Research Focus

Molecular Cellular Biology

* Molecular mechanisms of liver cancer development
* Effect of selenium deficiency dependent oxidative stress on HCC
* Identifications of novel targets of p53 tumor suppressor protein in HCC

Bioinformatics

* Genome annotation through machine learning techniques
* Protein and DNA motif data analysis
* Microarray data analysis
* Molecular Cellular Biology

Academic Degrees and Employment

Employment:

2007-Present Associate Professor, Bilkent University, Ankara Turkey
1999-2007 Assistant Professor, Bilkent University, Ankara Turkey
2004-2005 Assistant Professor (sabbatical leave) Virginia Bioinformatics Institute, Blacksburg, USA
1997-1999 Instructor, Bilkent University, Ankara Turkey
1992-1997 Research Assistant, Ecole Polytechnique, Palaiseau, France

Academic Degrees:

1997 Ph.D. Biochimie Univ. de Paris-Sud, Orsay, France
1994 DEA(M.Sc) Biochimie Univ. de Paris-Sud, Orsay, France
1992 M.D. Medicine Hacettepe Univ., Fac. of Medicine Ankara, Turkey

Graduate & Fellowship Program Affiliations

Department of Molecular Biology and Genetics

Summary of Requirements for Admission to Graduate Programs

Research Interests

Cancer is a multi-gene and multi-step disease with progressive and cumulative changes in the phenotype of tumor cells. Genetic changes associated with malignant transformation of cells occur on two type of genes, namely “oncogenes” and “tumor suppressor genes”. Oncogenes are either activated forms of cellular proto-oncogenes such as ras, or viral oncogenes such as E6 and E7 genes of some papillomaviruses. Activation of cellular proto-oncogenes occurs as a result of point mutations (ras, b-catenin…, gene amplification (N-myc, cyclin D…or chromosomal translocations (c-myc, c-abl… Inactivation of tumor suppressor genes involves more complex processes such as point mutations, chromosomal deletions, or functional inactivation of wild-type proteins by viral transforming proteins. Recently, Kinzler and Vogelstein proposed that tumor suppressor genes can be broadly divided into two groups, namely “gatekeepers” and “caretakers” (Kinzler & Vogelstein, 1998). According to this new grouping, gatekeepers are genes that directly regulate the growth of tumors, whereas caretakers are genes involved in maintaining genomic stability. The loss of caretaker function is not a direct cause of malignant tranformation, but the resulting genomic instability leads to downstream mutations on gatekeeper genes. Genetic changes detected in cancer cells are either germ-line cancer predisposition mutations, or they occur somatically in cancer cells, as a result of exposure to DNA damaging agents and/or error-prone DNA replication. Genetic changes of oncogenes and gatekeeper genes lead to permenant phenotypic aberrations on growth control pathways, such as cell cycle, apoptosis and senescence which reflect the phenotypic heterogeneity of tumor cells.

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Articles in Refereed Journals

* Tuncbilek, M.; Bilget Guven, E.; 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” Journal of Medicinal Chemistry, In print, 2012

* 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” Investigational New Drugs, Vol. 29, 1303-1313, 2011

* 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,  Vol. 344, 333-339, 2011

* Saraç OS, Atalay V, Cetin-Atalay R, “GOPred: GO molecular function prediction by combined classifiers” PLoS One. 5(8):e12382, 2010

* L. Carkacioglu, R. Cetin-Atalay, O. Konu, V. Atalay, T. Can, “Bi-k-Bi Clustering: Mining Large Scale Gene Expression Data Using Two-Level Biclustering,” accepted for publication in Int J of Data Mining and Bioinformatics

* B. Sayan, N.C.T. Emre, M.B. Irmak, M. Ozturk, R. Cetin-Atalay, “Monoclonal antibody 15B9 against p33ING1b tumor suppressor protein,” accepted for publication in Hybridoma

* F. Buontempo, T. Ersahin, S. Missiroli, S. Senturk, D. Etro, M. Ozturk, S. Capitani, R. Cetin- Atalay, M.L. Neri, “Inhibition of Akt signaling in hepatoma cells induces apoptotic cell death independent of Akt activation status,” Investigational New Drugs, vol. , pp. (2010) PubMed

