Omics Lab - People

Principal Investigator
Mehmet Koyuturk

Mehmet Koyuturk received his Ph.D. degree in Computer Science from Purdue University, and his B.S. and M.S. degrees from Bilkent University, respectively in Electrical Engineering and Computer Engineering. He is currently the Andrew R. Jennings Professor of Computing Sciences at Case Western Reserve University (CWRU). His research is on the development of algorithms for large-scale data mining and analysis, with particular emphasis on networks and graph-structured data. His research focuses on the analysis of biological networks, systems biology of complex diseases, and computational genomics. Mehmet also serves in the steering committee of CWRU's graduate programs in Systems Biology and Bioinformatics (SYBB). He is an associate editor for IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) and EURASIP Journal on Bioinformatics and Systems Biology, and has been serving regularly as a program committee member for prominent computational biology conferences, including RECOMB, ISMB, ACM-BCB, and APBC.


Current Graduate Students
Mengzhen Li is a Ph.D. student in Computer Science since 2020. Her research focuses on the computation and use of network embeddings for biological networks. Kaan Yorgancıoğlu is a Ph.D. student in Computer Science since 2020. He received his M.S. in Computer Science from Case Western Reserve University and his B.S. in Computer Engineering from Bilkent University. His research focuses on link prediction in big networks.
Serhan Yılmaz is a Ph.D. student in Computer Science since 2018. He received his B.S. in Electrical Engineering from Middle East Technical University and M.S. in Computer Engineering from Bilkent University. His research focuses on the development of computational tools for various inference and predictive modeling tasks in the context of cellular signaling. Filipa Blasco Tavares Pereira Lopes is a Ph.D. student in Systems Biology and Bioinformatics since 2019. She received her M.S. in Molecular Biology from Università degli Studi di Milano and her Bachelor degree in Chemistry from Universidade Nova de Lisboa. Her research focuses on understanding changes in cellular signaling that underlie the progression of Alzheimer's disease. Mehmet Koyuturk co-advise Filipa with Mark Chance from the Center for Proteomics and Bioinformatics and Xin Qi from the Physiology and Biophysics.

Sean Maxwell is a Ph.D. student in Computer Science since 2017. He is also a Research Computing Technologist at CWRU's High Performance Computing Center. He received his B.S in Computer Science abd M.S. in Systems Biology and Bioinformatics, both from Case Western Reserve University. Sean's research focuses on the development of high-performance software for analyzying and querying biological networks and quantum computing. Ahmad Maroof Karimi is a Ph.D. student in Computer Science since 2016. He received his BTech in Engineering from Aligargh Muslim University and M.S. in Computer Science from the University of Toledo. His research focuses on predictive modeling of the degradation and performance of photovoltaic systems by integrating various data sources. Mehmet Koyuturk co-advise Ahmad with Roger French at the Department of Materials Science and Engineering.
Tyler Cowman is a Ph.D. student in Computer Science since 2014. He received his B.S. in Bioengineering from the University of Illinois Urbana-Champaign. His research focuses on the development of data structures and algorithms for efficient compression and version control of biological networks. Zheng Zhu is a Master's student in Computer Science since 2018. He received his B.E. in Computer Software Engineering from East China Normal University. His research focuses on assessing diversity in social networks.
Thomas Varley is a B.S. student in Data Science & Analytics since 2018. His research focuses on the characterization of transcriptional programs that play a role in pre-term birth. Mehmet Koyuturk co-advise Tommy with Sam Mesiano from Reproductive Biology.

Alumni
Ahmet Hacıaliefendioğlu received his M.S. in Computer Science in 2020 from Case Western Reserve University. He received his B.S. in Computer and Informatics Engineering from Istanbul Technical University and in Information Systems from Binghamton University. His thesis focused on the development of computational algorithms and tools to integrate and mine various types of data on intimate partner violence. Mehmet Koyuturk co-advised Ahmet with Günnur Karakurt at the Department of Psychiatry. Dr. Zachary Stanfield received his Ph.D. in Systems Biology and Bioinformatics in 2019. He is currently a Chemical Exposure Modeling Scientist at the US Environmental Protection Agency in Raleigh, NC. Zach won the Doctoral Excellence Award in Biomedical Sciences in 2020 with his dissertation on characterizing the transcriptional signaling of human parturition through integrative analysis of myometrial tissues and cell lines. Mehmet Koyuturk co-advised Zach with Sam Mesiano from Reproductive Biology.

Yidi Huang received his MS in Computer Science in 2019. He is currently a research intern at Harvard Medical School. His thesis was on characterizing the disease-site microbiome of acute myoleid leukemia patients. Mehmet Koyuturk co-advised Yidi with Thomas LaFramboise at the Department of Genetics and Genome Sciences. Dr. Daniel Savel received his Ph.D. in Computer Science in 2018. He is currently a Senior Bioinformatics Scientist at Natera in San Carlos, CA. Dan's dissertation was on characterizing the functional underpinnings of co-evolution patterns in the human genome.
Dr. Marzieh Ayati received her Ph.D. in Computer Science in 2018. She is currently an Assistant Professor of Computer Science at the University of Texas Rio Grande Valley. Her dissertation was on the development of algorithms that integrate omic data to drive personalized medicine, with particular focus on the analysis of phospho-proteomic data. Mehmet Koyuturk co-advised Marzieh with Mark Chance from the Center for Proteomics and Bioinformatics. Dr. Mustafa Coşkun received his Ph.D. in Computer Science in 2017. He is currently an Assistant Professor of Computer Engineering at Abdullah Gül University in Kayseri, Turkey. His dissertation was on the development of algebraic methods for real-time processing of proximity and link prediction queries in big networks.
Larry Liu received his M.S. in Systems Biology and Bioinformatics in 2017. He is currently a Data Systems Analyst at Cisco Meraki in San Francisco, CA. His thesis was on mining electronic health records data to characterize the interplay between intimate partner violence and traumatic brain injury. Mehmet Koyuturk co-advised Larry with Günnur Karakurt at the Department of Psychiatry. Dr. Matt Ruffalo received his Ph.D. in Computer Science in 2015. He is currently a Systems Scientist at the Computational Biology Department at Carnegie Mellon University. His dissertation was on the development of algorithms for feature extraction from omic data to facilitate effective machine learning in biomedical applications.
Dr. Sinan Erten received his Ph.D. in Computer Science in 2012. He is currently a Software Engineer at Facebook in Seattle, WA. His dissertation was on the development of network algorithms to prioritize candidate disease genes. Dr. Gökhan Yavaş received his Ph.D. in Computer Science in 2010. He is currently a Computer Scientist at the Food and Drug Administration in Jefferson, AR. His dissertation was on the development of algorithms to identify structural variants in the human genome. Mehmet Koyuturk co-advised Gökhan with Thomas LaFramboise at the Department of Genetics and Genome Sciences.
Dr. Salim Akhter Chowdhury received his M.S in Computer Science in 2010. He then received his Ph.D. in Computer Science Carnegie Mellon University. is currently a Data Analyst at Millenium Management in New York, NY. His thesis was on the development of algorithms to identify combinatorially dysregulated protein subnetworks in cancer.