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Journal Articles
- 2021
[j15]Hasan Balci, Metin Can Siper, Nasim Saleh, Ilkin Safarli, Ludovic Roy, Merve Kilicarslan, Rumeysa Ozaydin, Alexander Mazein
, Charles Auffray, Özgün Babur, Emek Demir, Ugur Dogrusoz:
Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps. Bioinform. 37(10): 1475-1477 (2021)- [j14]Özgün Babur, Augustin Luna, Anil Korkut, Funda Durupinar, Metin Can Siper, Ugur Dogrusoz, Alvaro Sebastian Vaca Jacome, Ryan Peckner, Karen E. Christianson, Jacob D. Jaffe, Paul T. Spellman, Joseph E. Aslan, Chris Sander, Emek Demir:
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge. Patterns 2(6): 100257 (2021) - 2020
- [j13]Igor V. Rodchenkov, Ozgun Babur, Augustin Luna, Bülent Arman Aksoy, Jeffrey V. Wong, Dylan Fong, Max Franz, Metin Can Siper, Manfred Cheung, Michael Wrana, Harsh Mistry, Logan Mosier, Jonah Dlin, Qizhi Wen, Caitlin O'Callaghan, Wanxin Li, Geoffrey Elder, Peter T. Smith, Christian Dallago, Ethan Cerami, Benjamin Gross, Ugur Dogrusoz, Emek Demir, Gary D. Bader, Chris Sander:
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Res. 48(Database-Issue): D489-D497 (2020) - 2018
- [j12]Marco Antonio Valenzuela-Escárcega, Özgün Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir, Clayton T. Morrison:
Large-scale automated machine reading discovers new cancer-driving mechanisms. Database J. Biol. Databases Curation 2018: bay098 (2018) - 2017
- [j11]Istemi Bahceci, Ugur Dogrusoz, Konnor C. La, Özgün Babur, Jianjiong Gao, Nikolaus Schultz:
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. Bioinform. 33(14): 2238-2240 (2017) - 2016
- [j10]Augustin Luna, Özgün Babur, Bülent Arman Aksoy, Emek Demir, Chris Sander:
PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinform. 32(8): 1262-1264 (2016) - 2014
- [j9]Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir:
Pattern search in BioPAX models. Bioinform. 30(1): 139-140 (2014) - [j8]Bülent Arman Aksoy, Emek Demir, Özgün Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander:
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. Bioinform. 30(14): 2051-2059 (2014) - 2013
- [j7]Emek Demir, Özgün Babur, Igor V. Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander:
Using Biological Pathway Data with Paxtools. PLoS Comput. Biol. 9(9) (2013) - 2011
- [j6]Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor V. Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander:
Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 39(Database-Issue): 685-690 (2011) - 2010
- [j5]Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander:
ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinform. 26(3): 429-431 (2010) - 2009
- [j4]Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur:
Algorithms for effective querying of compound graph-based pathway databases. BMC Bioinform. 10: 376 (2009) - 2006
- [j3]Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak:
Patikaweb: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinform. 22(3): 374-375 (2006) - 2004
- [j2]Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay:
An ontology for collaborative construction and analysis of cellular pathways. Bioinform. 20(3): 349-356 (2004) - 2002
- [j1]Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk:
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways. Bioinform. 18(7): 996-1003 (2002)
Conference and Workshop Papers
- 2016
- [c1]Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir:
Collaborative Workspaces for Pathway Curation. ICBO/BioCreative 2016
Coauthor Index
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