Hakan Ferhatosmanoglu

 

            Associate Professor                                                     Department of Computer Science and Engineering

            The Ohio State University                                          Phone:  (614) 292-6377         

            2015 Neil Ave. Room 689                                          Email: hakan@cse.ohio-state.edu

            Columbus, Ohio 43210-1277                                      http://www.cse.ohio-state.edu/~hakan

 

http://www.cse.ohio-state.edu/../Owner/Desktop/cv-bio/

RESEARCH INTERESTS:

            Database Systems and Applications

Scientific, multimedia, and high dimensional data management

Bioinformatics

 

WORK EXPERIENCE:

            Associate Professor, Computer Science and Engineering, Ohio State University (OSU), 2007- present

            Courtesy/Participating Faculty, Biomedical Informatics, Biophysics, and Mathematical Biosciences Institute, OSU.          

Visiting Associate Professor, Computer Engineering, Bilkent University, 2009.

Assistant Professor, Computer Science and Engineering, OSU, 2001-2007.

Research Intern at AT&T Labs- Research, Florham Park, New Jersey, Summer 1999.

Graduate Research Associate, Computer Science, University of California, Santa Barbara, 1997-2001.

Graduate Teaching Associate of Operating Systems, Database Management Systems, Foundations of Computer Science, Discrete Mathematics, Automata Theory and Formal Languages courses. 1997-1999.

Software Consultant at Bilkent University Computer Center, Ankara, Turkey. 1997.


EDUCATION:

Ph.D. Computer Science, University of California, Santa Barbara. 2001.

Dissertation: Efficient Retrieval and Scalable Storage of Multi-dimensional Data.

Co-advisors: Divyakant Agrawal and Amr El Abbadi.

B.S. Computer Science, Bilkent University, Ankara, Turkey. 1997.

Full scholarship awarded for undergraduate education.

 

HONORS AND AWARDS:

·         Early Career Principal Investigator Award, US Department of Energy, 2003.

·         Large Interdisciplinary Grant Award, Office of Research, OSU, 2004.

·         NSF CAREER Award, 2006.

·         Lumley Research Accomplishment Award, OSU College of Engineering, 2007.

·         IBM Faculty Award, 2010.

 

 

RESEARCH FUNDING:

 

·         NSF Collaborative Systems, NSF Advances in Biological Informatics, NSF Cyber-infrastructure, US Department of Energy, Ohio Aerospace Institute, NSF Research Infrastructure, Ohio Board of Regents, IBM, Pfizer, Inc.

 

PUBLICATIONS:

1.      Smolign: A Spatial Motifs Based Protein Multiple Structural Alignment Method, H. Sun, A. Sacan, H. Ferhatosmanoglu, Y. Wang, IEEE/ACM Transactions on Computational Biology and Bioinformatics, to appear.

2.      Crowd-sourced Sensing and Collaboration Using Twitter. M. Demirbas, C. Akcora, M. Bayir, Y. Yilmaz, H. Ferhatosmanoglu. Proceedings of IEEE WoWMoM, 2010, Montreal, Canada.

3.      Identifying Breakpoints in Public Opinion. C. Akcora, M. Bayir, M. Demirbas, H. Ferhaosmanoglu. Social Media Analytics, KDD Workshop Proceedings, June 2010 (20.7%)

4.      Short Text Classification in Twitter to Improve Information Filtering. E. Demir, D. Fuhry, B. Sriram, H. Ferhatosmanoglu, M. Demirbas. Proceedings of the ACM SIGIR 2010, Geneva, Switzerland, July 2010, 841-842.

5.      Relationship Preserving Feature Selection for Unlabelled Clinical Trials Time-Series, F. Altiparmak, M. Gibas, H. Ferhatosmanoglu. Proceedings of 1st ACM International Conference on Bioinformatics and Computational Biology, August 2010, New York.

6.      MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs. A. Sacan, N. Ferhatosmanoglu, H. Ferhatosmanoglu. BMC Bioinformatics 10:304, September 2009.

7.      Secondary Bitmap Indexes with Vertical and Horizontal Partitioning . G. Canahuate, T. Apaydin, A. Sacan, H. Ferhatosmanoglu. EDBT, March 2009, pp 600-611.

