Mehmet Koyutürk

Andrew R. Jennings Professor of Computing Sciences Professor, Computer and Data Sciences Department
Develops algorithms for transforming "big" biological data into systems biology knowledge
Office: 512 Olin Phone Number: (216) 368-2963 Email: mehmet.koyuturk@case.edu

Education

Ph.D., Computer Science, Purdue University, 2006

Research Interests

Bioinformatics and Computational Biology

Teaching Interests

Algorithms, Bioinformatics, Data Mining & Analysis, Discrete Mathematics, Data Structures

Publications

Ayati, M., Chance, M., & Koyutürk, M. (2020). Co-Phosphorylation Networks Reveal Subtype-Specific Signaling Modules in Breast Cancer. Bioinformatics.
Deznabi, I., Arabaci, B., Koyutürk, M., & Tastan, O. (2020). DeepKinZero: zero-shot learning for predicting kinase–phosphosite associations involving understudied kinases. Bioinformatics, 36 (12), 3652-3661.
Karimi, A., Fada, J., Parrilla, N., Pierce, B., Koyutürk, M., French, R. H., & Braid, J. H. (2020). Generalized and Mechanistic PV Module Performance Prediction From Computer Vision and Machine Learning on Electroluminescence Images. IEEE Journal of Photovoltaics, 10 (3), 878-887.
Liu, D., Skomorovska, Y., Song, Y., Bowler, E., Harris, P., Ravasz, M., Bailey, S., Ayati, M., Tamai, K., Koyutürk, M., Yuan, X., Wang, Z., Wang, Y., & Ewing, R. (2019). ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1. Cancer Biology and Therapy, 20 (1), 90-100.
Qiao, S., Koyutürk, M., & Ozsoyoglu, M. (2018). Querying of Disparate Association and Interaction Data in Biomedical Applications. Computational Biology and Bioinformatics, IEEE-ACM Transactions on, 15 (4), 1052-1065.
Qiao, S., Koyutürk, M., & Ozsoyoglu, M. (2018). Querying of Disparate Association and Interaction Data in Biomedical Applications. Computational Biology and Bioinformatics, IEEE-ACM Transactions on, 15 (4), 1052-1065.
Maxwell, S., Chance, M., & Koyutürk, M. (2017). Linearity of network proximity measures: implications for set-based queries and significance testing. Bioinformatics, 33 (9), 1354--1361.
Wiredja, D., Koyutürk, M., & Chance, M. (2017). The KSEA App: a web-based tool for kinase activity inference from quantitative phosphoproteomics. Bioinformatics.
Wiredja, D., Ayati, M., Mazhar, S., Sangodkar, J., Maxwell, S., Schlatzer, D., Narla, G., Koyutürk, M., & Chance, M. (2017). Phosphoproteomics Profiling of Nonsmall Cell Lung Cancer Cells Treated with a Novel Phosphatase Activator. Proteomics.
Stanfield, Z., Coskun, M., & Koyutürk, M. (2017). Drug Response Prediction as a Link Prediction Problem. Scientific Reports, 7
Cowman, T., & Koyutürk, M. (2017). Prioritizing tests of epistasis through hierarchical representation of genomic redundancies. Nucleic Acids Research.
Ayati, M., & Koyutürk, M. (2016). PoCos: Population Covering Locus Sets for Risk Assessment in Complex Diseases. PLoS computational biology, 12 (11), e1005195.
Ni, J., Koyutürk, M., Tong, H., Haines, J., Xu, R., & Zhang, X. (2016). Disease gene prioritization by integrating tissue-specific molecular networks using a robust multi-network model. BMC bioinformatics, 17 (1), 453.
Qiao, S., Koyutürk, M., & Ozsoyoglu, Z. M. (2016). Querying of Disparate Association and Interaction Data in Biomedical Applications. IEEE/ACM transactions on computational biology and bioinformatics.
Savel, D., LaFramboise, T., Grama, A., & Koyutürk, M. (2016). Pluribus - Exploring the Limits of Error Correction Using a Suffix Tree. Computational Biology and Bioinformatics, IEEE-ACM Transactions on [15455963].
Niazi, M., Yao, K., Zynger, D., Clinton, S., Chen, J., Koyutürk, M., LaFramboise, T., & Gurcan, M. (2016). Visually Meaningful Histopathological Features for Automatic Grading of Prostate Cancer. IEEE Transactions on Information Technology in Biomedicine [10897771].
Ruffalo, M., Koyutürk, M., & Sharan, R. (2015). Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PLoS Computational Biology.
Hu, D., & Koyutürk, M. (2015). Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction. Cancer Informatics.
Yavas, G., Koyutürk, M., Gould, M., McMahon, S., & LaFramboise, T. (2014). DB2: a probabilistic approach for accurate detection of tandem duplication breakpoints using paired-end reads.. BMC genomics, 15 (1), 175.
