• Education
• Experience
• Publication
• Research
• Courses
• Professional
• Misc

Education

• PhD (January 2005): Department of Computer Engineering, Middle East Technical University, Ankara, Turkey.

• MSc (August 1999): Department of Computer Engineering, Middle East Technical University, Ankara, Turkey.

• BSc (June 1996): Department of Computer Science&Engineering, Hacettepe University, Ankara, Turkey.

Experience

• March 2007 - ... : Assistant Professor, TOBB University of Economics and Technology, Ankara, Turkey.
• June 2006 - March 2007: Postdoctoral fellow, Institute of Information Science and Technology (ISTI-CNR), Pisa, Italy.
• September 2005 - June 2006: Postdoctoral fellow, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.
• January 2004 - September 2005: Senior software engineer, Aselsan Inc. Ankara, Turkey.
• December 2002 - December 2003: Research & Teaching assistant, University of Calgary, Calgary, AB, Canada.
• August 2001-November 2002: Military service, Turkish Land Forces Hq. Ankara, Turkey.
• August 1997-July 2001: (Senior) software engineer, Aselsan Inc. Ankara, Turkey.
• August 1996 - August 1997: Research&Teaching assistant, Hacettepe University, Ankara, Turkey.
  

Publication

• O. Abul. "Controlling Discrete Genetic Regulatory Networks", PhD thesis, Dept. of Computer Engineering, Middle East Technical University, Ankara, 2005. Advisors: Professors Faruk Polat and Reda Alhajj.
• O. Abul. "Multi-agent Reinforcement Learning using Function Approximation", Masters thesis, Dept. of Computer Engineering, Middle East Technical University, Ankara, 1999. Advisor: Prof. Faruk Polat.

• K. Klepper, G.K. Sandve, O. Abul, J. Johansen, V. Walseng and F. Drablos, "Assessment of composite motif discovery methods",  BMC Bioinformatics, Vol.9, No.123, 2008.
• G.K. Sandve, O. Abul, V. Walseng and F. Drablos, "Improved Benchmarks for Computational Motif Discovery",  BMC Bioinformatics, Vol.8, No.163, 2007.
• O. Abul, R. Alhajj and F. Polat. "A Powerful Approach for Effective Finding of Significantly Differentially Expressed Genes", IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol.3, No.3, pp. 220-231, 2006.
• O. Abul, R. Alhajj, F. Polat and K. Barker. "Finding differentially expressed genes
  for pattern generation", Bioinformatics, Vol.21, No.4, pp. 445-450, 2005.
• F. Polat and O. Abul. "Learning Sequences of Compatible Actions Among Agents",
  Artificial Intelligence Review, Kluwer, Vol.17:1, pp. 21-37, March 2002.
• O. Abul, F. Polat and R. Alhajj. "Multi-Agent Reinforcement Learning Using Func-
  tion Approximation", IEEE Transactions on Systems, Man and Cybernetics-C, Vol.30,
  No. 4, pp. 485-497, Nov. 2000.

