Journal Papers

• 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. Microarray Designer Web Server
• Integrated Search and Alignment of Protein Structures. A. Sacan, I. H. Toroslu, and H. Ferhatosmanoglu. Bioinformatics, vol. 24, no. 14, December 2008, pp. 2872-9. Vorometric Web Server
• 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, 9 : 344. EPO Web Server
• 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. CellTrack Web Server
• 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.
• 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.
• LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins. A. Sacan, O. Ozturk, H. Ferhatosmanoglu, Y. Wang. Bioinformatics, Vol. 23, No. 6, pp. 709-716, March 2007. LFM-Pro Software

• 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.
• Access Structures for Angular Similarity Queries. T. Apaydin and H. Ferhatosmanoglu. IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 16, no. 6, 14 pp. 1512-1525, November 2006.
• High Dimensional Nearest Neighbor Searching. H. Ferhatosmanoglu, E. Tuncel, D. Agrawal, A. El Abbadi. Information Systems Journal, Volume 31, Issue 6, September 2006, pp. 512-540.
• Efficient Parallel Processing of Range Queries through Replicated Declustering. H. Ferhatosmanoglu, A. Tosun, G. Canahuate, A. Ramachandran. Distributed and Parallel Databases Journal, vol. 20, no. 2, pp. 117-148, September 2006.
• Online Summarization of Dynamic Time Series Data. U. Ogras and H. Ferhatosmanoglu. Very Large Databases (VLDB) Journal, 15(1): 84-98 (January 2006).
• 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).
• 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, 17(1): 75-101 (2005).
• Vector Space Indexing for Biosequence Similarity Searches. O. Ozturk and H. Ferhatosmanoglu. International Journal on Artificial Intelligence Tools, Special Issue on Selected Papers from the IEEE Symposium on BioInformatics and BioEngineering (BIBE) II, 14(5): 811-826 (2005).
• Dimensionality Reduction and Similarity Computation using Inner Product Approximations. O. Egecioglu, H. Ferhatosmanoglu, U. Ogras. IEEE Transactions on Knowledge and Data Engineering (TKDE) 16(6): 714-726 (June 2004).

