Graduate Advising

I usually work with Ph.D. and M.S. students in the Computer Science (CS) and Systems Biology and Bioinformatics (SYBB) programs. My research is application-focused with specific attention to biology, while I am also excited about applying what I learned from dealing with biological data to other domains - with particular interest in socially responsible computing. I also work on fundamental problems in computing that arise from these applications. I enjoy working with students who come from diverse academic backgrounds and I frequently co-advise students with domain scientists focused on specific applications. Graduate students (and undergraduate students planning to pursue a BS/MS degree) who are interested in algorithms, data science, scientific computing, and the applications of these in biology and other fields, may consider working with me. Please note that I do not commit to working with a student before interacting with them in a classroom context.

Current Graduate Students

	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. Serhan was the inaugural recipient of CWRU Computer and Data Sciences' Outstanding Graduate Research Award in 2022.
Mengzhen Li is a Ph.D. student in Computer Science since 2020. She also received her master's degree in Computer Science from CWRU. Mengzhen's research focuses on the computation and use of network embeddings and network alignment for biological networks.
	Çerağ Oğuztüzün is a Ph.D. student in Computer Science since 2021. She received her B.S. in Computer Engineering from Bilkent University. Çerağ's research focuses on developing machine learning models for various inference and prediction tasks in the context of intimate partner violence. I co-advise Çerağ with Günnur Karakurt at the Department of Psychiatry.
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.
	Alex Useloff is an M.S. student in Computer Science. He received his B.S in Data Science and Analytics in 2022. His research focuses on characterizing the interplay between gene regulatory network inference and identification of cell types using single cell omic data. Alex is currently a Data Engineering Analyst at Avanade.
Morgan Gillaspie is an M.S. student in Computer Science. He received his B.S/ in Data Science and Analytics in 2022. Morgan's research focuses on constructing canonical graph representations for disparate network-structured data to mitigate bias in machine learning tasks.

Alumni

	Sean Maxwell received his M.S in Systems Biology and Bioinformatics in 2014 and his M.S. in Computer Science in 2023. He is also a Research Computing Technologist at CWRU's High Performance Computing Center. Sean's research focuses on the development of high-performance software for analyzying and querying biological networks.
Filipa Blasco Tavares Pereira Lopes received her Ph.D. in Systems Biology and Bioinformatics in 2022. Filipa's dissertation was on characterizing the changes in cellular signaling that underlie the progression of Alzheimer's disease. She is currently a post-doctoral researcher at the Center for Proteomics and Bioinformatics at CWRU School of Medicine. I co-advised Dr. Lopes with Mark Chance from the Center for Proteomics and Bioinformatics and Xin Qi from the Physiology and Biophysics.
	Julian Robinson received his B.S/M.S. in Computer Science in 2022. His master's thesis focused on characterizing the effect of negative sampling in the evaluation of link prediction algorithms. Julian is currently a Software Engineer at Google.
Phan Trinh Ha received his B.S/M.S. in Computer Science in 2022. His master's thesis was on the development of machine learning models to detect intimate partner violence from unstructured text. Phan is currently a Software Engineer at Microsoft.
	Kameron Mackenzie received his B.S./M.S. in Computer Science in 2022. His master's thesis was on the development of machine learning models to predict treatment outcomes for intimate partner violence. Kameron is currently a Quantitative Research Analyst at PIMCO.
Thomas Varley received his B.S. in Data Science & Analytics in 2021 and M.S. in Computer Science in 2022. His master's thesis focused on the identification of maternal-fetal origins of cells at the maternal-fetal interface. He is currently a Software Engineer at Salesforce. I co-advised Tommy with Sam Mesiano from Reproductive Biology.
	Ahmet Mert Hacıaliefendioğlu received his M.S. in Computer Science in 2020. He is currently a Senior Software Engineer at Triverus Consulting. His master's thesis focused on the development of computational algorithms and tools to subtype intimate partner violence by integrating disparate sources and types of data. I co-advised Ahmet with Günnur Karakurt at the Department of Psychiatry.
Dr. Tyler Cowman received his Ph.D. in Computer Science in 2019. His dissertation was on the development of data structures and algorithms for efficient compression and version control of biological networks. Dr. Cowman is currently a Specialist Software Engineer at L3 Harris.
	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, North Carolina. 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. I co-advised Dr. Stanfield 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. I 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. Dr. Savel'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. Dr. Ayati's 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. I co-advised Dr. Ayati with Mark Chance from the Center for Proteomics and Bioinform atics.
	Dr. Mustafa Coşkun received his Ph.D. in Computer Science in 2017. He is currently an Associate Professor of Artificial Intelligence and Big Data Engineering at Ankara University, Turkey. Dr. Coşkun's 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. I 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. Dr. Ruffalo's 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. Dr. Erten's 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, Arkansas. His dissertation was on the development of algorithms to identify structural variants in the human genome. I co-advised Dr. Yavaş 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 from Carnegie Mellon University. is currently a Data Analyst at Millenium Management in New York. Dr. Chowdhury's master's thesis was on the development of algorithms to identify combinatorially dysregulated protein subnetworks in cancer.

Undergraduate Advising

If I am assigned as your academic advisor, please stop by my office (Olin 512) to introduce yourself.

During registration periods, I hold "advising office hours" where you can stop by to discuss your questions at the presence of other students, which provides an opportunity to exchange information with your peers. I post the time of these office hours on this webpage and via e-mail. If you are not available on posted times and/or would like to have a one-to-one meeting with me, please send me an e-mail to set up an appointment. If you have a brief question, you can also ask it to me via e-mail.

If you would like your registration hold to be removed but you do not have any questions and/or intend to meet in person, please send me an e-mail listing the courses you plan to take next semester and explain how these align with your requirements, constraints, and long-term goals.