Liu, Y., Koyutürk, M., Maxwell, S., & Chance, M. (2014). Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing. BMC Genomics, 15 (685).
Kahveci, T., Salem, S., & Koyutürk, M. (2013). Guest Editorial for Special Section on BIOKDD. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 10 (5), 1199--1200.
Patel, V., Gokulrangan, G., Chowdhury, S., Chen, Q., Sloan, A., Koyutürk, M., Barnholtz-Sloan, J., & Chance, M. (2013). Network signatures of survival in glioblastoma multiforme.. PLoS computational biology, 9 (9), e1003237.
Erten, S., Chowdhury, S., Guan, X., Nibbe, R., Barnholtz-Sloan, J., Chance, M., & Koyutürk, M. (2012). Identifying stage-specific protein subnetworks for colorectal cancer.. BMC proceedings, 6 Suppl 7 , S1.
Ruffalo, M., Koyutürk, M., Ray, S., & LaFramboise, T. (2012). Accurate estimation of short read mapping quality for next-generation genome sequencing.. Bioinformatics (Oxford, England), 28 (18), i349-i355.
Bebek, G., Koyutürk, M., Price, N., & Chance, M. (2012). Network biology methods integrating biological data for translational science.. Briefings in bioinformatics, 13 (4), 446-59.
Liu, Y., Koyutürk, M., Barnholtz-Sloan, J., & Chance, M. (2012). Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases.. BMC systems biology, 6 , 65.
Liu, Y., Maxwell, S., Feng, J., Zhu, X., Elston, R., Koyutürk, M., & Chance, M. (2012). Gene, pathway and network frameworks to identify epistatic interactions of single nucleotide polymorphisms derived from GWAS data.. BMC systems biology, 6 Suppl 3 , S15.
Koyutürk, M. (2012). Using protein interaction networks to understand complex diseases. IEEE Computer, 45 (3), 31-38.
Liu, Y., Koyutürk, M., Maxwell, S., Zhao, Z., & Chance, M. (2012). Integrative analysis of common neurodegenerative diseases using gene association, interaction networks and mRNA expression data.. AMIA Summits on Translational Science proceedings AMIA Summit on Translational Science, 2012 , 62-71.
Saha, S., Roman, T., Galante, A., Koyutürk, M., & Ewing, R. (2012). Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks.. International journal of computational biology and drug design, 5 (3-4), 185-205.
Erten, S., Bebek, G., & Koyutürk, M. (2011). Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks.. Journal of computational biology, 18 (11), 1561-74.
Ruffalo, M., LaFramboise, T., & Koyutürk, M. (2011). Comparative analysis of algorithms for next-generation sequencing read alignment.. Bioinformatics (Oxford, England), 27 (20), 2790-6.
Erten, S., Bebek, G., Ewing, R., & Koyutürk, M. (2011). DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization.. BioData mining, 4 , 19.
Nibbe, R., Chowdhury, S., Koyutürk, M., Ewing, R., & Chance, M. (2011). Protein-protein interaction networks and subnetworks in the biology of disease.. Wiley interdisciplinary reviews. Systems biology and medicine, 3 (3), 357-67.
Chowdhury, S., Nibbe, R., Chance, M., & Koyutürk, M. (2011). Subnetwork state functions define dysregulated subnetworks in cancer.. Journal of computational biology, 18 (3), 263-81.
Bebek, G., Chance, M., Koyutürk, M., Price, N., Francisco, M., Bustamante, C., Leal, S., Foster, J., Moore, J., Bernauer, J., & Others, J. (2011). Pacific symposium on biocomputing 2011. Unknown Journal.
Liu, Y., Patel, S., Nibbe, R., Maxwell, S., Chowdhury, S., Koyutürk, M., Zhu, X., Larkin, E., Buxbaum, S., Punjabi, N., Gharib, S., Redline, S., & Chance, M. (2011). Systems biology analyses of gene expression and genome wide association study data in obstructive sleep apnea.. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
Carbunar, B., Ramanathan, M., Koyutürk, M., Jagannathan, S., & Grama, A. (2010). Optimal Tag Coverage and Tag Report Elimination. RFID SYSTEMS.
Erten, S., Li , X., Bebek, G., Li, J., & Koyutürk, M. (2009). Phylogenetic analysis of modularity in protein interaction networks.. BMC bioinformatics, 10 , 333.
Yavas, G., Koyutürk, M., Ozsoyoglu, Z. M., Gould, M. M., & LaFramboise, T. M. (2009). An optimization framework for unsupervised identification of rare copy number variation from SNP array data. Genome Biol, 10 (10), R119.