Refereed Conference Papers

• Secondary Bitmap Indexes with Vertical and Horizontal Partitioning . G. Canahuate, T. Apaydin, A. Sacan, H. Ferhatosmanoglu , EDBT, March 2009, pp 600-611.
• Mutual Information Based Extrinsic Similarity for Microarray Analysis. D. Ucar, F. Altiparmak, H. Ferhatosmanoglu, S. Parthasarathy: BICoB, April 2009, pp. 424-436.
• 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.
• Analysis of Basic Data Reordering Techniques. T. Apaydin, A. Tosun, H. Ferhatosmanoglu: SSDBM, 20^th Scientific and Statistical Data Management Conference, pp. 517-524, July 2008.
• Dynamic Data Organization for Bitmap Indices. T. Apaydin, G. Canahuate, H. Ferhatosmanoglu, A. Tosun, 3rd International Conference on Scalable Information Systems, June 2008.
• A General Framework for Modeling and Processing Optimization Queries. M. Gibas, N. Zheng, H. Ferhatosmanoglu, VLDB '07, pp. 1069-1080.
• 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.
• A Multi-Metric Similarity Based Analysis of Microarray Data. F. Altiparmak, S. Erdal, O.  Ozturk, H. Ferhatosmanoglu. The IEEE International Conference on Bioinformatics and Biomedicine  (BIBM),  2007
• Enhanced Partial Order Curve Comparison over Multiple Protein Folding Trajectories. H. Sun, H. Ferhatosmanoglu, M. Ota, Y. Wang, CSB 2007 (to appear).
• Update Conscious Bitmap Indices. G. Canahuate, M. Gibas, H. Ferhatosmanoglu. International Conference on Scientific and Statistical Database Management (SSDBM), Banff, Canada, 2007/July, to appear.
• Approximate Encoding for Direct Access and Query Processing over Compressed Bitmaps. T. Apaydin, G. Canahuate, H. Ferhatosmanoglu, A. Tosun. 32^nd International Conference on Very Large Data Bases (VLDB ’06), Seoul, Korea, September, 2006, pp. 846-857. (Acceptance rate: 13.2%).
• Predicting the Binding Affinity of MHC class II Peptides. F. Altiparmak, A. Akalin, H. Ferhatosmanoglu. LSS Computational Systems Bioinformatics Conference (CSB ’06). Stanford, California, USA. (to appear) (Acceptance rate: 19%).
• Indexing Incomplete Databases. G. Canahuate, M. Gibas, H. Ferhatosmanoglu. 10^th International Conference on Extending Database Technology (EDBT ’06). Munich, Germany, March, 2006, pp. 884-901. (Acceptance rate: 16%).
• Compressing Bitmap Indices by Data Reorganization. A. Pinar, T. Tao, H. Ferhatosmanoglu. 21^st IEEE International Conference on Data Engineering (ICDE ’05). Tokyo, Japan, April 2005, pp. 310-321. (Acceptance rate: 13%).
• Replicated Declustering of Spatial Data. H. Ferhatosmanoglu, A. Tosun, A. Ramachandran. 23rd ACM SIGMOD-SIGACT-SIGART Symposium on Principles of Database Systems (PODS ‘04), pp. 125-135. Paris, France, June 2004. (Acceptance rate: 16%)
• 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), pp. 366-378.
• 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. (Acceptance rate: 15%)
• 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. (Acceptance rate: 15%)
• Peer-to-Peer Spatial Queries in Sensor Networks. M. Demirbas and H. Ferhatosmanoglu. 3rd IEEE International Conference on Peer-to-Peer Computing (P2P '03), pp.32-39. Linköping, Sweden, September 2003.
• Efficient k-NN Search on Streaming Data Series. X. Liu and H. Ferhatosmanoglu. 8th International Symposium on Spatial and Temporal Databases (SSTD '03), pp. 83-101. Santorini, Greece, July 2003.
• 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), pp. 553-558. Stanford, CA, August 2003.
• Effective Indexing and Filtering for Similarity Search in Large Biosequence Databases. O. Ozturk and H. Ferhatosmanoglu. IEEE International Symp. on Bioinformatics and Bioengineering (BIBE '03), pp. 359-366. Washington, DC. March 2003.
• VQ-Index: An Index Structure for Similarity Searching in Multimedia Databases. E. Tuncel, H. Ferhatosmanoglu, K. Rose. ACM Multimedia (ACM MM '02), pp. 543-552. Juan Les Pins, France, December 2002. (Acceptance rate: 14%)
• Vulnerabilities in Similarity Search based Systems. A. Tosun and H. Ferhatosmanoglu. 11th ACM International Conference on Information and Knowledge Management (CIKM '02) , pp. 110-117. Mc Lean, VA, November 2002.
• Optimal Parallel I/O Using Replication. A. Tosun and H. Ferhatosmanoglu. Proceedings of International Conference on Parallel Processing Workshops (ICPPW '02), pp. 506-513. Vancouver, Canada, August 2002.
• Efficient Processing of Conical Queries. H. Ferhatosmanoglu, D. Agrawal, A. El Abbadi. Proceedings of the 10th ACM International Conference on Information and Knowledge Management (CIKM '01), pp. 1-8. Atlanta, USA, November 2001.
• Optimal Partitioning for Efficient I/O in Spatial Databases. H. Ferhatosmanoglu, D. Agrawal, A. El Abbadi. European Conference on Parallel Computing (Euro-Par '01), Parallel I/O and Storage Technology, pp. 889-900. Manchester, United Kingdom, August 2001.
• Constrained Nearest Neighbor Queries. H. Ferhatosmanoglu, I. Stanoi, D. Agrawal, A. El Abbadi. 7th International Symposium on Spatial and Temporal Databases (SSTD '01), pp. 257-278. Los Angeles, CA, USA, July 2001.
• Approximate Nearest Neighbor Searching in Multimedia Databases. H. Ferhatosmanoglu, E. Tuncel, D. Agrawal, A. El Abbadi. 17th IEEE International  Conference on Data Engineering (ICDE), pp. 503-511. Heidelberg, Germany, April 2001. (Acceptance rate: 16%)
• Vector Approximation based Indexing for Non-uniform High Dimensional Data Sets. H. Ferhatosmanoglu, E. Tuncel, D. Agrawal, A. El Abbadi. Proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM), pp. 202-209, Washington, DC, USA, November 2000.
• Dimensionality Reduction and Similarity Distance Computation by Inner Product Approximations. O. Egecioglu and H. Ferhatosmanoglu. Proceedings of the 9th ACM International Conference on Information and Knowledge Management (CIKM), pp. 219-226, Washington, DC, USA, November 2000.
• Clustering Declustered Data for Efficient Retrieval.  H. Ferhatosmanoglu, D. Agrawal, A. El Abbadi. Proceedings of the 8th ACM International Conference on Information and Knowledge Management (CIKM), pp. 343-350, Kansas City, Missouri, USA, November 1999.
• Circular Data-space Partitioning for Similarity Queries and Parallel Disk Allocation.   O. Egecioglu, H. Ferhatosmanoglu. Proceedings of the 11th IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS), pp. 194-200, Boston, USA, November 1999.
• Concentric Hyperspaces and Disk Allocation for Fast Parallel Range Searching.  H. Ferhatosmanoglu, D. Agrawal, A. El Abbadi. Proceedings of the 15th IEEE International Conference on Data Engineering (ICDE), pp. 608-615, Sydney, Australia, March 1999. (Acceptance rate: 15%). 
  

Recent Workshop Papers

• 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.
• Combining Mining Results from Multiple Sources in Clinical Trials and Microarray Applications. F. Altiparmak, O. Ozturk, S. Erdal, H. Ferhatosmanoglu, D. C. Trost. MMIS workshop at the ACM International Conference on Knowledge Discovery and Data Mining (SIGKDD), 2007.
• Incremental Quantization for Aging Data Streams. F. Altiparmak, D. Chiu, H. Ferhatosmanoglu. DSMM workshop at IEEE International Conference on Data Mining (ICDM), 2007.