2017

1. Begik, O. Oyken, M. Alican, T.C. Can, T. and Erson-Bensan, E. Alternative Polyadenylation Patterns for Novel Gene Discovery and Classification in Cancer. Neoplasia. 19, 574-582 (2017).
2. Hawash MM, Kahraman DC, Eren F, Cetin Atalay R*, Baytas SN*. Synthesis and biological evaluation of novel pyrazolic chalcone derivatives as novel hepatocellular carcinoma therapeutics. Eur J Med Chem. Mar 31;129:12-26. (2017)
3. Kahraman DC., Hanquet G., Jeanmart L., Lanners S., Šramel, P, Bohác A and Cetin-Atalay R., Quinoides and VEGFR2 TKIs influence the fate of hepatocellular carcinoma and its cancer stem cells, Med. Chem. Commun., DOI:10.1039/C6MD00392C (2017)
4. Koyuncu C, Cetin-Atalay R, and Gunduz-Demir C. Object Oriented Segmentation of Cell Nuclei inFluorescence Microscopy Images, IEEE Transactions on Medical Imaging, accepted, 2017
5. Rifaioglu AS, Doğan T, Sarac OS, Ersahin T, Rabie Saidi, Atalay MV, Jesus Martin M and Cetin-Atalay R. Large-scale automated multi-functional annotation of protein sequences and an experimental case study validation on PTEN transcript variants, PLOS Computational Biology, under review
   

   2016

6. Akgun, H., Us Yilmaz, D., Cetin Atalay, R., Gozen, D., A Series of 2, 4 (1H, 3H)-Quinazolinedione Derivatives: Synthesis and Biological Evaluation as Potential Anticancer Agents. Lett. Drug Des. Discov. 13, 64–76 (2016).
7. Aytaç, P. S., Durmaz, I., Houston, D. R., Cetin-Atalay, R*. & Tozkoparan, B. Novel triazolothiadiazines act as potent anticancer agents in liver cancer cells through Akt and ASK-1 proteins. Bioorg. Med. Chem. 24, 858–872 (2016).
8. Doğan, T., MacDougall, A., Saidi, R., Poggioli, D., Bateman, A., O’Donovan, C., & Martin, M. J. UniProt-DAAC: Domain Architecture Alignment and Classification, a New Method for Automatic Functional Annotation in UniProtKB. Bioinformatics, 32(15): 2264-2271 (2016).
9. Durmaz, I. I, Bilget Guven E, Ersahin E, Ozturk M, Calis I, Cetin-Atalay R. Liver cancer cells are sensitive to Lanatoside C induced cell death independent of their PTEN status. Phytomedicine 23, 42–51 (2016).
10. Koyuncu, C. F., Akhan, E., Ersahin, T., Cetin-Atalay, R. & Gunduz-Demir, C. Iterative h-minima-based marker-controlled watershed for cell nucleus segmentation. Cytom. Part A 89, 338–349 (2016).
11. Mumcuoglu, M., Gurkan-Alp, A. S., Buyukbingol, E. & Cetin-Atalay, R. Retinoid N-(1H-benzo[d]imidazol-2-yl)-5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalene-2-carboxamide induces p21-dependent senescence in breast cancer cells. Steroids 108, 31–38 (2016).
12. Tofighi, M., Yorulmaz O., Köse K Yıldırım D.C., Çetin-Atalay R., and A Çetin A.E Phase and TV Based Convex Sets for Blind Deconvolution of Microscopic Images. IEEE J. Sel. Top. Signal Process. 10, 81–91 (2016).
    