* B. Sayan, N.C.T. Emre, M.B. Irmak, M. Ozturk, R. Cetin-Atalay, “Nuclear Exclusion of p33ING1b Tumor Suppressor Protein: Explored in HCC Cells Using a New Highly Specific Antibody,” Hybridoma, vol. 28, pp. 1-6 (2009) PubMed

* O.S. Sarac, O. Gursoy-Yuzugullu, R. Cetin-Atalay, V. Atalay, “Subsequence based feature map for protein function classification,” Computational Biology and Chemistry, vol. 32, pp. 122-130 (2008) PubMed

* N. Ozturk, E. Erdal, M. Mumcuoglu, K.C. Akcali, O. Yalcin, S. Senturk, A. Arslan-Ergul, B. Gur, I. Yulug, R. Cetin-Atalay, C. Yakicier, T. Yagci, M. Tez, M. Ozturk, Proceedings of National Academy of Sciences USA, vol. 103, pp. 2178-2183 (2006) PubMed

* B.D. Aguda, G. Cracium, R. Cetin-Atalay, “Data sources and computational approaches for Generating Models of Gene Regulatory Networks,” Reviews in Computational Chemistry, vol. 21, pp. 381-411 (2005) PubMed

* V. Atalay, R.C. Atalay, “Implicit motif distribution based hybrid computational kernel for sequence classification,” Bioinformatics, vol. 21, pp. 1429-1436 (2005) PubMed

* E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, R. Cetin-Atalay, “An Ontology for Collaborative Construction and Analysis of Cellular Pathways,” Bioinformatics, vol. 20, pp. 349-356 (2004) PubMed

* P. Dincer, B. Balci, Y.Yuva, B. Talim, M. Brockington, D. Dincel, S. Torelli, B.B. Sue, G. Kale, G. Haliloglu, F.O. Gerceker, R.C. Atalay, C. Yakicier, C. Longman, F. Muntoni, H. Topaloglu, “A novel form of recessive limb girdle muscular dystrophy with mental retardation and abnormal expression of alpha-dystroglycan,” Neuromuscular Disorders, vol. 13, pp. 771-778 (2003) PubMed

* M.B. Irmak, G. Ince, M. Ozturk, R. Cetin-Atalay, “Acquired tolerance of hepatocellular carcinoma cells to selenium deficiency: a selective survival mechanism?,” Cancer Research, vol. 63, pp. 6707-6715 (2003) PubMed

* A. Kocatas, A. Gursoy, R. Cetin-Atalay, “Application of Data Mining Techniques to Protein-Protein Interaction Prediction,” Lecture Notes in Computer Science, vol. 2869, pp. 316-323 (2003) PubMed

* M. Ozarar, V. Atalay, R. Cetin-Atalay, “Prediction of Protein Subcellular Localization Based on Primary Sequence Data,” Lecture Notes in Computer Science, vol. 2869, pp. 611-618 (2003) PubMed

* A. Atalay, T. Crook, M. Ozturk, I. Yulug, “Identification of genes induced by BRCA1 in breast cancer cells,” Biochemical and Biophysical Research Communications, vol. 299, pp. 839-846 (2002) PubMed

* E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, M. Ozturk, “PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways,” Bioinformatics, vol. 18, pp. 996-1003 (2002) PubMed

* E. Yildiz, A. Oztan, F. Sar, E. Pinartbasi, R. Cetin-Atalay, M. Ozturk, “Molecular characterization of a full genome Turkish Hepatits C Virus 1b isolate (HCV-TR1): a predominant viral form in Turkey,” Virus Genes, vol. 25, pp. 169-177 (2002) PubMed

* E. Yolcu, B.S. Sayan, T. Yagci, R. Cetin-Atalay, T. Soussi, N. Yurdusev, M. Ozturk, “A monoclonal antibody against DNA binding helix of p53 protein,” Oncogene, vol. 20, pp. 1398-1401 (2001) PubMed

* R. CetinAtalay, M. Ozturk, “p53 mutations as fingerprints of environmental carcinogens,” Pure and Applied Chemistry, vol. 72, pp. 995-999 (2000) PubMed

* M.N. Gurcan, M. Koyuturk, H.S. Yildiz, R. Cetin-Atalay, A.E. Cetin, “Identification of relative protein bands in polyacrylamide gel electrophoresis (PAGE) using mult- iresolution snake algorithm,” Biotechniques, vol. 26, pp. 1162-1169 (1999) PubMed

