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Ahmet Sacan

Ahmet Sacan, PhD

Teaching Professor
School of Biomedical Engineering, Science & Health Systems

Office: Bossone 702
Phone: 215.895.1804
Website: Sacan Bioinformatics Lab


Ahmet Sacan is currently an Associate Teaching Professor at Drexel University, School of Biomedical Engineering, Science and Health Systems. Ahmet received his BSc degrees in Computer Science and in Cellular and Molecular Biology from University of Michigan, Ann Arbor (2001). He received his PhD from the Computer Engineering Department of the Middle East Technical University (Turkey, 2008). He spent several years as a visiting scholar and Post-Doctoral Researcher at the Bioinformatics Research Group of the Ohio State University (2006-2008).

His research interests lie broadly in the areas of Structural Bioinformatics, Imaging Informatics, and Bitmap Indices. He is specifically focused on similarity search, data mining, and analysis of biomolecular databases; protein folding and docking; automated detection, tracking, and modeling of live cells in digital microscopy imaging; and maintenance and indexing of data warehouses. Besides his research interests, he has worked as system administrator and software developer and has contributed in the development of a number of online learning technologies. A list of his software products, publications, and details of his accomplishments and qualifications can be found at


  • PhD in Computer Engineering, Middle East Technical University, Ankara, Turkey (2001-2008)
  • BS in Computer Science, University of Michigan (1997-2001)
  • BS in Cell & Molecular Biology, University of Michigan (1997-2001)

Research Interests

Bioinformatics, analysis of genomic and proteomic databases, machine learning, and biomarker discovery for chronic pain syndromes.


  • MicroRNA modulation in complex regional pain syndrome. Irina Orlova, Guillermo Alexander, Rehman Qureshi, Ahmet Sacan, Alessandro Graziano, James E. Barrett, Robert Schwartzman, and Seena Ajit. Neurology. 2011 (to appear).
  • Smolign: A Spatial Motifs Based Multiple Protein Structures Alignment Method. Hong Sun, Ahmet Sacan, Hakan Ferhatosmanoglu, and Yusu Wang. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2011.
  • Comparing the Yeast Retrograde Response and NF-kB Stress Responses. Visish Srinivasan, Andres Kriete, Ahmet Sacan, and S. Michal Jazwinski. Aging Cell, 2010.
  • Sequence alignment reveals possible MAPK docking motifs on HIV proteins. Perry Evans, Ahmet Sacan, Lyle Ungar, Aydin Tozeren. PLoS ONE, 5(1):e8942, 2010.
  • MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs. Ahmet Sacan, Nilgun Ferhatosmanoglu, Hakan Ferhatosmanoglu. BMC Bioinformatics, 10:304-309, 2009.
  • Integrated Search and Alignment of Protein Structures. Ahmet Sacan, I. Hakki Toroslu, and Hakan Ferhatosmanoglu. Bioinformatics, 24(24):2872-2879, 2008.
  • CellTrack: An Open-Source Software for Cell Tracking and Motility Analysis. Ahmet Sacan, Hakan Ferhatosmanoglu, and Huseyin Coskun. Bioinformatics, 24(14):1647-1649, 2008.
  • LFM-Pro: A Tool for Detecting Significant Local Structural Sites in Proteins. Ahmet Sacan, Ozgur Ozturk, Hakan Ferhatosmanoglu, and Yusu Wang. Bioinformatics, 23(6):709-716, 2007.