9.      Integrated Search and Alignment of Protein Structures. A. Sacan, I. Toroslu, H. Ferhatosmanoglu. Bioinformatics, vol. 24, no. 14, December 2008, pp. 2872-9.

10.  CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis. A. Sacan, H. Ferhatosmanoglu, H. Coskun, Bioinformatics, vol. 24, no. 14, July 2008, pp. 1647-1649.

11.  An Enhanced Partial Order Curve Comparison Algorithm and its Application to Analyzing Protein Folding Trajectories. H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang. BMC BioInformatics 2008, Vol. 9 : 344, August 2008. (Impact factor: 3.78) doi:10.1186/1471-2105-9-344.

12.  Incremental Maintenance of Online Summaries Over Multiple Streams. F. Altiparmak, E. Tuncel, H. Ferhatosmanoglu. IEEE Transactions on Knowledge and Data Engineering (TKDE), Volume 20, Issue 2, Feb. 2008, pp. 216-229.

13.  Online Index Recommendations for High-Dimensional Databases using Query Workloads. M. Gibas, G. Canahuate, H. Ferhatosmanoglu. IEEE Transactions on Knowledge and Data Engineering (TKDE), Volume 20, Issue 2, Feb. 2008, pp. 246-260.

14.  Distance-based indexing of residue contacts for protein structure retrieval and alignment. Sacan, A.; Toroslu, I.H.; Ferhatosmanoglu, H.; BioInformatics and BioEngineering, BIBE, 8th IEEE International Conference, Oct. 2008, pp. 1 – 7.

15.  Dynamic Data Organization for Bitmap Indices. T. Apaydin, G. Canahuate, H. Ferhatosmanoglu, A. Tosun, 3rd International ICST Conference on Scalable Information Systems, InfoScale, June 2008.

16.  Analysis of Basic Data Reordering Techniques. T. Apaydin, A. Tosun, H. Ferhatosmanoglu, 20th Conference on Scientific and Statistical Data Management, SSDBM, July 2008, pp. 517-524.

17.  Automated Data Discovery in Similarity Score Queries. Altiparmak F., Tosun A. S., Ferhatosmanoglu H., Sacan A., 13th International Conference on Database Systems for Advance Applications (DASFAA), New Delhi, India, March 2008, pp. 440-451.

18.  A General Framework for Modeling and Processing Optimization Queries. M. Gibas, N. Zheng, H. Ferhatosmanoglu, VLDB ’07, Vienna, Austria, September, 2007, pp. 1069-1080.

19.  LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins. A. Sacan, O. Ozturk, H. Ferhatosmanoglu, Y. Wang. Bioinformatics, Volume 23, Number 6, pp. 709-716, March 2007.

20.  Enhanced Partial Order Curve Comparison over Multiple Protein Folding Trajectories. H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang, Life Sciences Society Computational Systems Biology (CSB ’07), San Diego, CA, August 2007,  pp. 299-310.

23.  Data Space Mapping for Efficient I/O in Large Multi-dimensional Databases. H. Ferhatosmanoglu, A. Ramachandran, D. Agrawal, A. El Abbadi. Information Systems Journal, vol. 32, no. 1, pp. 83-103, March 2007.

24.  Access Structures for Angular Similarity Queries. T. Apaydin and H. Ferhatosmanoglu. IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 16, no. 6, pp. 1512-1525, November 2006.

25.  Approximate Encoding for Direct Access and Query Processing over Compressed Bitmaps. T. Apaydin, G. Canahuate, H. Ferhatosmanoglu, A. Tosun. 32nd International Conference on Very Large Data Bases (VLDB ’06), Seoul, Korea, September 2006, pp. 846-857. (Accept-rate: 13.2%)

26.  High Dimensional Nearest Neighbor Searching. H. Ferhatosmanoglu, E. Tuncel, D. Agrawal, A. El Abbadi. Information Systems Journal, vol. 31, no. 6, pp. 512-540, September 2006.

27.  Information Mining over Heterogeneous and High Dimensional Time Series Data in Clinical Trials Databases. F. Altiparmak, H. Ferhatosmanoglu, S. Erdal, C. Trost. IEEE Transactions on Information Technology in Biomedicine, 10(2): 254- 263 (April 2006). 