    2015

13. Çikla-Süzgün, P., Kaushik-Basu, N., Basu, A., Arora, P., Talele, T.T., Durmaz, I., Çetin-Atalay, R., Küçükgüzel, S.G., Anti-cancer and anti-hepatitis C virus NS5B polymerase activity of etodolac 1, 2, 4-triazoles. J. Enzyme Inhib. Med. Chem. 30, 778-85 (2015)
14. Demir, Z., Guven, E.B., Ozbey, S., Kazak, C., Cetin Atalay, R.*, Tuncbilek, M., Synthesis of novel substituted purine derivatives and identification of the cell death mechanism. Eur. J. Med. Chem. 89, 701–720 (2015).
15. Ece Gurdal, E., Buclulgan, E., Durmaz, I., Cetin-Atalay, R., Yarim, M., Synthesis and Anticancer Activity Evaluation of Some Benzothiazole-Piperazine Derivatives. Anti-Cancer Agents Med. Chem. (Formerly Curr. Med. Chem. Agents) 15, 382–389 (2015).
16. Ersahin, T., Tuncbag, N., Cetin-Atalay, R., The PI3K/AKT/mTOR interactive pathway. Mol. Biosyst. Mol. BioSyst., 11, 1946-1954 (2015).
17. Keskin, N., Deniz, E., Eryilmaz, J., Un, M., Batur, T., Ersahin, T., Cetin Atalay, R., Sakaguchi, S., Ellmeier, W., Erman, B., PATZ1 Is a DNA Damage-Responsive Transcription Factor That Inhibits p53 Function. Mol. Cell. Biol. 35, 1741–1753 (2015).
18. Önen-Bayram, F.E., Buran, K., Durmaz, I., Berk, B., Cetin-Atalay, R., 3-Propionyl-thiazolidine-4-carboxylic acid ethyl esters: a family of antiproliferative thiazolidines. Medchemcomm 6, 90–93, (2015).
19. Pennakalathil, J., Özgün, A., Durmaz, I., Cetin-Atalay, R., Tuncel, D., 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 (2015).
20. Stucchi, M., Cairati, S., Cetin-Atalay, R., Christodoulou, M.S., Grazioso, G., Pescitelli, G., Silvani, A., Yildirim, D.C., Lesma, G., 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 (2015).
21. Vojtičková, M., Dobiaš, J., Hanquet, G., Addová, G., Cetin-Atalay, R., Yildirim, D.C., Boháč, A., Ynamide Click chemistry in development of triazole VEGFR2 TK modulators. Eur. J. Med. Chem. 103, 105–122 (2015).
    

    2014

22. Ersahin, T., Carkacioglu, L., Can, T., Konu, O., Atalay, V., Cetin-Atalay, R., Identification of Novel Reference Genes Based on MeSH Categories. PLoS One 28 e93341 (2014).
23. Gezici Ö, Durmaz I, Bilget Güven E, Ünal Ö, Özgün A, Cetin-Atalay R, and Tuncel D. Dual Functionality of Conjugated Polymer Nanoparticles as an Anticancer Drug Carrier and a Fluorescent Probe for Cell Imaging, Royal Society of Chemistry Advances, 4, 1302-1309 (2014).
24. Gurdal, E.E., Durmaz, I., Cetin-Atalay, R., Yarim, M., Cytotoxic activities of some benzothiazole-piperazine derivatives. J. Enzyme Inhib. Med. Chem. 30, 649-54. (2014).
25. Kucukoglu, K., Mete, E., Cetin-Atalay, R., Gul, H.I., Synthesis of 3-aroyl-4-aryl-1-isopropylamino-4-piperidinols and evaluation of the cytotoxicities of the compounds against human hepatoma and breast cancer cell lines. J. Enzyme Inhib. Med. Chem. 30, 564-568 (2014).
26. Kose, K., Cetin-Atalay, R. & Cetin, A.E. (2014) Editorial, Special issue on microscopic image processing. Signal, Image and Video Processing, 8 1-2. (2014).
27. Simioni C., Martelli A.M., Cani A., Cetin-Atalay R., McCubrey J.A., Capitani S., and Neri L.M. The AKT Inhibitor MK-2206 is Cytotoxic in Hepatocarcinoma Cells Displaying Hyperphos-phorylated AKT-1 and Synergizes with Conventional Chemotherapy Oncotarget, 4, 1496-506 (2014).
28. Turan, I.S., Cakmak, F.P., Yildirim, D.C., Cetin-Atalay, R., Akkaya, E.U., Near-IR Absorbing BODIPY Derivatives as Glutathione-Activated Photosensitizers for Selective Photodynamic Action. Chem. Eur. J. 20, 16088–16092 (2014).
    