* 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, PubMed

* 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 13, 5113-5120, 1994 PubMed

Chapters in Books

* Ozturk M and Cetin-Atalay R, Biology of Hepatocellular Carcinoma, Gastrointestinal Cancers, A Companion to Sleisenger & Fordtran’s GI and Liver Disease, edited by Anil K. Rustgi, James M. Crawford, Chapter 43, W.B. Saunders, Harcourt Philadelphia, January 2003 Ozturk M, Cetin-Atalay R,

* “Molecular Biology of Liver Cancer” in Encyclopedia of Molecular Cell Biology and Molecular Medicine, Volume 7, 2nd Edition, Edited by Robert A. Meyers, John Wiley & Sons, ISBN: 3-527-30549-1, March 2005 Ozturk M., Erdal E., Ozturk N., Cetin-Atalay R. and Irmak B.,

* “Liver cell biology: differentiation and malignant transformation” in State of the Art of Hepatology Edited by Blum, and Manns ISBN: 0792387953 Kluwer Academic Publishers 2004

Refreed Proceedings and Published Conference Abstracts

* Z. Isik, V. Atalay and R. Cetin-Atalay. “Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data”, Journal of Machine Learning Research (JMLR) Workshop and Conference Proceedings,  8:44-54, 2010

* Zerrin Isik, Volkan Atalay, Cevdet Aykanat, Rengul Cetin-Atalay, Lecture Notes in Electrical Engineering, Proceedings of the 25th International Symposium on Computer and Information Sciences Vol. 62, pp.91-94, September 2010.

* “HP2SLs: a database for subcellular localizations of human proteome” FEBS journal June 2006 – Vol. 273 p248, Bilen B., Atalay V., Ozturk M. and Cetin-Atalay R.

* “CAPRIS: a database for cancer gene promoter related motif search” FEBS journal June 2006 – Vol. 273 p248, Iskar M., Erdem A., Erdem E., Dickerman A., Ozturk M., Atalay V. and Cetin-Atalay R.

* “Autosomal recessive limb-girdle muscular dystrophy with severe mental retardation: a new phenotype with glycosylation defects of alpha-dystroglycan” Neuromuscular Disorders 12 (7-8): 721-721 OCT 2002, Dincer P, Balci B, Yuva Y, Talim B, Brockington M, Dincel D, Gerceker FO, Haliloglu G, Atalay RC, Yakicier C, Muntoni F, Topaloglu H

Non-refereed proceedings

* Aslıgul Kucukdumlu, Meral Tuncbilek, Ebru Bilget Guven, Rengul Cetin Atalay, Synthesis and Biological Activity of Some New Substituted Purine Derivatives in Human Cancer Cells, International Symposium on Advances in Synthetic and Medicinal Chemistry, St. Petersburg, Russia, August 21-25, 2011

* Zeynep Ates-Alagoz, Meral Tunçbilek, Rengül Atalay, Synthesis and Biological Activity of Some New Substituted Purine Derivatives in Human Cancer Cells, 239th ACS National Meeting, San Francisco, CA, United States, March 21-25, 2010.

* O S Sarac, R. Cetin-Atalay, and V. Atalay. “GOPred: Combining classifiers on the GO”, in the Proceedings of MLSB08, the Second International Workshop on Machine Learning in Systems Biology, Brussels on September 13-14 2008

* O.S. Sarac, Ö. Gürsoy-Yüzügüllü,, R. Cetin-Atalay and V. Atalay, “Protein Function Annotation by Subsequence based Feature Map”, Automated Function Prediction (AFP) and Biosapiens Special Interest Group (SIG) meeting at ISMB/ECCB 2007, Vienna, Austria, July 19-20, 2007.

* Z.Sokmen, M.Ozturk, V.Atalay, R.Cetin Atalay, “A Hybrid Method For The Identification of Expression Patterns From Microarray Data”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007.

* O.Sinan Sarac, O.Gursoy-Yuzugullu, R.Cetin-Atalay and V. Atalay, “Function Annotation via a Discriminative Classifier Database on GO hierarchy”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007.

* O.Sinan Sarac, P.Bezek, R.Cetin-Atalay, V.Atalay, “Spectral Clustering based Subsequence Feature Map for Protein Classification”, 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), Oakland, California, USA, April 21-25, 2007.