29.  Indexing Incomplete Databases. G. Canahuate, M. Gibas, H. Ferhatosmanoglu. 10th International Conference on Extending Database Technology (EDBT ’06). Munich, Germany, March 2006, pp. 884-901.

30.  Online Summarization of Dynamic Time Series Data. U. Ogras and H. Ferhatosmanoglu. VLDB Journal, 15(1): 84-98, January 2006.

31.  Compressing Bitmap Indices by Data Reorganization. A. Pinar, T. Tao, H. Ferhatosmanoglu. 21st IEEE International Conference on Data Engineering (ICDE ’05). Tokyo, Japan, April 2005, pp. 310-321.

32.  Vector Space Indexing for Biosequence Similarity Searches. O. Ozturk and H. Ferhatosmanoglu. International Journal on Artificial Intelligence Tools, 14(5):  811-826 (2005).

33.  Optimal Data-Space Partitioning of Spatial Data for Parallel I/O. H. Ferhatosmanoglu, D. Agrawal, O. Egecioglu, and A. El Abbadi. Distributed and Parallel Databases (DAPD), 17(1): 75-101 (2005).

34.  Replicated Declustering of Spatial Data. H. Ferhatosmanoglu, A. Tosun, A. Ramachandran. 23rd ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems (PODS ‘04), June 2004, Paris, France, pp. 125-135.

35.  Dimensionality Reduction and Similarity Computation using Inner Product Approximations. O. Egecioglu, H. Ferhatosmanoglu, U. Ogras. IEEE Transactions on Knowledge and Data Engineering (TKDE). June 2004 (vol. 16, no.6), pp. 714-726.

36.  A Time-Series Analysis of Gene Expression Data. S. Erdal, O. Ozturk, D. Armbruster, H. Ferhatosmanoglu, W. Ray. IEEE International Symp. On Bioinformatics and Bioengineering (BIBE ’04), Taiwan, March 2004, pp. 366-378.

37.  High Dimensional Reverse Nearest Neighbor Queries. A. Singh, H. Ferhatosmanoglu, A. Tosun. 12th ACM International Conference on Information and Knowledge Management (CIKM'03), pp. 91-98. New Orleans, LA, November 2003.

38.  Dimensionality Reduction using Magnitude and Shape Approximations. Umit Ogras, Hakan Ferhatosmanoglu. 12th ACM International Conference on Information and Knowledge Management (CIKM'03), pp. 99-107. New Orleans, LA, November 2003.

39.  Peer-to-Peer Spatial Queries in Sensor Networks. M. Demirbas and H. Ferhatosmanoglu. 3rd IEEE International Conference on Peer-to-Peer Computing (P2P '03), Linkφping, Sweden. September 2003, pp. 32-39.

40.  Efficient k-NN Search on Streaming Data Series. X. Liu and H. Ferhatosmanoglu. 8th International Symposium on Spatial and Temporal Databases (SSTD '03), Santorini, Greece. July 2003, pp. 83-101.

41.  CoMRI: A Compressed Multi-Resolution Index Structure for Sequence Similarity Queries. H. Sun, O. Ozturk and H. Ferhatosmanoglu. IEEE Computer Society Bioinformatics Conference (CSB '03). Stanford, CA. August 2003, pp. 553-558.

43.  VQ-Index: An Index Structure for Similarity Searching in Multimedia Databases. E. Tuncel, H. Ferhatosmanoglu, K. Rose. ACM Multimedia, Juan Les Pins, France, pp. 543-552. December 2002.

44.  Vulnerabilities in Similarity Search based Systems. A. Tosun and H. Ferhatosmanoglu. ACM International Conference on Information and Knowledge Management (CIKM ‘02), Mc Lean, VA, pp. 110-117. November 2002.

45.  Optimal Parallel I/O Using Replication. A. Tosun, H. Ferhatosmanoglu. In proceedings of International Workshops on Parallel Processing (ICPPW ‘02), Vancouver, Canada, pp. 506-513. August 2002.