    2013

29. Arslan S., Ersahin T., Cetin-Atalay R., Gunduz-Demir C. Perceptual Watersheds for Cell Segmentation in Fluorescence Microscopy Images IEEE Transactions on Medical Imaging 32, 1121-31 (2013).
30. Gurdal E. E., Yarim M., Durmaz I., Cetin-Atalay R. Cytotoxic Activities of some Novel Benzhydrylpiperazine Derivatives Drug Research/ Arzneimittelforschung, 63, 1-8 (2013).
31. Keskin M.F., Suhre A., Kose K., Ersahin T., Cetin A.E. and Cetin-Atalay R. Image Classification of Human Carcinoma Cells Using Complex Wavelet-Based Covariance Descriptors PLoS One. 8 , e52807 (2013)
32. Kucukoglu K, Gul HI, Cetin-Atalay R. Baratli Y, Charles AL, Sukuroglu M, Gul M, Geny B. Synthesis of new N,N'-bis[1-aryl-3-(piperidine-1yl)propylidene]hydrazine dihydrochlorides and evaluation of their cytotoxicity against human hepatoma and breast cancer cells. J Enzyme Inhib Med Chem, 29, 420-6 (2013).
33. Yildiz G, Arslan-Ergul A, Bagislar S, Konu O, Yuzugullu H, Gursoy-Yuzugullu O, Ozturk N, Ozen C, Ozdag H, Erdal E, Karademir S, Sagol O, Mizrak D, Bozkaya H, Ilk HG, Ilk O, Bilen B, Cetin-Atalay R, Akar N, Ozturk M. Genome-Wide Transcriptional Reorganization Associated with Senescence-to-Immortality Switch during Human Hepatocellular Carcinogenesis. PLoS One. 15, e64016 (2013)
    

    2012

34. Gurkan-Alp A.S., Mumcuoglu M., Andac A.C. , Dayanc E., Cetin-Atalay R., Buyukbingol E. Synthesis, anticancer activities and molecular modeling studies of novel indole retinoid derivatives European Journal of Medicinal Chemistry, 58, 346-354 (2012).
35. Isik Z, Ersahin T, Atalay V, Aykanat C, Cetin-Atalay R., A signal transduction score flow algorithm for cyclic cellular pathway analysis, which combines transcriptome and ChIP-seq dataMolecular Biosystems Volume 812) October 2012, pp3224-3231.
36. Ligons D.L., Tuncer C., Linowes B.A., Akcay I.M., Kurtulus S., Deniz E., Atasever Arslan B., Cevik S.I., Keller H.R., Luckey M.A., Feigenbaum L., Möröy T., Ersahin T., Atalay R., Erman B., Park J.H. CD8 lineage specific regulation of interleukin-7 receptor expression by the transcriptional repressor Gfi1 Journal of Biological Chemistry 287, 34386-34399 (2012).
37. Koyuncu C.F., Arslan S., Durmaz I., Cetin-Atalay R., and Gunduz-Demir C. Smart markers for watershed-based cell segmentation, PLoS One 7 e48664 (2012).
38. Koksal M, Yarim M, Durmaz I, Cetin-Atalay R., Synthesis and Cytotoxic Activity of Novel 3-methyl-1-[(4-substitutedpiperazin-1-yl)methyl]- 1H-indole Derivatives Arzneimittel-forschung 62, 389-94 (2012).
39. Onen-Bayram FE, Durmaz I, Scherman D, Herscovici J, Cetin-Atalay R. A novel thiazolidine compound induces caspase-9 dependent apoptosis in cancer cells. Bioorganics and Medicinal Chemistry 20, 5094-5102, (2012).
40. Tuncbilek M, Guven EB, Onder T, Cetin Atalay R., Synthesis of novel 6-(4-substituted piperazine-1-yl)-9-(β-D-ribofuranosyl) purine derivatives, which lead to senescence-induced cell death in liver cancer cells J Med Chem. 55, 3058-3065 (2012).
41. Yarim M, Koksal M, Durmaz I, Atalay R. Cancer Cell Cytotoxicities of 1-(4-Substituted benzoyl)-4-(4-chlorobenzhydryl) piperazine Derivatives. Int J Mol Sci. 13, 8071-8085 (2012).
    

    2011

42. Buontempo F#, Ersahin T#, Missiroli S, Senturk S, Etro D, Ozturk M, Capitani S, Cetin-Atalay R.*, Neri ML. Inhibition of Akt signaling in hepatoma cells induces apoptotic cell death independent of Akt activation status Invest New Drugs, 29, 1303-1313, (2011).
43. Mete EB, Inci G, Cetin-Atalay R., Das U, Sahin A, Gul M, Kazaz C, and Dimmock JR The design and cytotoxic evaluation of some 1-aryl-3-isopropyl-amino-1-propanone hydrochlorides towards human Huh-7 hepatoma cells Archiv Der Pharmazie, 344, 333-339. (2011).
    

    2010

44. Carkacıoglu L., Cetin Atalay R., Konu O., Atalay V. and Can T. Bi-k-Bi Clustering : Mining Gene Expression Profiles Using An Association Pattern Discovery Approach Int. J. Data Mining and Bioinformatics, 4, 701-721. (2010).
45. Saraç O.S., Atalay V., Cetin-Atalay R. GOPred: GO molecular function prediction by combined classifiers PLoS One, 5, e12382 (2010).
    