* O.S. Sarac, V. Atalay, R. Cetin-Atalay, “Subsequence Feature Map for Protein Classification and Remote Homology Detection” accepted to be presented at the 5th European Conference on Computational Biology (ECCB), Eliat, Israel, September 10-13, 2006.

* L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, “Expression Pattern Analysis of Housekeeping Genes Across Large Number of Microarray Experiments”, accepted to be presented at the 5th European Conference on Computational Biology (ECCB), Eliat, Israel, September 10-13, 2006.

* O.S. Sarac, V. Atalay, R. Cetin-Atalay, “HMM-based subsequence feature map for Protein Classification and Remote Homology Detection”, accepted to be presented at the 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Forteleza, Brazil, August 6-10, 2006.

* B. Bilen, V. Atalay, M. Ozturk, R. Çetin-Atalay, “hP2SLs: A database for Subcellular Localizations of Human Proteome based on P2SL”, International Symposium on Health Informatics and Bioinformatics, Turkey ‘05, Antalya, Turkey, 10-12 November, 2005.

* Ö.S. Saraç, A. Tekeoglu, V. Atalay, R. Çetin-Atalay, “Implicit Motif-Based Sequence Classification for Genome and Proteome Annotation” International Symposium on Health Informatics and Bioinformatics, Turkey ‘05, Antalya, Turkey, 10-12 November, 2005.

* M. Iskar, M.E. Erdem, I.A. Erdem, S. Akman, A. Dickerman, V. Atalay, R. Çetin-Atalay, “CAPRIS: A Database for Cancer Gene Promoter Related Motif Search”, International Symposium on Health Informatics and Bioinformatics, Turkey ‘05 Antalya, Turkey, 10-12 November, 2005.

* 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”, Nov 22-24 2002, HUPO First World Congress, Human Proteome Organisation, Versailles, France Emre NCT., Gokay KE, Ozturk M. and Cetin-Atalay R.,

* “p33 ING1 protein interacts in vitro with C-terminal domain of p53 tumor suppressor protein” in the Proceedings of the EACR XVI-2000, Thessaloniki, Greece, 2000. Gurcan N., Yildiz S., Cetin R., Cetin E.A.,

* “Identification of relative protein bands in PAGE using multiresolution snake algorithm”, IEEE International Symposium on Time-Frequency and Time-Scale Analysis, Oct. 6-9, 1998 in Pittsburgh, Pennsylvania, USA.

* İrem Durmaz Ph.D. “Identification of novel kinase inhibitors”  2011-

* Deniz Cansen Yıldırım Ph.D. “analysis of kınase inhibitors in HCC”  2011-

* Ebru Bilget Guven Ph.D. “molecular identification novel cytotoxic kinase inhibitors in liver cancer” 1/2006-

* Tulin Ersahin Ph.D. “Identification of novel diagnostic and therapeutic targets involved in the PI3K/Akt signaling in hepatocellular carcinoma” 1/2008-

* Irem Durmaz M. Sc. “FGFR2 as a therapeutic candidate in liver cancer” 9/2009-present

* Pelin Gunay, MSc, Molecular analysis of  senescence associated protein phosphatases DUSP10 and MTMR11 protein, Graduated  July 27, 2009

* Guvanch Ovezmuradov M.Sc., Identifications of novel targets of p53 tumor suppressor protein in HCC, 9/2005- 9/2007

* Biter Bilen, M.Sc., Construction of model organisms proteome subcellular localization database, 9/2004-6/2007

* Omer Sinan Sarac, Ph.D. Implicit motif-based sequence classification for genome and proteome annotation (co supervisor with Volkan Atalay, Department of ComputerEngineering, Middle East Technical University) 9/2004-present

* Levent Carkacioglu, Ph.D. Large scale microarray data analysis (co supervisor with Volkan Atalay, Department of Computer Engineering, Middle East Technical University) 9/2003-present

* Burcu Irmak, Ph.D. “Identification of the mechanism that contributes to differential apoptotic response of HCC cells under selenium deficiency”, 9/1999-8/2003

* Deniz Dincel, M.Sc., “In vitro and in vivo analysis of p33 and p53 protein interactions”, 6/2000-1/2002

