Onur Sakarya, Ph.D., University of California

I'm now working at Applied Biosystems that became Life Technologies after its merger with Invitrogen.

2008 - 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, Ankara, Turkey

Tompkins-Macdonald GJ, Gallin WJ, Sakarya O, Degnan BM, Leys SP, Boland LM. Expression of a poriferan potassium channel: insights into the evolution of ion channels in metazoans. The Journal of Experimental Biology 2009; 212(6):761-7.
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)

Onur Sakarya, Dumitru Brinza, Yongming Sun, Eugene Spier, Francisco de la Vega, Fiona Hyland. SNP and error detection models in ligation based di-nucleotide sequencing. RECOMB 2009, Tucson, Arizona, 2009.
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.

EvolMAP: Ancestral genome content reconstruction, domain expansion trees, finding lineage-specific genes. Parallel version also available.