Cigdem Ak, Ph.D.
- Postdoctoral Researcher, CEDAR, OHSU Knight Cancer Institute, School of Medicine
Biography
My research focuses on developing computational methods to analyze complex biological data, with a focus on cancer biology and early detection. Using my background in mathematics, I specialize in scalable and interpretable machine learning to extract meaningful insights from large datasets.
I collaborate with clinicians and researchers to apply computational methods to real-world biomedical challenges. My current projects involve integrating different data types, analyzing spatial patterns in tissue samples from multiplex imaging, and leveraging existing databases for cancer research.
Beyond cancer, my earlier work focused on modeling spatiotemporal dynamics. During my PhD, I developed models for predicting changes across space and time, with applications in epidemiology. Building on this work, I later modeled the spread of COVID-19 using demographic and socioeconomic data to understand its impact on different communities.
Education and training
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Degrees
- Ph.D., 2019, Koc University
- MSc, 2014, École Polytechnique
- MSc, 2013, École Normale Supérieure
- B.S., 2012, Université Galatasaray
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Internship
- French National Institute for Research in Digital Science and Technology (Inria Lyon, Grenoble)
Memberships and associations:
- International Society for Computational Biology (ISCB)
- American Association for Cancer Research (AACR)
Areas of interest
- Interpretable Machine Learning
- Multiomic Integration
- Spatiotemporal modelling
- Precision Medicine
- Systems Biology
Additional information
Honors and awards
- Master Excellence Scholarship from Fondation Mathématique Jacques Hadamard, 2013
- The Ampère Scholarships of Excellence of the ENS de Lyon, 2012
Publications
Elsevier pure profileSelected publications
- Kupp, S., Vangordon, I., Eksi, S. E., Gonen, M., Esener, S., Ak, Ç.* Interpretable and integrative analysis of single-cell multiomics with scMKL Communications Biology, (8), 1160. (2025)
- Ak Ç., Sayar Z., Thibault G., Burlingame E.A., Kuykendall M.J., Eng J., Chitsazan A., Chin K., Adey A.C., Boniface C., Spellman P.T., Thomas G.V., Kopp R.P., Demir E., Chang Y.H., Stavrinides V., Eksi S.E. Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment iScience, 27 (9), art. no. 110668. (2024)
- Ors A., Chitsazan A.D., Doe A.R., Mulqueen R.M., Ak Ç., Wen Y., Haverlack S., Handu M., Naldiga S., Saldivar J.C., Mohammed H. Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer Nucleic Acids Research, 50 (20), pp. 11492 - 11508. (2022)
- Bektaş A.B., Ak Ç., Gönen M. Fast and interpretable genomic data analysis using multiple approximate kernel learning Bioinformatics, 38, pp. I77 - I83. (2022)
- Ak Ç.*, Chitsazan A.D., Gönen M., Etzioni R., Grossberg A.J. Spatial Prediction of COVID-19 Pandemic Dynamics in the United States ISPRS International Journal of Geo-Information, 11 (9), art. no. 470. (2022)
- Ak Ç., Ergönül Ö., Gönen M. A prospective prediction tool for understanding Crimean–Congo haemorrhagic fever dynamics in Turkey Clinical Microbiology and Infection, 26 (1), pp. 123.e1 - 123.e7. (2020)
- Ak Ç., Ergönül Ö., Gönen M. Structured Gaussian Processes with Twin Multiple Kernel Learning Proceedings of Machine Learning Research, 95, pp. 65 - 80. (2018)
- Ak Ç., Ergönül Ö., Şencan İ., Torunoğlu M.A., Gönen M. Spatiotemporal prediction of infectious diseases using structured Gaussian processes with application to Crimean–Congo hemorrhagic fever PLoS Neglected Tropical Diseases, 12 (8), art. no. e0006737. (2018)