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)

A Compound Graph Layout Algorithm for Biological Pathways. - Ugur Dogrusöz; Erhan Giral; Ahmet Cetintas; Ali Civril; Emek Demir (GD, 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)

An ontology for computer-aided modeling of cellular processes (Bilgisayar destekli hücresel yolak modellemesi) - Emek Demir (2005)

Patikaweb: 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)

Algorithms for effective querying of compound graph-based pathway databases. - Ugur Dogrusöz; Ahmet Cetintas; Emek Demir; Ozgun Babur (BMC Bioinform., 2009)

A layout algorithm for undirected compound graphs. - Ugur Dogrusöz; Erhan Giral; Ahmet Cetintas; Ali Civril; Emek Demir (Inf. Sci., 2009)

ChiBE: interactive visualization and manipulation of BioPAX pathway models. - Ozgun Babur; Ugur Dogrusöz; Emek Demir; Chris Sander (Bioinform., 2010)

BioPAX support in CellDesigner. - Huaiyu Mi; Anushya Muruganujan; Emek Demir; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Paul D. Thomas (Bioinform., 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)

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; et al. (Bioinform., 2012)

The BioPAX Validator. - Igor V. Rodchenkov; Emek Demir; Chris Sander; Gary D. Bader (Bioinform., 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)

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)

Pattern search in BioPAX models. - Özgün Babur; Bülent Arman Aksoy; Igor V. Rodchenkov; Selçuk Onur Sümer; Chris Sander; Emek Demir (Bioinform., 2014)

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)

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: 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)

Collaborative Workspaces for Pathway Curation. - Funda Durupinar-Babur; Metin Can Siper; Ugur Dogrusoz; Istemi Bahceci; Ozgun Babur; Emek Demir (ICBO/BioCreative, 2016)

PaxtoolsR: pathway analysis in R using Pathway Commons. - Augustin Luna; Özgün Babur; Bülent Arman Aksoy; Emek Demir; Chris Sander (Bioinform., 2016)

Large-scale automated machine reading discovers new cancer-driving mechanisms. - Marco Antonio Valenzuela-Escárcega; Özgün Babur; Gus Hahn-Powell; Dane Bell; Thomas Hicks 002; Enrique Noriega-Atala; Xia Wang; Mihai Surdeanu; Emek Demir; Clayton T. Morrison (Database J. Biol. Databases Curation, 2018)

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; et al. (J. Integr. Bioinform., 2019)

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; et al. (Nucleic Acids Res., 2020)

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)

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)

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)

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; et al. (Patterns, 2021)

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; et al. (Nucleic Acids Res., 2022)