1 Zafer Aydın Abdullah Gul University, Computer Engineering Department, Aşıkveysel Bulvarı, Erciyes Teknopark, No: 4/67-a Melikgazi, Kayseri, Turkey Mobile: +90 (507) URL: EDUCATION Ph.D. in Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, GA, USA Overall GPA: 4.0 / 4.0 Specialized Area: Machine Learning, Pattern Recognition, Bioinformatics, Computational Biology Thesis Title: Bayesian Models and Algorithms for Protein Secondary Structure and Beta-Sheet Prediction Advisor: Prof. Yucel Altunbasak Coadvisor: Prof. Mark Borodovsky M.S. in Electrical and Electronics Engineering, Overall GPA: 3.8 / 4.0 Specialized Area: Digital signal processing, time-frequency signal processing Thesis Title: A New Approach to Time-Frequency Localized Signal Design Advisor: Prof. Orhan Arikan B.Sc. in Electrical and Electronics Engineering, Overall GPA: 3.56 / 4.0 ACADEMIC EXPERIENCE Assistant Professor, Feb 2014-Present Abdullah Gul University, Istanbul, Turkey Assistant Professor, Sep 2011-Feb 2014 Bahcesehir University, Istanbul, Turkey Post-doctoral fellow, Sep 2008-Sep 2011 University of Washington, Seattle, WA, USA 1. Image analysis in C. elegans embryogenesis. Developed support vector machine classifiers for correcting annotation errors of StarryNite. 2. Prediction of local structure for proteins. Developed dynamic Bayesian networks, support vector machines and neural networks for protein secondary structure prediction, torsion class prediction, and beta-strand classification. Developed machine learning algorithms for sparse dynamic Bayesian network models. 3. DNA-protein interaction modeling for homing endonucleases. Developed neural network classifiers for discriminating cleavage sensitive and cleavage resistant sites for homing endonucleases.
2 4. Protein structure prediction with Rosetta. Fragment selection using torsion class predictions for abinitio structure prediction. Graduate Research Assistant, Aug 2002-Sep 2008 Georgia Institute of Technology, Atlanta, GA, USA Graduate Teaching Assistant, Sep 1999-Aug 2002 Undergraduate Teaching Assistant, Fall 1998 TEACHING EXPERIENCE 1. Introduction to Bioinformatics, Spring Circuit Theory I (Fall 2011, Spring 2012, Fall 2012) 3. Circuit Theory II (Spring 2012, Fall 2012, Fall 2013) 4. Machine Learning for Bioinformatics I (Spring 2013) 5. Programming for Bioengineering Research (Fall 2012) 6. Data Mining I (Fall 2013) INDUSTRIAL EXPERIENCE Summer Intern, 1998 Nortel Networks Netas, Istanbul, Turkey Summer Intern, 1997 Turkish Telecommunication, Ankara, Turkey HONORS AND DISTINCTIONS 1. Best researcher award, Multimedia Computing and Communications Lab (MCCL), Spring nd place award in EMBS Student Design Competition, 26 th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, San Francisco CA, Sep Honored to compete in the finals of Turkish Nationwide Intelligence Games organized by Turkish Intelligence Association, Ankara, Turkey, Received full-time scholarship from the Master s program of the Electrical and Electronics Engineering Department in, Received merit-based full four-year scholarship from the Electrical and Electronics Engineering Department in, Honored as 117th among over 1 million students in Turkish Nationwide University Entrance Examination, COMPUTER SKILLS 1. Proficient in C. 2. Comfortable with C Proficient in Matlab. 4. Competent with Python. 5. Comfortable with Perl.
3 6. Experienced with machine learning software: Graphical Models Toolkit (GMTK), libsvm, Torch. 7. Experienced with Bioinformatics software/tools: BLAST, PSI-BLAST, HMMER, SAM, HHSEARCH, GeneMark, PSIPRED, Porter, SSpro4, BetaPro, NNcon, USCS Genome Browser, Rosetta. 8. Experienced with HTML. 9. Proficient in Microsoft Word, Excel, Outlook, Powerpoint. 10. Comfortable with ACT, Goldmine. 11. Comfortable with Linux, UNIX, Windows. PROFESSIONAL ACTIVITIES 1. Reviewer for grant proposal panels: TUBITAK EEEAG Bioinformatics Panel 2012, Reviewer for fellowship panels: TUBITAK BIDEB 2214/2219 Informatics Panel Reviewer for international journals: Plos One, BMC Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics, JBCB, NEUNET, KAIS, NEUCOM, Turkish Journal of Electrical Engineering and Computer Sciences. 4. Reviewer for international conferences: RECOMB 2010, RECOMB 2009, IEEE-ICIP 2006, IEEE- ICASSP ADMINISTRATIVE WORK 1. PhD program coordinator, Electrical and Electronics Engineering Department of Bahcesehir University, Fall 2012-Spring Internship coordinator, Electrical and Electronics Engineering Department of Bahcesehir University, Fall 2011-Spring JOURNAL PUBLICATIONS 1. Cigdem Eroglu Erdem, Cigdem Turan and Zafer Aydin, BAUM-2: A multilingual audio-visual affective face database, Multimedia Tools and Applications, Zafer Aydin, Ajit Singh, Jeff Bilmes and William S Noble, Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure, BMC Bioinformatics, 12:154, Zafer Aydin, Hakan Erdogan and Yucel Altunbasak, Bayesian Models and Algorithms for Protein Beta-Sheet Prediction, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol 8, Issue: 2, Page(s): , Zafer Aydin, John I Murray, Robert H Waterston and William S Noble, Using machine learning to speed up manual image annotation: application to a 3D imaging protocol for measuring single cell gene expression in the developing C. elegans embryo, BMC Bioinformatics, vol. 11, no. 84, Zafer Aydin, Hakan Erdogan and Yucel Altunbasak, Bayesian Protein Secondary Structure Prediction with Near-Optimal Segmentations, IEEE Transactions on Signal Processing, vol. 55, Issue: 7, Part 1, Page(s): , Zafer Aydin and Yucel Altunbasak, A signal processing application in genomic research: protein secondary structure prediction, IEEE Signal Processing Magazine, vol. 23, Issue: 4, Page(s): , Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, Prediction of protein secondary structure for a single-sequence using hidden semi-markov models, BMC Bioinformatics, vol. 7, no. 178, 2006.