• O. Abul, F. Bonchi and M. Nanni. "Never Walk Alone: Uncertainty for Anonymity in Moving Objects Databases", IEEE 24th International Conference on Data Engineering (ICDE 2008), Cancun, Mexico, April 2008.
• O. Abul, G.K. Sandve and F. Drablos. "False Discovery Rates in Identifying Functional DNA Motifs", Proceedings of IEEE Symposium on Bioinformatics and Bioengineering (BIBE'07), Cambridge MA, Oct. 2007.
• O. Abul, M. Atzori, F. Bonchi and F. Giannotti. "Hiding Sensitive Trajectory Patterns", 6th International Workshop on Privacy Aspects of Data Mining, ICDM'07 Workshops, October 2007, Omaha, Nebreska.
• M. Atzori, F. Bonchi, F. Giannotti, D. Pedreschi and O. Abul. "Privacy-Aware Knowledge Discovery from Location Data",The International Workshop on Privacy-Aware Location-based Mobile Services (PALMS'07),Mannheim, Germany, May 2007.   
• O. Abul, M. Atzori, F. Bonchi and F. Giannotti. "Hiding Sequences", The 3rd International Workshop on Privacy Data Management, IEEE 23rd International Conference on Data Engineering (ICDE 2007), Istanbul, Turkey, April 2007. Also appears as a technical report of ISTI (acc. number 2006-TR-40). An extended abstract appears in Proceedings of Italian Symposium on Advanced Database Systems, SEBD'07.
• O. Abul, F. Polat and R. Alhajj. "Asymptotical Lower Limits on the Required Num-
  ber of Examples for Learning Boolean Networks", The 21st International Symposium
  on Computer and Information Sciences (ISCIS), Istanbul, Turkey, Nov. 2006 (LNCS,
  Vol 4263 pp. 154-164, Springer-Verlag).
• O. Abul, F. Polat and R. Alhajj. "Optimal Multi-Objective Control Method for
  Discrete Genetic Regulatory Networks", Proceedings of IEEE Symposium on Bioinfor-
  matics and Bioengineering (BIBE), Washington DC, Oct. 2006.
• G.K. Sandve, M. Nedland, O.B. Syrstad, L.A. Eidsheim, O. Abul and F. Drablos.
  "Accelerating Motif Discovery: Motif Matching on Parallel Hardware", 6th Workshop
  on Algorithms in Bioinformatics (WABI), Zurich-Switzerland, Sep. 2006 (LNCS, Vol
  4175 pp. 197-206 Springer-Verlag).
• O. Abul, G.K. Sandve and F. Drablos. "A Methodology for Motif Discovery Employ-
  ing Iterated Cluster Re-assignment", Computational Systems Bioinformatics Confer-
  ence (CSB), Stanford University CA, Aug. 2006 (Series on Advances in Bioinformatics
  and Computational Biology - Volume 4, 2006, Imperial College Press).
• O. Abul, G.K. Sandve and F. Drablos. "TSCAN: A two-step de novo Motif Discov-
  ery Method", The 3rd annual RECOMB Satellite Workshop on Regulatory Genomics
  (RECOMB-RG), Singapore, July. 2006.
• O. Abul, R. Alhajj and F. Polat. "Importance of Monitoring in Developing Optimal
  Control Policies for Probabilistic Boolean Genetic Networks", Proceedings of the In-
  ternational Conference on Information Processing and Management of Uncertainty in
  Knowledge-Based Systems (IPMU), Italy, July 2004.
• O. Abul, R. Alhajj and F. Polat. "Markov Decision Processes Based Optimal Con-
  trol Policies for Probabilistic Boolean Networks", Proceedings of IEEE Symposium on
  Bioinformatics and Bioengineering (BIBE), Taiwan, pp.337-344, May 2004.
• O. Abul, R. Alhajj, F. Polat and K. Barker. "Finding Differentially Expressed Genes:
  Pattern Generation using q-values", Proceedings of the ACM Annual Symposium on
  Applied Computing, Cyprus, Mar. 2004.
• O. Abul, A. Lo, R. Alhajj, F. Polat and K. Barker. "Cluster Validity Analysis Using
  Subsampling", Proceedings of IEEE International Conference on Systems, Man and
  Cybernetics, Washington DC, Oct. 2003.
• O. Abul, F. Polat and R. Alhajj. "Function Approximation Based Multi-Agent Re-
  inforcement Learning", Proceedings of IEEE International Conference on Tools with
  Artificial Intelligence (ICTAI-2000), IEEE Press, Nov 13, 2000, Vancouver, British
  Columbia, Canada, pp.36-39.

• O. Abul. "E-Saglik ve Mahremiyete Veri Madenciligi Kaynakli Tehdit", 2nd National E-Health congress-technical program, October 2007, Antalya, Turkey. (In Turkish).
• O. Abul, F. Bonchi, and M. Nanni. "Never Walk Alone: Trajectory anonymity via clustering", Technical Report ISTI-007/2007, ISTI-C.N.R., 2007. 
• M. Ege, O. Abul and O. Aslanturk. "Algoritmaları niçin analiz etmeliyiz?", Bilisim-2000 Conference, Istanbul, Turkey, 2000. (In Turkish).

Research

• Data Mining
• Bioinformatics
• Machine Learning

• Bioinformatics Group at NTNU led by Prof. Finn Drablos. link
• Pisa KDD laboratory at ISTI-CNR led by Prof.ssa Fosca Giannotti. link

Courses

• BIL212 -Data Structures (Spring 2007-2008)
• BIL013 -Data Structures and Data Management (Spring 2007-2008)
• BIL514 -Theory of Computation (Spring 2007-2008)

• BIL212 -Data Structures (Summer 2006-2007)
• BIL372 -Database Systems (Summer 2006-2007)
• BIL395 (BIL512) -Programming Languages (Fall 2007-2008)

Professional

• PC member: International Multi-Topic Conference (IMTIC'08)
• PC member: Int. Work. on Practical Privacy-Preserving Data Mining (P3DM '08), (in conjunction with SDM '08)
• PC member: IEEE Int. Conf. on Bioinformatics and Bioengineering (BIBE '07)  
• PC member: Int. Conf. on Health Informatics (HealthInf '07)
• Fellow member: Int. Society of Intelligent Biological Medicine (ISIMB)
• Editorial Board Member: International Journal of Computer Science and Software Technology (IJCSST)
• Editorial Board Member: Open Software Engineering Journal, Bentham.
• Reviewer: Knowledge and Information Systems Journal (KAIS), Springer.
• Reviewer: Data and Knowledge Engineering Journal (DKE), Elsevier.
• Reviewer: SIAM Conference on Data Mining (SDM 2008), Atlanta, Georgia.
• Reviewer: The 11th Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD 2007), China.
• Reviewer: International Conference on Data Mining (ICDM 2006), Hong Kong.
• Reviewer: International Symposium on Computer and Information Sciences (ISCIS 2005), Istan-
  bul, Turkey. 

Misc

• Turkish (native), English (fluent), Italian (intermediate), Norwegian (beginner).

• 18-month postdoctoral fellowship award by ERCIM.
• 1-year research associate grant by ADSA lab of University of Calgary.
• Several travel awards for conference attendances by ERCIM, NTNU, Aselsan, Univ. of Calgary, TOBB University.