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)

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)

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)

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

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)

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)

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)

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data. - Istemi Bahceci; Ugur Dogrusoz; Konnor C. La; Özgün Babur; Jianjiong Gao; Nikolaus Schultz (Bioinform., 2017)

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)

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)

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)

Strategies to include prior knowledge in omics analysis with deep neural networks. - Kisan Thapa; Meric Kinali; Shichao Pei; Augustin Luna; Özgün Babur (Patterns, 2025)