Ahmet Sacan

See my Curriculum Vitae for more detailed information.

Research Interests: Indexing and Data Mining in Biological Databases, Protein Sequence and Structure, Similarity Search, Protein Structure Modeling, Protein-Protein Interaction, Automated Cell Tracking

Software Development: The Software page lists some of the software I have developed.

Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. Integrated Search and Alignment of Protein Structures. Bioinformatics, doi: 10.1093/bioinformatics/btn545, 2008 (to appear).

Guadalupe Canahuate, Tan Apaydin, Ahmet Sacan, and Hakan Ferhatosmanoglu. Secondary Bitmap Indexes with Vertical and Horizontal Partitioning. 13th International Conference on Extending Database Technology (EDBT). Saint-Petersburg, Russia, March 2009 (to appear).

Ahmet Sacan, Nilgun Ferhatosmanoglu, and Hakan Ferhatosmanoglu. MaD: An Online Search Tool and Repository for Near–Optimal Microarray Experimental Designs. BMC Bioinformatics, (submitted).

Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, and Yusu Wang. Smolign: A Spatial Motifs Based Multiple Protein Structures Alignment Method. Bioinformatics, (under submission).

Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment. IEEE 8th International Symposium on Bioinformatics & Bioengineering (IEEE-BIBE2008).

Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. Contacts-based indexing, retrieval, and alignment of protein structures (Poster and demo). Fifth Midwest Database Research Symposium, Oct 2008.

Ahmet Sacan Similarity Search and Analysis of Protein Sequences and Structures: A Residue Contacts Based Approach. PhD Thesis. Advisors: I. Hakki Toroslu and Hakan Ferhatosmanoglu. Middle East Technical University, Aug 2008.

Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, and Yusu Wang. Smolign: A Spatial Motifs Based Multiple Protein Structures Alignment Method (poster presentation). Ohio Collaborative Conference on Bioinformatics (OCCBIO), Toledo, OH, 2008.

Ahmet Sacan, Hakan Ferhatosmanoglu, and Huseyin Coskun. CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis. Bioinformatics, 24(14):1647-1649, 2008.

Ahmet Sacan and I. Hakki Toroslu. Approximate Similarity Search in Genomic Sequence Databases using Landmark-Guided Embedding. 1st International Workshop on Similarity Search and Applications (SISAP, an ICDE-2008 workshop) April 11-12, 2008, Cancún, Mexico.

Fatih Altiparmak, Ali Tosun, Hakan Ferhatosmanoglu, and Ahmet Sacan. Automated Data Discovery in Similarity Score Queries. International Conference of Database Systems for Advanced Applications (DASFAA 2008), Lecture Notes in Computer Science, India, 2008.

Ahmet Sacan and I. Hakki Toroslu. Amino acid substitution matrices based on 4-body Delaunay contact profiles. IEEE 7th International Symposium on Bioinformatics & Bioengineering (IEEE-BIBE2007), 796-801, 2007.

Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang. LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins. Bioinformatics, 23(6):709-716, 2007.

Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang. LFM-Pro: a tool for mining family-specific sites in protein structure databases (Poster presentation). Third Midwest Database Research Symposium, Apr 2006.

Ahmet Sacan. Mapping Protein Sequences and Structures to Feature Spaces for Efficient Indexing. Proceedings of the International Symposium on Health Informatics and Bioinformatics 2005 (HIBIT 2005)