University of Washington, Seattle, WA
Post-Doctoral Fellow, 2008-Present

• Developing protein secondary structure prediction methods with dynamic Bayesian networks

• Developing SVM classifiers that find the annotation errors of C.elegans cells during embryonic development

Georgia Institute of Technology, Atlanta, GA
Graduate Research Assistant, 2002-2008

• Performed statistical analysis to analyze correlations in protein secondary structure.
• Developed and implemented hidden semi-Markov models for protein secondary structure prediction.
• Developed training methods to estimate HMM parameters.
• Derived a global scoring function from 3D structural alignments that jointly captures secondary structure and amino acid similarity.
• Developed and implemented HMMs for pairwise alignments of amino acid and secondary structure sequences.
• Developed and implemented N-Best algorithms to compute suboptimal segmentations of protein secondary structure.
• Developed a Bayesian model for protein β-sheets.
• Developed and implemented algorithms that find the optimum β-sheet architecture of a protein.

Nortel Networks Netas, Istanbul, Turkey
Summer Intern, Summer 1998

Turkish Telecommunication, Ankara, Turkey
Summer Intern, Summer 1997

1. MCCL best researcher award, Multimedia Computing and Communications Lab (MCCL), Georgia Institute of Technology, Spring 2007.

1. 2nd place award in EMBS Student Design Competition, 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, San Francisco CA, Sep 2004.

2. Received a full-time scholarship from the Master's Program of the Electrical and Electronics Engineering Department, Bilkent University, Ankara, Turkey, 1999.

3. Received a merit-based full four-year scholarship from the Electrical and Electronics Engineering Department, Bilkent University, Ankara, Turkey, 1995.

4. Honored as 117th among over 1 million students in Turkish Nationwide University Entrance Examination, 1995.

5. Honored to compete in the finals of Turkish Nationwide Intelligence Games, Turkish National Intelligence Association, Ankara, Turkey, 2000.

6. Ranked 1st in Intelligence Games, Istanbul Ataturk Science High School, which is among the best 3 high schools in Turkey, Istanbul, Turkey, 1993.

7. Ranked 6th among secondary school students in Turkish Nationwide Chess Tournament, Ministry of Education, Turkey, 1992.

1. Proficient in C for more than 5 years. Implemented HMMs, secondary structure prediction, pairwise alignment and numerical analysis algorithms.

2. Competent with C++.

3. Proficient in Matlab for more than 8 years. Implemented several engineering projects and simulation tools.

4. Competent with Python. Implemented several scripts for data formatting.

5. Competent with Perl. Implemented pairwise alignment algorithms, multiple sequence alignment using Gibbs sampling algorithm.

6. Experienced with BLAST. Competent with CLUSTALW. Knowledge of public databases including PDB, NCBI-NR, EMBL, Swiss-Prot, COGs, PFAM, CDD. Competent with bioinformatics software including GeneMark, PSIPRED, Porter, SSpro4, BetaPro, DSSP. 

7. Experienced in web design.

8. Proficient with Microsoft Word, Excel, Outlook, Powerpoint, Frontpage. Competent with ACT, Goldmine, and SQL.

9. Comfortable with Linux, UNIX, and Windows environments.

1. "Understanding the Book of Life: Non-Local Interaction Modeling for Protein Beta-Sheets and Its Integration to Protein Structure Prediction," funded by National Science Foundation (NSF) for three years, PI:Yucel Altunbasak, 2007.

2. "Understanding the Book of Life: Bayesian Protein Secondary Structure Analysis and Its Application to Protein Function Prediction," funded by National Science Foundation (NSF) for three years, PI:Yucel Altunbasak, 2005.

1. Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, "Protein secondary structure prediction with semi Markov HMMs," The Fourth Georgia Tech and University of Georgia International Conference on Bioinformatics, Nov 13-16, 2003.

1. "Genomics from an Engineering Perspective," Sabanci University, Istanbul, Turkey, 2003.

2. "Bayesian Protein Secondary Structure Prediction and Homology Detection with Residue-Based Alignments of Sequence and Secondary Structure," Arizona State University, Arizona, 2006.