* Hayreddin Bahsi, M.Sc., “Inferring phylogenetic tree by hierarchical SOM”, (co supervisor with Atilla Gursoy of Computer Engineering Department, Bilkent University), 1/2000-1/2002

* Emek Demir, M.Sc., PATIKA: a tool for modeling analyzing and querying cellular pathways, 9/1999-8/2001

* N. C.Tolga Emre, M.Sc., Identification of the role of p33ING1 Protein in the cellular activities of p53 Tumor supressor protein, 9/1997-8/1999

KANILTEK – Cancer Drug Technologies, Investigator, Turkish Governmental Planning Organization, 2006-2009 Genome annotation based on subsequence analysis, Co-principal investigator, Scientific and Technical Research Council of Turkey, 2005-2007

Molecular analysis of Selenium deficiency induced oxidative stress tolerance in cancer cells, Principalinvestigator, Scientific and Technical Research Council of Turkey, 2005-2008,

Cancer gene promoter related motif search (CAPRIS) database, Principal investigator, JHU-VBI Collaboration grant, Virginia Bioinformatics Institute 2004-2005,

PATIKA, cell signaling pathway database, Principal investigator, Scientific and Technical Research Council of Turkey, 2003-2004,

PATIKA, a tool for modeling analyzing and querying cellular pathways, Principal investigator, Bilkent University Research Found, 2001-2002,

Effect of selenium deficiency dependent oxidative stress on HCC, Principal investigator, Turkish Academy of Sciences, 2002-2005,

Identification of the interacting site of p33 protein on p53 tumor suppressor, Principal investigator, Scientific and Technical Research Council of Turkey, 2000-2001

UICC international cancer technology transfer fellowship (ICRETT), 2007
Turkish Academy of Sciences Young Investigator Award, 2002
French Government Ph.D. Scholarship, 1992-1997
PhD thesis, “Mention Très Honorable avec félicitations de jury”, 1997

Invited Lectures and Invited Talks

“Data sources and computational approaches for cell signaling pathway modeling”  at the 25th International Symposium on Computer and Information Sciences Sept 22-24, 2010,  Royal Society in London,

“Data- and model-driven hybrid approach to evaluate quantitatively biological activity of a specific cellular process” at the Design and Analysis of Single and Combinatorial Gene Perturbation Screens meeting, Sept 9 – 11, 2010, Lucy Cavendish College, Cambridge, UK

Biological sequence analysis using machine-learning techniques, 31st FEBS Congress Satellite Workshop, Istanbul, 2006

In slico representation of cancer cell signaling, Boston University, November 2004

P2SL: Protein subcellular localization tool, Virginia Bioinformatics Institute, February 2004.

Cancer Cell Signaling Database with PATIKA, Mathematical Bioscience Institute, Ohio Sate University, September 2003.

Proteomics, International Theoretical Course on Genetics and Molecular Biology of Stress Tolerance in Plants, Gebze, 2001

Proteomics: Protein Identification and Characterization, XVI National Congress of Biochemistry, Izmir, 2000

Biological sequence analysis and Bioinformatics, TUBITAK DNA/Cell Bank workshop, Ankara, 2000

EF-Tu as a Target of Antibiotics, Hacettepe University, Ankara, 1999

Functional Role of Noncatalytic Domains of EF-Tu, Bogazici University, Istanbul, 1999

Graduate Courses

MBG 513 Bioinformatics
MBG 512 Advanced Cellular Biology
MBG 515 Principles of Protein Structure
MBG 524 Seminars in Molecular Biology
MBG 623 Seminars in Molecular Genetics I
MBG 624 Seminars in molecular Genetics II
MBG 612 Special Topics in Molecular Biology I
MBG 613 Special Topics in Molecular Biology II

Undergraduate Courses

MBG 104 Introduction to Modern Biology
MBG 311 Biochemistry I
MBG 312 Biochemistry II
MBG 309 Introduction to Biochemistry
MBG 411 Molecular Biology of the Cell I
MBG 413 Biotechnology
MBG 326 Introduction to Bioinformatics
MBG 481 Protein Chemistry
MBG 430 Computer Applications in Molecular Biology

Volkan (Professor, METU – Dept. of Computer Eng.)
Mufitcan (11, BUPS grade5)
Sinem Naz (6,BUPS grade1 )