Publications

Journal Publications

  1. Mustafa Bıçakçı, Oğuzhan Ayyıldız, Zafer Aydın, Alper Baştürk, Seyhan Karaçavuş, Bülent Yılmaz, "Metabolic Imaging Based Sub-Classification of Lung Cancer," IEEE Access, 8:218470-218476, 25 November 2020.
  2. Nuh Azgınoğlu, Zafer Aydın, Mete Çelik, "Structural profile matrices for predicting structural properties of proteins," Journal of Bioinformatics and Computational Biology, 18(4):2050022-1-2050022-20, 10 July 2020.
  3. Rukiye Nur Kaçmaz, Bülent Yılmaz, Zafer Aydın, "Effect of interpolation on specular reflections in texture‐based automatic colonic polyp detection," International Journal of Imaging Systems and Technology, 1-9, 26 June 2020. 
  4. Ashrf Aoad, Zafer Aydın, "New modeling of reconfigurable microstrip antenna using hybrid structure of simulation driven and knowledge based artificial neural networks," Pamukkale University Journal of Engineering Sciences, 26(5):935-943, October 2020.
  5. Yasin Görmez, Zafer Aydın, Ramazan Karademir, Vehbi Çağrı Güngör, "A deep learning approach with Bayesian optimization and ensemble classifiers for detecting denial of service attacks," International Journal of Communication Systems, 33:e4401, 06 May 2020.
  6. Sena Büşra Yengeç Taşdemir, Kasım Tasdemir, Zafer Aydın, "A review of mammographic region of interest classification," WIREs Data Mining and Knowledge Discovery, 10:(5), e1357, 18 February 2020.
  7. Zafer Aydın, "Performance analysis of machine learning and bioinformatics applications on high performance computing systems," Academic Platform Journal of Engineering and Science, 8(1):1-14, 28 January 2020.
  8. Hilal Hacılar, Yasin Görmez, Burcu Bakır Güngör, Cengiz Gezer, Zafer Aydın, Vehbi Çağrı Güngör, "Classification of cardiovascular artery diseases using artificial neural network," International Journal of Bioscience, Biochemistry and Bioinformatics, 10(1):34-41, January 2020.
  9. Oğuzhan Ayyıldız, Zafer Aydın, Bülent Yılmaz, Seyhan Karaçavuş, Kübra Şenkaya, Semra İçer, Arzu Taşdemir, Eser Kaya, "Lung cancer subtype differentiation from positron emission tomography images," Turkish Journal of Electrical Engineering and Computer Sciences, 28(1):262-274, 27 January 2020.
  10. Sema Atasever, Zafer Aydın, Hasan Erbay, Mostafa Sabzekar, "Sample reduction strategies for protein secondary structure prediction," Applied Sciences, 9(20):4429, 2019. 
  11. Zafer Aydın, Nuh Azgınoğlu, Halil İbrahim Bilgin, Mete Çelik, "Developing structural profile matrices for protein secondary structure and solvent accessibility prediction," Bioinformatics, 35(20):4004-4010, 2019.
  12. Fourati et al. "A crowdsourced analysis to identify ab initio molecular signatures predictive of susceptibility to viral infection," Nature Communications, 9(1):1-11, 2018.
  13. Zafer Aydın, Oğuz Kaynar, Yasin Görmez, "Dimensionality reduction for protein secondary structure and solvent accesibility prediction," Journal of Computational Biology and Bioinformatics, 16(5):1850020-1-1850020-16, 2018.
  14. Vehbi Çağrı Güngör, Zafer Aydın, Ramazan Karademir, “Intelligent anomaly detection techniques for denial of service attacks,” International Journal of Computer and Communication Enginering, 7(2): 20-31, 2018.
  15. Mostafa Sabzekar, Mahmoud Naghibzadeh, Mahdie Eghdami, Zafer Aydın, "Protein beta-sheet prediction using an efficient dynamic programming algorithm," Computational Biology and Chemistry, 70:142-155, 2017.
  16. Oğuz Kaynar, Zafer Aydın, Yasin Görmez, “Sentiment analizinde öznitelik düşürme yöntemlerinin oto kodlayıcı derin öğrenme makinaları ile karşılaştırılması,” Gazi Üniversitesi Bilişim Teknolojileri Dergisi, 10(3):319-326, 2017.
  17. Ashrf Aoad, Murat Şimşek, Zafer Aydın, "Knowledge based response correction method for design of reconfigurable N-shaped microstrip patch antenna using inverse ANNs," International Journal of Numerical Modeling: Electronic Networks, Devices and Fields, 30:e2129, 2017.
  18. Zafer Aydın, David Baker, William Stafford Noble, "Template scoring methods for protein torsion angle prediction," Communications in Computer and Information Science, 574:206-223, 2015.
  19. Çiğdem Eroğlu Erdem, Çiğdem Turan, Zafer Aydın, "BAUM-2: A multilingual audio-visual affective face database," Multimedia Tools and Applications, 74(18): 7429-7459, 2015.
  20. Ashrf Aoad, Murat Şimşek 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.
  21. Zafer Aydın, Ajit Singh, Jeff Bilmes, William Stafford Noble, "Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure," BMC Bioinformatics , 12:154, 2011.
  22. Zafer Aydın, Yücel Altunbaşak, Hakan Erdoğan, "Bayesian models and algorithms for protein beta-sheet prediction," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8(2):395-409, 2011.
  23. Zafer Aydın, John Isaac Murray, Robert H Waterston, William Stafford 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.
  24. Zafer Aydın, Yücel Altunbaşak, Hakan Erdoğan, "Bayesian protein secondary structure prediction with near-optimal segmentations," IEEE Transactions on Signal Processing, 55(7):3512-3525, 2007.
  25. Zafer Aydın, Yücel Altunbaşak, "A signal processing application in genomic research: protein secondary structure prediction," IEEE Signal Processing Magazine, 23(4):128-131, 2006.
  26. Zafer Aydın, Yücel Altunbaşak, Mark Borodovsky, "Protein secondary structure prediction for a single-sequence using hidden semi-Markov models," BMC Bioinformatics, 7:178, 2006.

