Emek Demir

Publication Activity (10 Years)

Years Active: 2002-2022
Publications (10 Years): 10

Top Topics

Biological Entities

Description Language

Systems Biology

Top Venues

J. Integr. Bioinform.

Nucleic Acids Res.

Publications

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 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) (2022)
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) (2021)
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) (2021)
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) (2021)
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) (2021)
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) (2020)
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)
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 (2018)
Augustin Luna, Özgün Babur, Bülent Arman Aksoy, Emek Demir, Chris Sander
PaxtoolsR: pathway analysis in R using Pathway Commons. Bioinform. 32 (8) (2016)
Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir
Collaborative Workspaces for Pathway Curation. ICBO/BioCreative (2016)
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)
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)
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)
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) (2014)
Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir
Pattern search in BioPAX models. Bioinform. 30 (1) (2014)
Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader
The BioPAX Validator. Bioinform. 29 (20) (2013)
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)
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) (2012)
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) (2011)
Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas
BioPAX support in CellDesigner. Bioinform. 27 (24) (2011)
Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander
ChiBE: interactive visualization and manipulation of BioPAX pathway models. Bioinform. 26 (3) (2010)
Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur
Algorithms for effective querying of compound graph-based pathway databases. BMC Bioinform. 10 (2009)
Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir
A layout algorithm for undirected compound graphs. Inf. Sci. 179 (7) (2009)
Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak
: a Web interface for analyzing biological pathways through advanced querying and visualization. Bioinform. 22 (3) (2006)
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) (2004)
Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir
A Compound Graph Layout Algorithm for Biological Pathways. Graph Drawing (2004)
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) (2002)