Publications

Journal Publications

1. Zafer Aydin, David Baker, and William Stafford Noble, "Template Scoring Methods for Protein Torsion Angle Prediction," Communications in Computer and Information Science, vol. 574, pp. 206-223, 2015.

2. Ashrf Aoad, Murat Simsek and Zafer Aydin, "Knowledge Based Response Correction Method for Design of Reconfigurable N-Shaped Microstrip Patch Antenna Using Inverse ANNs," accepted to International Journal of Numerical Modeling: Electronic Networks, Devices and Fields, 2015.

3. Cigdem Eroglu Erdem, Cigdem Turan and Zafer Aydin, "BAUM-2: A multilingual audio-visual affective face database," Multimedia Tools and Applications, 74(18): 7429-7459, 2015.

4. Ashrf Aoad, Murat Simsek and Zafer Aydin, "Design of a Reconfigurable 5-Fingers Shaped Microstrip Patch Antenna by Artificial Neural Networks," International Journal of Advanced Research in Computer Science and Software Engineering (IJARCSSE), 4(10): 61-70, 2014.

5. 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, 2011.

6. Zafer Aydin, Yucel Altunbasak and Hakan Erdogan, "Bayesian models and algorithms for protein beta-sheet prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2):395-409, 2011.

7. 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, 11:84, 2010.

8. Zafer Aydin, Yucel Altunbasak and Hakan Erdogan, "Bayesian protein secondary structure prediction with near-optimal segmentations," IEEE Transactions on Signal Processing, 55(7):3512-3525, 2007.

9. Zafer Aydin and Yucel Altunbasak, "A signal processing application in genomic research: protein secondary structure prediction," IEEE Signal Processing Magazine, 23(4):128-131, 2006.

10. Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, "Protein secondary structure prediction for a single-sequence using hidden semi-Markov models," BMC Bioinformatics, 7:178, 2006.

Conference Publications

1. Zafer Aydin, Huseyin Emre Erdem, Ömmu Gülsüm Uzut, "Identifying Discriminative Scores of HMM-profile Alignments by Feature Selection," 9th International Symposium on Health Informatics and Bioinformatics (HIBIT'15), Mugla, Turkey, October 2015.

2. Ashrf Aoad, Murat Simsek and Zafer Aydin, "Development of Knowledge Based Response Correction for a Reconfigurable N-Shaped Microstrip Antenna Design," IEEE MTT-S International Conference on Numerical Electromagnetic and Multiphysics Modeling and Optimization (NEMO'15), Ottawa, Canada, August 2015.

3. Muhammed Yasin, Tolga Göze, İhsan Özcan, Vehbi Cagri Gungor and Zafer Aydin, "Short Term Electricity Load Forecasting: A Case Study of Electric Utility Market in Turkey," International Istanbul Smart Grid Congress And Exhibition (ICSG Istanbul'15), April 2015.

4. Zafer Aydin, David Baker and William Stafford Noble, "Constructing structural profiles for protein torsion angle prediction," In Proc. 6th International Conference on Bioinformatics Models, Methods and Algorithms (BIOINFORMATICS'15), pages 26-35, Lisbon, Portugal, January 2015.

5. Ashrf Aoad, Zafer Aydın and Erdal Korkmaz, "Design of a tri band 5-fingers shaped microstrip patch antenna with an adjustable resistor," IEEE International Conference on Antenna Measurements and Applications (CAMA'15) , pages 1-4, Antibes Juan-les-Pins, France, November 2014.

6. 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 Applications Conference (SIU'13), pages 1-4, Girne, Turkish Republic of Northern Cyprus, April 2013.

7. 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 Proc. 13th International Conference on Bioinformatics and Computational Biology (BIOCOMP'12), pages 477-483, Las Vegas, NV USA, July 2012.

8. Eser Aygun, Caner Komurlu, Zafer Aydin and Zehra Cataltepe, "Protein function prediction with amino acid and sequence and secondary structure alignment scores," International Symposium on Health Informatics and Bioinformatics (HIBIT'08), Istanbul, Turkey, May 2008.

9. Zafer Aydin, Isa Kemal Pakatci, Hakan Erdogan and Yucel Altunbasak, "Training set reduction methods for protein secondary structure prediction in single-sequence condition," In Proc. 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBS'07), pages 5025-5028, Lyon, France, August 2007.

10. Zafer Aydin, Hakan Erdogan and Yucel Altunbasak, "Protein fold recognition using residue-based alignments of sequence and secondary structure," In Proc. IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP '07), volume 1, pages I349-I352, Honolulu, HI USA, April 2007.

11. 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'07), pages 1-4, Eskisehir, Turkey, June 2007.

12. Zafer Aydin, Toygar Akgun and Yucel Altunbasak, "A modified stack decoder for protein secondary structure prediction," In Proc. IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP'05), volume 4, pages iv/737-iv/740, Philadelphia, PA USA, March 2005.

13. Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, "Protein secondary structure prediction with semi Markov HMMs," In Proc. 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '04), volume 2, pages 2964-2967, San Francisco, CA USA, Sep 2004.

14. Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, "Protein secondary structure prediction with semi Markov HMMs," In Proc. IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP'04), volume 5, pages V - 577-580, Montreal, Quebec, Canada, May 2004.

15. Ahmet Kemal Ozdemir, Zafer Aydin and Orhan Arikan, "A New approach to time-frequency localized signal design," In Proc. IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP '02), volume 2, pages 1229-1232, Orlando, FL USA, May 2002.