1. 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. [pdf]

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

3. Zafer Aydin, John I Murray, Robert H Waterston, 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, 2010. [pdf].

4. Zafer Aydin, Yucel Altunbasak and Hakan Erdogan, "Bayesian protein secondary structure prediction with near-optimal segmentations," IEEE Transactions on Signal Processing, vol. 55, Issue 7, Part 1, Page(s): 3512-3525, 2007. [pdf].

5. 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): 128-131, 2006. [pdf] [pdf: extended version].

6. Zafer Aydin, Yucel Altunbasak and Mark Borodovsky, "Protein secondary structure prediction for a single-sequence using hidden semi-Markov models," BMC Bioinformatics, vol. 7, no. 178, 2006. [pdf] [IPSSP web-server].

1. 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), May 2008. [doc]

2. 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 (EMBS'07), page(s) 5025-5028, Aug 2007. [pdf]

3. Zafer Aydin, Hakan Erdogan and Yucel Altunbasak, "Protein fold recognition using residue-based alignments of sequence and secondary structure," in Proceedings of the IEEE International Conference on Acoustics Speech and Signal Processing (ICASSP '07), vol. 1, page(s): I349-I352, April 2007. [pdf]

4. 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 (SUI'2007). [doc]

5. 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 2005. [pdf]

6. 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): 2964-2967, Sep 2004. [pdf]

7. 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 - 577-580, May 17-21, 2004. [pdf]

8. 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): 1229-1232, May 13-17, 2002. [pdf]