4 JOURNAL MANUSCRIPTS IN PREPARATION 1. Zafer Aydin and Serap Aydin, Detection of paradoxical and psychophysiological insomnia by support vector machines and entropy measures derived from EEG signals, in revision, Turkish Journal of Electrical Engineering and Computer Sciences, Zafer Aydin, David Baker and William Stafford Noble, Accurate prediction of torsion angle classes improves protein structure prediction, in preparation Ashraf Awad, Erdal Korkmaz, Neslihan S. Sengor, Murat Simsek and Zafer Aydin, "Modeling a reconfigurable 5-Fingers shaped microstrip patch antenna by artificial neural networks," in preparation, CONFERENCE PUBLICATIONS 1. Cigdem Turan, Can Kansin, Sara Zhalehpour, Zafer Aydin and Cigdem Eroglu Erdem, A Method for Extraction of Affective Audio-Visual Facial Clips from Movies, IEEE Signal Processing and Communication Applications Conference (SIU 2013), Girne, Turkish Republic of Northern Cyprus, April Zafer Aydin, James Thompson, Jeff Bilmes, David Baker and William Stafford Noble, "Protein torsion angle class prediction by a hybrid architecture of Bayesian and neural networks," in Proceedings of the 13th International Conference on Bioinformatics and Computational Biology (BIOCOMP'12), Page(s): , July Eser Aygun, Caner Komurlu, Zafer Aydin, Zehra Cataltepe, Protein Function Prediction with Amino Acid Sequence and Secondary Structure Alignment Scores, HIBIT 2008, Istanbul, Turkey. 4. Zafer Aydin, Isa Kemal Pakatci, Hakan Erdogan and Yucel Altunbasak, Training Set Reduction Methods for Protein Secondary Structure Prediction in Single-Sequence Condition, in Proceedings of the 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'07), Page(s): , Aug Zafer Aydin, Hakan Erdogan and Yucel Altunbasak, Protein Fold Recognition using Residue-Based Alignments of Sequence and Secondary Structure, in Proceedings of the IEEE Int. Conf. on Acoustics Speech and Signal Processing (ICASSP 2007), vol. 1, Page(s): I349-I352, April Isa Kemal Pakatci, Zafer Aydin, Hakan Erdogan and Yucel Altunbasak, Training Set Reduction Methods for Single-Sequence Protein Secondary Structure Prediction, IEEE Signal Processing and Communication Applications Conference (SIU 2007), Eskisehir Turkey, June Zafer Aydin, Toygar Akgun and Yucel Altunbasak, A Modified Stack Decoder for Protein Secondary Structure Prediction, in Proceedings of the IEEE Int. Conf. on Acoustics Speech and Signal Processing (ICASSP'05), vol. 4, Page(s): iv/737-iv/740, March Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, Protein secondary structure prediction with semi Markov HMMs, in Proceedings of the 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'04), vol. 2, Page(s): , Sep Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, Protein secondary structure prediction with semi Markov HMMs, in Proceedings of the IEEE Int. Conf. on Acoustics Speech and Signal Processing (ICASSP'04), vol. 5, Page(s): V , May Ahmet Kemal Ozdemir, Zafer Aydin and Orhan Arikan, A New approach to time-frequency localized signal design, in Proceedings of the IEEE Int. Conf. on Acoustics Speech and Signal Processing (ICASSP'02), vol. 2, Page(s): , May CONSULTANCY 1. Design of a Telemetric Embedded System with Multi Protocol Communication Interface, Non Technical Loss Detection and Demand Forecasting, The Scientific and Technological Research
5 Council of Turkey (TUBITAK), 1501 Industrial Research and Development Project Grant Program, PI: Cafer Kockan, June 2013-June BOOK CHAPTERS 1. Protein Yapı Tahmini (Protein Structure Prediction) ed: Jens Allmer, Bioinformatics II, in preparation, POSTER SESSIONS 1. Zafer Aydin, Sheila Reynolds, Jeff Bilmes and William S Noble, A Dynamic Bayesian Network Approach for Protein Secondary Structure Prediction, The 13 th Annual International Conference on Research in Computational Molecular Biology (RECOMB), Tucson, Arizona, 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 REFERENCES Available upon request.