Emek Demir

According to our database, Emek Demir authored at least 28 papers between 2002 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2022

The reactome pathway knowledgebase 2022.

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

Nucleic Acids Res., 2022

2021

Causal interactions from proteomic profiles: Molecular data meet pathway knowledge.

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

Patterns, 2021

A flexible search system for high-accuracy identification of biological entities and molecules.

Max Franz, Jeffrey V. Wong, Metin Can Siper, Christian Dallago, John M. Giorgi, Emek Demir, Chris Sander, Gary D. Bader

J. Open Source Softw., 2021

Systematic interrogation of mutation groupings reveals divergent downstream expression programs within key cancer genes.

Michal R. Grzadkowski, Hannah D. Holly, Julia Somers, Emek Demir

BMC Bioinform., 2021

Newt: a comprehensive web-based tool for viewing, constructing and analyzing biological maps.

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

Bioinform., 2021

2020

Pathway Commons 2019 Update: integration, analysis and exploration of pathway data.

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

Nucleic Acids Res., 2020

2019

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

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

J. Integr. Bioinform., 2019

2018

Large-scale automated machine reading discovers new cancer-driving mechanisms.

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

Database J. Biol. Databases Curation, 2018

2016

PaxtoolsR: pathway analysis in R using Pathway Commons.

Augustin Luna, Özgün Babur, Bülent Arman Aksoy, Emek Demir, Chris Sander

Bioinform., 2016

Collaborative Workspaces for Pathway Curation.

Funda Durupinar-Babur, Metin Can Siper, Ugur Dogrusoz, Istemi Bahceci, Ozgun Babur, Emek Demir

Proceedings of the Joint International Conference on Biological Ontology and BioCreative, 2016

2015

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Anatoly A. Sorokin, Nicolas Le Novère, Augustin Luna, Tobias Czauderna, Emek Demir, Robin Haw, Huaiyu Mi, Stuart L. Moodie, Falk Schreiber, Alice Villéger

J. Integr. Bioinform., 2015

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

Stuart L. Moodie, Nicolas Le Novère, Emek Demir, Huaiyu Mi, Alice Villéger

J. Integr. Bioinform., 2015

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2 .

Huaiyu Mi, Falk Schreiber, Stuart L. Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly A. Sorokin, Alice Villéger

J. Integr. Bioinform., 2015

2014

Pattern search in BioPAX models.

Özgün Babur, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir

Bioinform., 2014

Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles.

Bülent Arman Aksoy, Emek Demir, Özgün Babur, Weiqing Wang, Xiaohong Jing, Nikolaus Schultz, Chris Sander

Bioinform., 2014

2013

Using Biological Pathway Data with Paxtools.

Emek Demir, Özgün Babur, Igor V. Rodchenkov, Bülent Arman Aksoy, Ken I. Fukuda, Benjamin E. Gross, Selçuk Onur Sümer, Gary D. Bader, Chris Sander

PLoS Comput. Biol., 2013

The BioPAX Validator.

Igor V. Rodchenkov, Emek Demir, Chris Sander, Gary D. Bader

Bioinform., 2013

2012

Software support for SBGN maps: SBGN-ML and LibSBGN.

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

Bioinform., 2012

2011

Pathway Commons, a web resource for biological pathway data.

Ethan G. Cerami, Benjamin E. Gross, Emek Demir, Igor V. Rodchenkov, Özgün Babur, Nadia Anwar, Nikolaus Schultz, Gary D. Bader, Chris Sander

Nucleic Acids Res., 2011

BioPAX support in CellDesigner.

Huaiyu Mi, Anushya Muruganujan, Emek Demir, Yukiko Matsuoka, Akira Funahashi, Hiroaki Kitano, Paul D. Thomas

Bioinform., 2011

2010

ChiBE: interactive visualization and manipulation of BioPAX pathway models.

Ozgun Babur, Ugur Dogrusöz, Emek Demir, Chris Sander

Bioinform., 2010

2009

A layout algorithm for undirected compound graphs.

Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Inf. Sci., 2009

Algorithms for effective querying of compound graph-based pathway databases.

Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur

BMC Bioinform., 2009

2006

Patika<i>web</i>: a Web interface for analyzing biological pathways through advanced querying and visualization.

Ugur Dogrusöz, E. Z. Erson, Erhan Giral, Emek Demir, Ozgun Babur, Ahmet Cetintas, R. Colak

Bioinform., 2006

2005

An ontology for computer-aided modeling of cellular processes (Bilgisayar destekli hücresel yolak modellemesi)

Emek Demir

PhD thesis, 2005

2004

An ontology for collaborative construction and analysis of cellular pathways.

Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, A. Ayaz, Gürcan Gülesir, Gurkan Nisanci, Rengül Çetin-Atalay

Bioinform., 2004

A Compound Graph Layout Algorithm for Biological Pathways.

Ugur Dogrusöz, Erhan Giral, Ahmet Cetintas, Ali Civril, Emek Demir

Proceedings of the Graph Drawing, 12th International Symposium, 2004

2002

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

Emek Demir, Ozgun Babur, Ugur Dogrusöz, Attila Gürsoy, Gurkan Nisanci, Rengül Çetin-Atalay, Mehmet Ozturk

Bioinform., 2002