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ORCIDEmek Demir
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2020 – today
- 2022
[j25]Marc Gillespie
, Bijay Jassal, Ralf Stephan, Marija Milacic, Karen Rothfels, Andrea Senff-Ribeiro, Johannes Griss, Cristoffer Sevilla, Lisa Matthews, Chuqiao Gong, Chuan Deng, Thawfeek M. Varusai, Eliot Ragueneau, Yusra Haider, Bruce May, Veronica Shamovsky, Joel Weiser, Timothy Brunson, Nasim Sanati, Liam Beckman, Xiang Shao, Antonio Fabregat, Konstantinos Sidiropoulos, Julieth Murillo, Guilherme Viteri, Justin Cook, Solomon Shorser, Gary D. Bader, Emek Demir, Chris Sander, Robin Haw, Guanming Wu, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The reactome pathway knowledgebase 2022. Nucleic Acids Res. 50(D1): 687-692 (2022)- 2021
- [j24]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) - [j23]Michal R. Grzadkowski, Hannah D. Holly, Julia Somers, Emek Demir:
Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes. BMC Bioinform. 22(1): 233 (2021) - [j22]Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader:
A flexible search system for high-accuracy identification of biological entities and molecules. J. Open Source Softw. 6(67): 3756 (2021) - [j21]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
- [j20]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)
2010 – 2019
- 2019
- [j19]Adrien Rougny, Vasundra Touré, Stuart L. Moodie, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Ugur Dogrusoz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly A. Sorokin, Falk Schreiber, Augustin Luna:
Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0. J. Integr. Bioinform. 16(2) (2019) - 2018
- [j18]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) - 2016
- [j17]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) - [c2]Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir:
Collaborative Workspaces for Pathway Curation. ICBO/BioCreative 2016 - 2015
- [j16]Huaiyu Mi, Falk Schreiber, Stuart L. Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly A. Sorokin, Alice Villéger:
Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 . J. Integr. Bioinform. 12(2) (2015) - [j15]Stuart L. Moodie, Nicolas Le Novère, Emek Demir, Huaiyu Mi, Alice Villéger:
Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3. J. Integr. Bioinform. 12(2) (2015) - [j14]Anatoly A. Sorokin, Nicolas Le Novère, Augustin Luna, Tobias Czauderna, Emek Demir, Robin Haw, Huaiyu Mi, Stuart L. Moodie, Falk Schreiber, Alice Villéger:
Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2. J. Integr. Bioinform. 12(2) (2015) - 2014
- [j13]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) - [j12]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
- [j11]Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader:
The BioPAX Validator. Bioinform. 29(20): 2659-2660 (2013) - [j10]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) - 2012
- [j9]Martijn P. van Iersel, Alice Villéger, Tobias Czauderna, Sarah E. Boyd, Frank T. Bergmann, Augustin Luna, Emek Demir, Anatoly A. Sorokin, Ugur Dogrusöz, Yukiko Matsuoka, Akira Funahashi, Mirit I. Aladjem, Huaiyu Mi, Stuart L. Moodie, Hiroaki Kitano, Nicolas Le Novère, Falk Schreiber:
Software support for SBGN maps: SBGN-ML and LibSBGN. Bioinform. 28(15): 2016-2021 (2012) - 2011
- [j8]Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas:
BioPAX support in CellDesigner. Bioinform. 27(24): 3437-3438 (2011) - [j7]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
- [j6]Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander:
ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinform. 26(3): 429-431 (2010)
2000 – 2009
- 2009
- [j5]Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur:
Algorithms for effective querying of compound graph-based pathway databases. BMC Bioinform. 10: 376 (2009) - [j4]Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir:
A layout algorithm for undirected compound graphs. Inf. Sci. 179(7): 980-994 (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) - 2005
- [b1]Emek Demir:
An ontology for computer-aided modeling of cellular processes (Bilgisayar destekli hücresel yolak modellemesi). İhsan Doğramacı Bilkent University, Turkey, 2005 - 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) - [c1]Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir:
A Compound Graph Layout Algorithm for Biological Pathways. GD 2004: 442-447 - 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)
Coauthor Index
aka: Özgün Babur
aka: Ugur Dogrusöz
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