Onur Sakarya

Kosik Lab, Room 5107, Bio II, Neuroscience Research Institute
University of California, Santa Barbara, Santa Barbara, CA, 93117

Education:

• 2008 (expected) - Ph.D., Computer Science, University of California, Santa Barbara
  
• 2006 - M.A., Molecular, Cellular and Developmental Biology, University of California, Santa Barbara
  
• 2004 - B.S., Computer Engineering and Information Science, Bilkent University, Turkey
  
• 2000 - High School degree, Mathematical Sciences, Bornova Anatolian High School, Izmir, Turkey
  
  

Publications:

• Sakarya O, Kosik KS, and Oakley TH. Reconstructing ancestral genome content based on symmetrical best alignments and Dollo parsimony. Bioinformatics 2008 24(5): 606-612
  
• Sakarya O, Armstrong KA, Adamska M, Adamski M, Wang IF, Tidor B, Degnan BM, Oakley TH, and Kosik KS, A post-synaptic scaffold at the origin of the animal kingdom. PLoS ONE 2007. 2: p. e506
  
• Babur O, Demir E, Ayaz A, Dogrusoz U, Sakarya O. Pathway activity inference using microarray data. Technical report 2004, Bilkent Center for Bioinformatics (BCBI)

Research Posters:

• Onur Sakarya, Kenneth S. Kosik, Todd H. Oakley. Detecting gene duplications and losses using symmetrical best hit parsimony. Fifth Annual RECOMB Satellite Workshop in Comparative Genomics, San Diego, 2007.
• Onur Sakarya, Kathryn A. Armstrong, Maja Adamska, I-Fan Wang, Dan Morse, Bruce Tidor, Bernard M. Degnan, Todd H. Oakley, Kenneth S. Kosik. Defining the Proto-synapse for a Synthetic Biology Approach to Information Transfer. Institute for Collaborative Biotechnologies Annual Meeting, Santa Barbara, 2006 and 2007.
• E. Orias, O. Sakarya, O. Egecioglu. Gene Duplication by Pre-scan Rna Retrotransposition: A Proposed Novel Mechanism of Ciliate Genome Evolution. Ciliate Molecular Biology Conference, Italy 3-8 August, 2005.
• C. Aksay, A. Ayaz, O. Babur, C. Bilgin, A. Cetintas, A. Civril, R. Colak, G. Cozen, E. Demir, U. Dogrusoz, Z. Erson, O. Gerdaneri, E. Giral, G. Gulesir, G. Nisanci, O. Sakarya, and H. Yildirim, "PATIKA: An informatics infrastructure for cellular networks", ISMB 2004, Scotland, July 31 - August 4, 2004.
• O. Babur, E. Demir, A. Ayaz, U. Dogrusoz, O. Sakarya, "Microarray Data Analysis and Pathway Activity Inference in PATIKA", ISMB 2004, Scotland, July 31 - August 4, 2004.

Supported Software:

• EvolMAP: Ancestral genome content reconstruction, domain expansion trees, finding lineage-specific genes

Email: onur@cs.ucsb.edu