46.  Approximate Nearest Neighbor Searching in Multimedia Databases. H. Ferhatosmanoglu, E. Tuncel, D. Agrawal, A. El Abbadi.  In proceedings of the 17th IEEE International Conference on Data Engineering (ICDE ‘01), Heidelberg, Germany. April 2001. (A.r.: 15%)

47.  Efficient Processing of Conical Queries. H. Ferhatosmanoglu, D. Agrawal and A. El Abbadi. In proceedings of the 10th ACM International Conference on Information and Knowledge Management (CIKM ‘01), Atlanta, pp. 1-8. November 2001.

49.  Constrained Nearest Neighbor Queries. H. Ferhatosmanoglu, I. Stanoi, D. Agrawal, A. El Abbadi. 7th International Symposium on Spatial and Temporal Database (SSTD ‘01), Los Angeles, CA, pp. 257-276. July 2001.

50.  Vector Approximation based Indexing for Non-uniform High Dimensional Data Sets. H. Ferhatosmanoglu, E. Tuncel, D. Agrawal, A. El Abbadi. In proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM ‘00), Washington, DC, pp. 202-209. November 2000.

51.  Dimensionality Reduction and Similarity Computation by Inner Product Approximations. O. Egecioglu and H. Ferhatosmanoglu.  In proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM ‘00), Washington, DC, pp. 219-226.  November 2000.

52.  Clustering Declustered Data for Efficient Retrieval. H. Ferhatosmanoglu, D. Agrawal, A. El Abbadi. In proceedings of the 8th ACM International Conference on Information and Knowledge Management (CIKM ‘99), Kansas City, Missouri, pp. 343-350. November 1999.

53.  Concentric Hyperspaces and Disk Allocation for Fast Parallel Range Searching. H. Ferhatosmanoglu, D. Agrawal, A. El Abbadi. In proceedings of the 15th IEEE International Conference on Data Engineering (ICDE ‘99), Sydney, Australia, pp. 608-615. March 1999.

Others

54.  Bitmap-based Index Structures. G. Canahuate, H. Ferhatosmanoglu. Encyclopedia of Database Systems 2009: 248-251.

55.  Michael Gibas, Hakan Ferhatosmanoglu: Indexing, High Dimensional. Encyclopedia of GIS, pp. 502-507, February 2008.

56.  Investigating the use of Extrinsic Similarity Measures for Microarray Analysis. D. Ucar, F. Altiparmak, H. Ferhatosmanoglu, S. Parthasarathy. Proceedings of the BIOKDD workshop at the ACM International Conference on Knowledge Discovery and Data Mining (SIGKDD), 2007.

 

 

PROFESSIONAL SERVICES:

 