Conference Publications

  1. Zafer Aydın, Vehbi Çağrı Güngör, “A novel feature design and stacking approach for non technical electricity loss detection,” IEEE Innovative Smart Grid Technologies – Asia (ISGT Asia), 867-872, 2018.
  2. Sena Büşra Yengeç Taşdemir, Kasım Taşdemir, Zafer Aydın, "ROI detection in mammogram images using wavelet-based Haralick and HOG features," IEEE International Conference on Machine Learning Applications, Orlando, Florida, 2018.
  3. Yunus Emre Işık, Yasin Görmez, Oğuz Kaynar, Zafer Aydın, “NSEM: Novel Stacked Ensemble Method for Sentiment Analysis,” International Conference on Artificial Intelligence and Data Processing (IDAP), 1-4, 2018.
  4. Zafer Aydın, Oğuz Kaynar, Yasin Görmez, Yunus Emre Işık, “Comparison of machine learning classifiers for protein secondary structure prediction,” IEEE 26th Signal Processing and Communication Applications Conference (SIU), 1-4, 2018.
  5. Zafer Aydın, Oğuz Kaynar, Yasin Görmez, “Comparison of NR and Uniclust databases for protein secondary structure prediction,” IEEE 26th Signal Processing and Communication Applications Conference (SIU), 1-4, 2018.
  6. Nuh Azgınoğlu, Mehmet Akif Eren, Mete Çelik, Zafer Aydın, “Ceph-based storage server application,” IEEE 6th International Symposium on Digital Forensics and Security (ISDFS), 1-4, 2018.
  7. Zafer Aydın, Ömmu Gülsüm Uzut, “Combining Classifiers for Protein Secondary Structure Prediction,” IEEE International Conference on Computational Intelligence and Communication Networks, Girne, Cyprus, pp. 29-33, 2017.
  8. Zafer Aydın, Oğuz Kaynar, Yasin Görmez, “Feature Selection for Protein Dihedral Angle Prediction,” IEEE International Conference on Computational Intelligence and Communication Networks, Girne Cyprus, pp. 48-52, 2017.
  9. Nuh Azgınoğlu, Umut Atasever, Zafer Aydın, Mete Çelik, Hasan Erbay, “Open Source SLURM Computer Cluster System Design and a Sample Application, IEEE International Conference on Computer Science and Engineering, Antala Turkey, 2017.
  10. Ashrf Aoad, Murat Şimşek, 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.
  11. Muhammed Yasin, Tolga Göze, İhsan Özcan, Vehbi Çağrı Güngör, Zafer Aydın, "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.
  12. Zafer Aydin, David Baker, 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.
  13. Ashrf Aoad, Zafer Aydın, 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.
  14. Çiğdem Turan, Can Kansın, Sara Zhalehpour, Zafer Aydın, Çiğdem Eroğlu 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.
  15. Zafer Aydın, James Thompson, Jeff Bilmes, David Baker, 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.
  16. Eser Aygün, Caner Kömürlü, Zafer Aydın, Zehra Çataltepe, "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.
  17. Zafer AydIn, İsa Kemal Pakatçı, Hakan Erdoğan, Yücel Altunbaşak, "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.
  18. Zafer Aydın, Hakan Erdoğan, Yücel Altunbaşak, "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.
  19. İsa Kemal Pakatçı, Zafer Aydın, Hakan Erdoğan, Yücel Altunbaşak, "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.
  20. Zafer Aydın, Toygar Akgün,Yücel Altunbaşak, "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.
  21. Zafer Aydın, Yücel Altunbaşak, 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.
  22. Zafer Aydın, Yücel Altunbaşak, 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.
  23. Ahmet Kemal Özdemir, Zafer Aydın, Orhan Arıkan, "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.