Improved Duplication Models for Proteome Network Evolution. - Gürkan Bebek; Petra Berenbrink; Colin Cooper; Tom Friedetzky; Joseph H. Nadeau; Süleyman Cenk Sahinalp (Systems Biology and Regulatory Genomics, 2005)

The degree distribution of the generalized duplication model. - Gürkan Bebek; Petra Berenbrink; Colin Cooper; Tom Friedetzky; Joseph H. Nadeau; Süleyman Cenk Sahinalp (Theor. Comput. Sci., 2006)

PathFinder: mining signal transduction pathway segments from protein-protein interaction networks. - Gürkan Bebek; Jiong Yang (BMC Bioinform., 2007)

Phylogenetic analysis of modularity in protein interaction networks. - Sinan Erten; Xin Li; Gürkan Bebek; Jing Li 002; Mehmet Koyutürk (BMC Bioinform., 2009)

PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. - Gürkan Bebek; Vishal N. Patel; Mark R. Chance (BMC Bioinform., 2010)

Session Introduction. - Gürkan Bebek; Mehmet Koyutürk; Mark R. Chance; Nathan D. Price 001 (Pacific Symposium on Biocomputing, 2011)

Disease Gene Prioritization Based on Topological Similarity in Protein-Protein Interaction Networks. - Sinan Erten; Gürkan Bebek; Mehmet Koyutürk (RECOMB, 2011)

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. - Sinan Erten; Gürkan Bebek; Rob M. Ewing; Mehmet Koyutürk (BioData Min., 2011)

BiC: a web server for calculating bimodality of coexpression between gene and protein networks. - George C. Linderman; Vishal N. Patel; Mark R. Chance; Gürkan Bebek (Bioinform., 2011)

Vavien: An Algorithm for Prioritizing Candidate Disease Genes Based on Topological Similarity of Proteins in Interaction Networks. - Sinan Erten; Gürkan Bebek; Mehmet Koyutürk (J. Comput. Biol., 2011)

Microenvironmental genomic alterations reveal signaling networks for head and neck squamous cell carcinoma. - Gürkan Bebek; Mohammed Orloff; Charis Eng (J. Clin. Bioinform., 2011)

Network biology methods integrating biological data for translational science. - Gürkan Bebek; Mehmet Koyutürk; Nathan D. Price 001; Mark R. Chance (Briefings Bioinform., 2012)

MAGNET: MicroArray Gene expression and Network Evaluation Toolkit. - George C. Linderman; Mark R. Chance; Gürkan Bebek (Nucleic Acids Res., 2012)

Session introduction. - Gürkan Bebek; Mehmet Koyutürk; Thomas LaFramboise; Benjamin J. Raphael; Mark R. Chance (Pacific Symposium on Biocomputing, 2013)

Drug Intervention Response Predictions with Paradigm (DIRPP) Identifies Drug Resistant Cancer Cell Lines and Pathway Mechanisms of Resistance. - Douglas Brubaker; Analisa Difeo; Yanwen Chen; Taylor Pearl; Kaide Zhai; Gürkan Bebek; Mark R. Chance; Jill S. Barnholtz-Sloan (Pacific Symposium on Biocomputing, 2014)

Frequent Subgraph Mining of Personalized Signaling Pathway Networks Groups Patients with Frequently Dysregulated Disease Pathways and Predicts Prognosis. - Arda Durmaz; Tim A. D. Henderson; Douglas Brubaker; Gürkan Bebek (PSB, 2017)

Frequent Subgraph Mining of Functional Interaction Patterns Across Multiple Cancers. - Arda Durmaz; Tim A. D. Henderson; Gürkan Bebek (PSB, 2021)