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  2. Doğan, T. (2018). HPO2GO: Prediction of Human Phenotype Ontology Term Associations for Proteins Using Cross Ontology Annotation Co-occurrences. PeerJ 6:e5298.
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  4. Demirel, H.C., Doğan, T. & Tuncbag, N. (2018). A Structural Perspective on Modulation of Protein-Protein Interactions with Small Molecules. Current Topics in Medicinal Chemistry, 18(8):700-713. (
  5. Rifaioglu, A.S., Doğan, T., Saraç, Ö.S., Ersahin, T., Saidi, R., Atalay, M.V., Martin, M.J. and Cetin‐Atalay, R. (2018). Large‐scale automated function prediction of protein sequences and an experimental case study validation on PTEN transcript variants. Proteins: Structure, Function, and Bioinformatics, 86(2), 135-151. (
  6. Rifaioglu, A.S., Doğan, T., Martin, M.J., Cetin-Atalay, R. and Atalay, M.V. (2017). Multi-task Deep Neural Networks in Automated Protein Function Prediction. arXiv preprint arXiv:1705.04802 [Currently under peer review].
  7. Doğan, T., MacDougall, A., Saidi, R., Poggioli, D., Bateman, A., O’Donovan, C. and Martin, M. J. (2016). UniProt-DAAC: Domain Architecture Alignment and Classification, a New Method for Automatic Functional Annotation in UniProtKB. Bioinformatics, 32(15): 2264-2271. (
  8. Aytaç, P.S., Durmaz, I., Houston, D.R., Cetin-Atalay, R., Tozkoparan, B., 2016. Novel triazolothiadiazines act as potent anticancer agents in liver cancer cells through Akt and ASK-1 proteins. Bioorg. Med. Chem, 2016 in print
  9. Akgun, H., Us Yilmaz, D., Cetin Atalay, R., Gozen, D., 2016. A Series of 2, 4 (1H, 3H)-Quinazolinedione Derivatives: Synthesis and Biological Evaluation as Potential Anticancer Agents. Lett. Drug Des. Discov. 13, 64–76.
  10. Ece Gurdal, E., Buclulgan, E., Durmaz, I., Cetin-Atalay, R., Yarim, M., 2015. Synthesis and Anticancer Activity Evaluation of Some Benzothiazole-Piperazine Derivatives. Anti-Cancer Agents Med. Chem. (Formerly Curr. Med. Chem. Agents) 15, 382–389.
  11. Ersahin, T., Ozturk, M., Cetin-Atalay, R., 2015. Molecular Biology of Liver Cancer, in: Meyers, R.A. (Ed.), Encyclopedia of Molecular Cell Biology and Molecular Medicine: Translational Medicine: Cancer. Wiley-VCH Verlag GmbH & Co. KGaA.
  12. Vojtičková, M., Dobiaš, J., Hanquet, G., Addová, G., Cetin-Atalay, R., Yildirim, D.C., Boháč, A., 2015. Ynamide Click chemistry in development of triazole VEGFR2 TK modulators. Eur. J. Med. Chem. 103, 105–122.
  13. Demir, Z., Guven, E.B., Ozbey, S., Kazak, C., Atalay, R.C., Tuncbilek, M., 2015. Synthesis of novel substituted purine derivatives and identification of the cell death mechanism. Eur. J. Med. Chem. 89, 701–720.
  14. Çikla-Süzgün, P., Kaushik-Basu, N., Basu, A., Arora, P., Talele, T.T., Durmaz, I., Çetin-Atalay, R., Küçükgüzel, S.G., 2015. Anti-cancer and anti-hepatitis C virus NS5B polymerase activity of etodolac 1, 2, 4-triazoles*. J. Enzyme Inhib. Med. Chem. 1–8.
  15. Pennakalathil, J., Özgün, A., Durmaz, I., Cetin-Atalay, R., Tuncel, D., 2015. pH-responsive near-infrared emitting conjugated polymer nanoparticles for cellular imaging and controlled-drug delivery. J. Polym. Sci. Part A Polym. Chem. 53, 114–122.
  16. Önen-Bayram, F.E., Buran, K., Durmaz, I., Berk, B., Cetin-Atalay, R., 2015. 3-Propionyl-thiazolidine-4-carboxylic acid ethyl esters: a family of antiproliferative thiazolidines. Medchemcomm 6, 90–93.
  17. Keskin, N., Deniz, E., Eryilmaz, J., Un, M., Batur, T., Ersahin, T., Atalay, R.C., Sakaguchi, S., Ellmeier, W., Erman, B., 2015. PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function. Mol. Cell. Biol. 35, 1741–1753.
  18. Ersahin, T., Tuncbag, N., Cetin-Atalay, R., 2015. The PI3K/AKT/mTOR interactive pathway. Mol. Biosyst. doi:10.1039/c5mb00101c
  19. Stucchi, M., Cairati, S., Cetin-Atalay, R., Christodoulou, M.S., Grazioso, G., Pescitelli, G., Silvani, A., Yildirim, D.C., Lesma, G., 2015. Application of the Ugi reaction with multiple amino acid-derived components: synthesis and conformational evaluation of piperazine-based minimalist peptidomimetics. Org. Biomol. Chem. 13, 4993–5005.
  20. Durmaz, I., Guven, E.B., Ersahin, T., Ozturk, M., Calis, I., Cetin-Atalay, R., 2015. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine in print
  21. Akbas, C.E., Bozkurt, A., Cetin, A.E., Cetin-Atalay, R., Uner, A., 2015. Multiplication-free Neural Networks, in: Signal Processing and Communications Applications Conference (SIU), 2015 23th. pp. 2416–2418.
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