Bell, T Hicks, ...
Database 2018, 2018
622018
ChiBE: interactive visualization and manipulation of BioPAX pathway models
O Babur, U Dogrusoz, E Demir, C Sander
Bioinformatics 26 (3), 429-431, 2010
612010
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
392017
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles
BA Aksoy, E Demir, Ö Babur, W Wang, X Jing, N Schultz, C Sander
Bioinformatics 30 (14), 2051-2059, 2014
382014
SBGNViz: a tool for visualization and complexity management of SBGN process description maps
M Sari, I Bahceci, U Dogrusoz, SO Sumer, BA Aksoy, Ö Babur, E Demir
PloS one 10 (6), e0128985, 2015
322015
Integrating biological pathways and genomic profiles with ChiBE 2
Ö Babur, U Dogrusoz, M Çakır, BA Aksoy, N Schultz, C Sander, E Demir
BMC genomics 15 (1), 1-9, 2014
322014
Discovering modulators of gene expression
Ö Babur, E Demir, M Gönen, C Sander, U Dogrusoz
Nucleic acids research 38 (17), 5648-5656, 2010
322010
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), 100257, 2021
302021
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Articles 1–20