A qualitative study of large-scale recommendation algorithms for biomedical knowledge bases. - Noei, Ehsan; Hayat, Tsahi; Perrie, Jessica; Colak, Recep; Hao, Yanqi; Vembu, Shankar; Lyons, Kelly A.; Molyneux, Sam (Int. J. Digit. Libr., 2021)

Implementing Recommendation Algorithms in a Large-Scale Biomedical Science Knowledge Base. - Perrie, Jessica; Hao, Yanqi; Hayat, Zack; Colak, Recep; Lyons, Kelly A.; Vembu, Shankar; Molyneux, Sam (CoRR, 2017)

Novel Machine Learning Models for Identification, Characterization and Prioritization of Phenotype-Genotype Associations. - Colak, Recep (2016)

JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. - Colak, Recep; Kim, TaeHyung; Kazan, Hilal; Oh, Yoomi; Cruz, Miguel; Valladares-Salgado, Adan; Peralta, Jesus; Escobedo, Jorge; Parra, Esteban J.; Kim, Philip M.; Goldenberg, Anna (Bioinform., 2016)

ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity. - Witvliet, Daniel K.; Strokach, Alexey; Giraldo-Forero, Andrés Felipe; Teyra, Joan; Colak, Recep; Kim, Philip M. (Bioinform., 2016)

Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing. - Colak, Recep; Kim, TaeHyung; Michaut, Magali; Sun, Mark G. F.; Irimia, Manuel; Bellay, Jeremy; Myers, Chad L.; Blencowe, Benjamin J.; Kim, Philip M. (PLoS Comput. Biol., 2013)

Inferring cancer subnetwork markers using density-constrained biclustering. - Dao, Phuong; Colak, Recep; Salari, Raheleh; Moser, Flavia; Davicioni, Elai; Schönhuth, Alexander; Ester, Martin (Bioinform., 2010)

Exploratory Analysis of Co-Change Graphs for Code Refactoring. - Khosravi, Hassan; Colak, Recep (2009)

Dense Graphlet Statistics of Protein Interaction and Random Networks. - Colak, Recep; Hormozdiari, Fereydoun; Moser, Flavia; Schönhuth, Alexander; Holman, J.; Ester, Martin; Sahinalp, Süleyman Cenk (2009)

Mining Cohesive Patterns from Graphs with Feature Vectors. - Moser, Flavia; Colak, Recep; Rafiey, Arash; Ester, Martin (2009)