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Graduate AdvisingI 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, though I am excited about applying what I learned from dealing with biological data to other domains. 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
|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.|
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. I co-advise Filipa with Mark Chance from the Center for Proteomics and Bioinformatics and Xin Qi from the Physiology and Biophysics.
Ahmet Hacıaliefendioğlu is an M.S. student in Computer Science since 2018. He received his B.S. in Computer and Informatics Engineering from Istanbul Technical University and in Information Systems from Binghamton University. His research focuses on the development of computational algorithms and tools to integrate and mine various types of data on intimate partner violence. I co-advise Ahmet with Günnur Karakurt at the Department of Psychiatry.
|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.|
|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.|
|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.|
|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.|
|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.|
|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. I co-advise Ahmad with Roger French at the Department of Materials Science and Engineering.|
|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. I co-advise Tommy with Sam Mesiano from Reproductive Biology.|
|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. I 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. 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. 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. I co-advised Marzieh 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 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. 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. 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. I 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.|
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.