    2009 and ...

46. Sayan B., Emre N.C.T., Irmak M.B., Ozturk M. and Cetin-Atalay R. Nuclear exclusion of p33ING1b tumor suppressor protein: explored in HCC cells using a new highly specific antibody, Hybridoma 28, 1-6 (2009).
    
47. Sarac O.S., Gürsoy-Yüzügüllü O., Cetin-Atalay R., Atalay V. Subsequence-based feature map for protein function classification Comput Biol Chem. 32, 122-130 (2008).
    
48. Ozturk N., Erdal E., Mumcuoglu M., Akcali K.C., Yalcin O., Senturk S., Arslan-Ergul A., Gur B., Yulug I., Cetin-Atalay R., Yakicier C., Yagci T., Tez M., Ozturk M. Reprogramming of replicative senescence in hepatocellular carcinoma-derived cells Proc Natl Acad Sci U S A. 103, 2178-2183 (2006).
    
49. Atalay V and Cetin-Atalay R., Implicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification Bioinformatics 21, 1429-36, (2005).
    
50. Demir E., Babur O., Dogrusoz U., Gursoy A., Ayaz A. Gulesir G., Nisanci G. and Cetin-Atalay R., An Ontology for Collaborative Construction and Analysis of Cellular Pathways. Bioinformatics, 20, 349–356 (2004).
    
51. Dinçer P., Balcı B., Talim B., Brockington M., Yuva Y., Dinçel D.,Torelli S., Brown S., Haliloğlu G., Özbaş Gerçeker F., Cetin Atalay R., Yakıcıer C., Muntoni F., Topaloğlu H. A novel form of limb-girdle muscular dystrophy and mental retardation with reduced a-dystroglycan, Neuromuscular Disorders, 13, 771–778 (2003).
52. Irmak MB, Ince G, Ozturk M, Cetin-Atalay R., Acquired tolerance of hepatocellular carcinoma cells to selenium deficiency: a selective survival mechanism? Cancer Research, 63, 6707-6715 (2003).
53. Kocatas A., Gursoy A. and Atalay R., Application of Data Mining Techniques to Protein-Protein Interaction Prediction Lecture Notes in Computer Science, Volume 2869, April 2003, pp.316-323.
54. Ozarar M., Atalay V. and Cetin Atalay R., Prediction of Protein Subcellular Localization Based on Primary Sequence Data Lecture Notes in Computer Science, 2869, 611 – 618 (2003).
    
55. Yildiz E., Oztan A., Sar F., Pinarbasi E., Cetin-Atalay R., Akkiz H., and Ozturk M. Molecular characterization of a full genome Turkish hepatitis C virus 1b isolate (HCV-TR1): a predominant viral form in Turkey, Virus Genes 25, 169-177 (2002).
56. Demir E, Babur O, Dogrusoz U., Gursoy A., Nisanci G., Cetin-Atalay R. and Ozturk M. PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways Bioinformatics 18, 996-1003 (2002).
    
57. Yolcu E., Sayan B.S., Yagci T., Cetin-Atalay R., Soussi T., Yurdusev N. and Ozturk M. A monoclonal antibody against DNA binding helix of p53 protein Oncogene, 20, 1398-1401 (2001).
    
58. Cetin-Atalay R. and Ozturk M p53 mutations as fingerprints of environmental carcinogenesis by. Pure Appl. Chem. 72, 995-999, (2000)
    
59. Gurcan N., Koyutürk M., Yildiz S., Cetin-Atalay R., Cetin E.A. Identification of relative protein bands in PAGE using multiresolution snake algorithm, Biotechniques, 26, 1162-1169 (1999).
    
60. Cetin R., Anborgh P.H., Cool R.H. and Parmeggiani A. Functional role of the non catalytic domains of elongation factor Tu in the interactions with ligands, Biochemistry, 37, 486-495 (1998)
    
61. Cetin R., Krab I.M., Anborgh P.H., Cool R.H., Watanabe T., Sugiyama T., Izaki K. and Parmeggiani A. Enacyloxin IIa, an inhibitor of protein biosynthesis that acts on elongation factor Tu and the ribosome EMBO Journal, 15, 2604-2611 (1996).
    
62. Zeef L.A.H. Bosch L., Anborgh P.H., Cetin R., Parmeggiani A. and Hilgenfeld R. Pulvomycin resistant mutants of E. coli elongation factor Tu EMBO Journal, 135113-5120 (1994).