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Rengul Cetin-Atalay, MD PhD Associate Professor Department of Molecular Biology and Genetics, Faculty of Science, Bilkent University Born: Ankara, 1968 Address: Bilkent Main Campus |
Research Interests
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 HCCGenome annotation through machine learning techniques
Protein and DNA motif data analysis
Microarray data analysis
Molecular Cellular Biology
Employment History
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
Scholarly Publications
Articles in Refereed Journals
- “Subsequence based feature map for protein function classification” , Journal of Computational Biology and Chemistry, O.S. Sarac, Ö. Gürsoy-Yüzügüllü, R. Cetin-Atalay, V. Atalay, In press
- “Reprogramming of replicative senescence in hepatocellular carcinoma-derived cells.” Proc Natl Acad Sci U S A. Feb 14;103(7):2178-83 2006, Ozturk N, Erdal E, Mumcuoglu M, Akcali KC, Yalcin O, Senturk S, Arslan-Ergul, A, Gur B, Yulug I, Cetin-Atalay R., Yakicier C, Yagci T, Tez M, Ozturk M.,
- “Implicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification.” Bioinformatics, 21(8): 1429-1436, 2005, Atalay V. and Cetin-Atalay R.,
- “An Ontology for Collaborative Construction and Analysis of Cellular Pathways.” Bioinformatics, Vol. 20 no. 3 349356, 2004, Demir E., Babur O., Dogrusoz U., Gursoy A., Ayaz A., Gulesir G., Nisanci G. and Cetin-Atalay R.,
- “Acquired tolerance of hepatocellular carcinoma cells to selenium deficiency: a selective survival mechanism?” Cancer Res., Oct 15; 63, 6707-15 2003, Irmak MB, Ince G, Ozturk M, Cetin-Atalay R.,
- “A novel form of limb-girdle muscular dystrophy and mental retardation with reduced a-dystroglycan.”, Neuromuscular Disorders, 13, 771778, 2003, Dinçer P., Balc¦ B., Talim B., Brockington M., Yuva Y., Dinçel D.,Torelli S., Brown S., Halilogšlu G., Özbas¸ Gerçeker F., Cetin Atalay R., Yak¦c¦er C., Muntoni F., Topalogšlu H.,
- “Prediction of Protein Subcellular Localization Based on Primary Sequence Data.” Lecture Notes in Computer Science, Vol. 2869, 611 618, 2003, Özarar M., Atalay V. and Cetin Atalay R.,
- “Application of Data Mining Techniques to Protein-Protein Interaction Prediction.”, Lecture Notes in Computer Science, Vol. 2869, 316 323, 2003, Kocatas A., Gursoy A. and Atalay R.,
- “Molecular characterization of a full genome Turkish hepatitis C virus 1b isolate (HCV-TR1): a predominant viral form in Turkey”, Virus Genes 25:2, 169-177, 2002, Yildiz E., Oztan A., Sar F., Pinarbasi E., Cetin-Atalay R., Akkiz H., and Ozturk M.,
- “PATIKA: An integrated visual environment for collaborative construction and analysis of cellular pathways”, Bioinformatics 18:7, 996-1003, 2002, Demir E., Babur O., Dogrusoz U., Gursoy A., Nisanci G., Cetin-Atalay R. and Ozturk M.,
- “A monoclonal antibody against DNA binding helix of p53 protein”, Oncogene, 20, 1398-401, 2001, Yolcu E., Sayan B. S., Yagci T., Cetin-Atalay R., Soussi T., Yurdusev N. and Ozturk M.,
- “p53 mutations as fingerprints of environmental carcinogenesis”, Pure Appl. Chem. 72:6, 995-999, 2000, Cetin-Atalay R. and Ozturk M.,
- “Identification of relative protein bands in PAGE using multiresolution snake algorithm”, Biotechniques, 26, 1162-1169, 1999, Gurcan N., Yildiz S., Cetin-Atalay R., Cetin E.A,
- “Functional role of the non catalytic domains of elongation factor Tu in the interactions with ligands”, Biochemistry, 37, 486-495, 1998, Cetin R., Anborgh P.H., Cool R.H. 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, Cetin R., Krab I.M., Anborgh P.H., Cool R.H., Watanabe T., Sugiyama T., Izaki K. and Parmeggiani A.,
- "Pulvomycin resistant mutants of E. coli elongation factor Tu", EMBO Journal 13, 5113-5120, 1994, Zeef L.A.H., Bosch L., Anborgh P.H., Cetin R., Parmeggiani A. and Hilgenfeld R.,
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
Rewievs
- Aguda B.D., Craciun G., Cetin-Atalay R., Data Sources and Computational Approaches for Generating Models of Gene Networks, Reviews in Computational Chemistry, Volume 21 April 2005 Kenny B. Lipkowitz (Editor), Donald B. Boyd (Editor), John Wiley & Sons, Inc.
Published conference Abstracts
- “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
- 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.
Graduate Student Supervision
Sponsored Research
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, Principal investigator, 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
Professional Awards and Honors
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
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
Teaching
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
Family
Volkan (Professor, METU - Dept. of Computer Eng.)
Mufitcan (11, BUPS grade5)
Sinem Naz (6,BUPS grade1 )
