Publications

*Corresponding Author

Postdoc papers

• Ak, Ç., Sayar, Z., Thibault, G., Burlingame, E., Eng, J., Chitsazan, A., Adey, A., Boniface, C., Spellman, P., Thomas, G., Kopp, R., Chang, Y. H., Stavrinides, V., Demir, E., and Eksi, S. E.
  Multiplex imaging of localized prostate tumors reveals altered spatial organization of AR-positive cells in the microenvironment
  iScience, 2024, 110668, ISSN 2589-0042, https://doi.org/10.1016/j.isci.2024.110668.

• Ait Ahmad, K., Ak, Ç., Thibault G., Chang, Y. H., Eksi, S. E.
  Automated segmentation of tumor innervating neuronal fibers
  Heliyon, 2024, e41209, https://doi.org/10.1016/j.heliyon.2024.e41209.

• Ors, A., Chitsazan A. D., Doe, A. R., Mulqueen R. M., Ak, Ç., Wen Y., Haverlack, M., Handu, M., Naldiga, S., Saldivar, J. C., and Mohammed H.
  Estrogen regulates divergent transcriptional and epigenetic cell states in breast cancer
  Nucleic Acids Research, 2022, Volume 50, Issue 20, Pages 11492–11508, https://doi.org/10.1093/nar/gkac908.

• Bektaş, A. B., Ak, Ç., Gönen, M.
  Fast and interpretable genomic data analysis using multiple approximate kernel learning
  Bioinformatics, 2022, vol. 38, Issue Supplement 1, Pages i77–i83, https://doi.org/10.1093/bioinformatics/btac241.

• Ak, Ç.*, Chitsazan, A., Gönen, M., Grossberg, A., Etzioni, R.
  Spatial prediction of COVID 19 pandemic dynamics in the United States
  ISPRS International Journal of Geo Information, 2022, 11(9), 470, https://doi.org/10.3390/ijgi11090470.

PhD papers

• Ak, Ç., Ergönül, Ö., Gönen, M.
  A prospective prediction tool for understanding Crimean–Congo haemorrhagic fever dynamics in Turkey <br) Clinical Microbiology and Infection, 2020, 26(1):123.e1 123.e7. https://doi.org/10.1016/j.cmi.2019.05.006.

• Ak, Ç., Ergönül, Ö., Gönen, M.
  Structured Gaussian processes with twin multiple kernel learning
  Proceedings of The 10th Asian Conference on Machine Learning, 2018, PMLR 95:65 80. https://proceedings.mlr.press/v95/ak18a/ak18a.pdf.

• 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, 2018, vol. 12, no. 8, p. e0006737. https://doi.org/10.1371/journal.pntd.0006737.

Latest works in preperation

• Kupp, S., Vangordon, I., Eksi, S. E., Gonen, M., Esener, S., Ak, Ç.*
  [scMKL: Knowledge based machine learning to enhance the interpretability of single cell multi omics analysis]
  Currently in revision at Communications Biology, 2025.

• Ak, Ç.*, Szczepanski, N., Doe, A., Chitsazan, A., Yardımcı, G. G.
  [EpiConfig: Multimodal topic modeling for single cell multiomics]
  Proceedings AACR, 2025.

• Ak, Ç.*, Ait Ahmad, K., Kupp, S., Wang, M., Thibault G., Chang, Y. H., Eksi, S. E.
  [Investigating the spatial interactions of neural and immune cells in localized prostate cancer via new spatial analysis tools]
  

• Mohebnasab, M., Ak, Ç., Williams, T., Corless, C., Morgan, T.
  [Functional PTEN mutations in progestin resistant de novo endometrial intraepithelial neoplasia]
  Archives of Pathology & Laboratory Medicine, 2021, 145 (9): e2–e194.

• Grieco, J. P., Sener, G., Theison, H., Riesterer, J. L., Kuykendall, M. J., Makkawi, R., Davies, A. E., McGann, J., Ak, Ç., Eksi, S. E.
  [Upregulated NRXN1 expression mediates neuronal phenotypic plasticity in prostate cancer through mitochondrial shuttling at cellular adhesion sites]
  Currently in revision at Nature Communications, 2024.