Program Committee Member

  • VLDB 2012, 38th International Conference on Very Large Data Bases.
  • SIGMOD 2011 (Demonstration), 22nd ACM SIGMOD International Conference on Management of Data, June 2011.
  • ICDE 2011, 27th IEEE International Conference on Data Engineering, April 2011.
  • ICDM 2011, 10th IEEE International Conference on Data Mining, Vancouver, Canada, 2011.
  • SIGMOD 2010, 21st ACM SIGMOD International Conference on Management of Data, June 2010 (Also in organizing committee).
  • ICDM 2010, 10th IEEE International Conference on Data Mining, Sydney, Australia, 2010.
  • SIGSPATIAL 2010, 18th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems (ACM GIS), San Jose, CA, 2010.
  • SIGHINF 2010, 1st ACM International Health Informatics Symposium, Washington, DC, 2010.
  • ISCIS 2009, Track Program Chair, Bioinformatics and Bioengineering, 24th International Symp. On Computer and Information Sciences, 2009.
  • SSDBM 2009, 21st International Conference on Scientific and Statistical Database Management, June 2009.
  • ICDE 2009, 25th International Conference on Data Engineering, Shanghai, China, March 2009.
  • SSTD 2009, 21st International Symp. on Spatial and Temporal Databases, Aalborg, Denmark, July 2009.
  • ICDM 2008, IEEE International Conference on Data Mining, Pisa, Italy, December 2008.
  • SAC 2008, 23rd Annual ACM Symposium on Applied Computing, Mobile Computing and Applications, Brazil, March 2008.
  • IEEE CSE 2008, 9th IEEE International Conference on Computational Science and Engineering, Brazil, June 2008
  • DASFAA 2008. 13th International Conference on Database Systems for Advanced Applications, Delhi, India, March, 2008.
  • KDD 2007. 13th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, San Jose, August, 2007.
  • ICDE 2007. 23rd IEEE International Conference on Data Engineering, Istanbul, Turkey, April 2007.
  • DASFAA 2007. 12th International Conference on Database Systems for Advanced Applications, Bangkok , Thailand, April 2007.
  • KDD 2006. 12th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Philadelphia, August 2006.
  • IEEE WirelessCom 2006, Mobile Computing Symposium, Toronto, Canada, June 2006.
  • MDM 2006. Workshop on Mobile Location-Aware Sensor Networks, Nara, Japan, May 2006.
  • DASFAA 2006. 11th International Conference on Database Systems for Advanced Applications, Singapore, April 2006.
  • IEEE BIBE 2005. 5th IEEE Symposium on Bioinformatics and Bioengineering, Minneapolis, Minnesota, October 2005.
  • SAC 2006. 20th ACM Symposium on Applied Computing, Mobile Computing and Applications, Dijon, France, March 2006.
  • CISSE 2005. International Joint Conferences on Computer, Information, and Systems Sciences, and Engineering, December 2005.
  • IEEE BIBE 2005. 5th IEEE Symposium on Bioinformatics and Bioengineering, Minneapolis, Minnesota, October 2005.
  • BIOKDD 2005. 5th International Workshop on Data Mining in Bioinformatics (BIOKDD), Chicago, IL, August 2005.
  • SAC 2005. 20th ACM Symposium on Applied Computing, Mobile Computing and Applications, Santa Fe, New Mexico, March 2005.
  • IEEE WirelessCom 2005. Symposium on Mobile Computing. Maui, Hawaii, June 2005.
  • ICDE 2004. 20th IEEE International Conference on Data Engineering, Boston, Mass., USA, March 2004.
  • BIBE 2004. IEEE International Symposium on Bioinformatics and Bioengineering, Taiwan, Taichung, Taiwan, ROC, May 2004.
  • ACM SAC 2004. ACM Symposium on Applied Computing, special track on Mobile Computing and Applications (SAC-MCA), Nicosia, Cyprus, March 2004.
  • IEEE ICDE 2003. 19th IEEE International Conference on Data Engineering, Bangalore, India, March 2003.
  • ACM SAC 2003. ACM Symposium on Applied Computing, special track on Mobile Computing and Applications (SAC-MCA), Melbourne, Florida, March 2003.
  • IEEE BIBE 2003. IEEE International Symposium on Bioinformatics and Bioengineering, Washington, DC, March 2003.
  • ACM CIKM 2002. Conference on Information and Knowledge Management, McLean, VA, November 2002 (Also in organization committee).

Panelist and Reviewer for Proposals

NSF: Information & Intelligent Systems (IIS), Information Integration and Informatics, Division of Biological Infrastructure; Canada National Research Council; TUBITAK.

Editorial Board

·         Distributed and Parallel Databases Journal

·         International Journal of Data Engineering

·         The Turkish Journal of Electrical Engineering & Computer Sciences

Reviewer for Journals and Conferences

·         ACM Transactions on Database Systems (TODS)

·         IEEE Transactions on Knowledge and Data Engineering (TKDE)

·         Very Large Databases Journal (VLDB Journal)

·         Bioinformatics (Oxford)

·         IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

·         IEEE Transactions on Information Technology in Biomedicine

·         Parallel and Distributed System

·         International Journal on Information Processing Letters (IPL)

·         Information Sciences

·         Data and Knowledge Engineering

·         The Computer Journal

·         IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)

 

Reviewer for Books

 

·         Fundamentals of Database Systems, by Elmasri & Navathe, Addison Wesley.

·         An Information Systems Project Guide (working title), Prentice Hall.

 

      Departmental Service

·      Recruitment Coordinator

·      Colloquium Coordinator

·      Semester Conversion Committee                                                       

·      Advisory Committee

·      Faculty Search, Graduate Studies, and Computer Systems