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

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)

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)

DORMAN: Database of Reconstructed MetAbolic Networks. - Furkan Ozden; Metin Can Siper; Necmi Acarsoy; Tugrulcan Elmas; Bryan Marty; Xinjian Qi; A. Ercüment Çiçek (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Cytoscape.js 2023 update: a graph theory library for visualization and analysis. - Max Franz; Christian Tannus Lopes; Dylan Fong; Mike Kucera; Manfred Cheung; Metin Can Siper; Gerardo Huck; Yue Dong; Selçuk Onur Sümer; Gary D. Bader (Bioinform., 2023)