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)

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

Cytoscape.js: a graph theory library for visualisation and analysis. - Max Franz; Christian Tannus Lopes; Gerardo Huck; Yue Dong; Selçuk Onur Sümer; Gary D. Bader (Bioinform., 2016)

MutationAligner: a resource of recurrent mutation hotspots in protein domains in cancer. - Nicholas Paul Gauthier; Ed Reznik; Jianjiong Gao; Selçuk Onur Sümer; Nikolaus Schultz; Chris Sander; Martin L. Miller (Nucleic Acids Res., 2016)

A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. - Yasin Senbabaoglu; Selçuk Onur Sümer; Francisco Sánchez-Vega; Debra Bemis; Giovanni Ciriello; Nikolaus Schultz; Chris Sander (PLoS Comput. Biol., 2016)

G2S: a web-service for annotating genomic variants on 3D protein structures. - Juexin Wang; Robert Sheridan; Selçuk Onur Sümer; Nikolaus Schultz; Dong Xu 002; Jianjiong Gao (Bioinform., 2018)

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)