Bioinformatics

1. Mohamad M.S., Omatu S., Yoshioka M., Deris S. (2010), A Three-Stage Method to Select Informative Genes for Cancer Classification. International Journal of Innovative Computing, Information and Control. Vol. 6, No.1, pp. 117-125.
2. Mohamad M.S., Omatu S., Deris S., Yoshioka M. (2010), An Enhancement of Binary Particle Swarm Optimization based on the Proposed Constraint and Rule for Selecting a Small Subset of Informative Genes. Far East Journal of Mathematical Sciences. Vol. 38, No. 2, pp. 253-264. Pushpa Publishing House.
3. M.S. Mohamad, S. Omatu, S. Deris, M. Yoshioka. (2009). Three-Stage Method for Selecting Informative Genes for Cancer Classification. IEEJ Transactions on Electrical and Electronic Engineering. Vol. 4, No. 6, pp. 725-730. Wiley InterScience.
4. Rosfuzah R., Razib M.O., Zuraini A.S., Shahreen K., Hishammuddin A., Jumail T., Rohayanti H. and Zalmiyah Z. (2009), Incorporating multiple genomics features with the utilization of interacting domain patterns to improve protein-protein interactions prediction, Information Sciences (Elsevier), Accepted for Publication, ISSN 0020-0255 [2008 Impact Factor: 3.095]
5. Mohamad, M.S., Omatu, S., Yoshioka, M., Deris, S., A cyclic hybrid method to select a smaller subset of informative genes for cancer classification, International Journal of Innovative Computing, Information and Control, Vol. 5, No. 8, 2009, 2189-2202.
6. Umi K.H., Zuraini A. S., Razib M. O., Rohayanti H., Shafry M. R., Hishammudin A., Jumail T., Zalmiyah Z., SPlitSSI-SVM: An algorithm to reduce the misleading and increase the strength of domain signal, Computers in Biology and Medicine, 39(11). 2009,1013-1019 [2008 Impact Factor: 1.272]
7. Mohamad M.S., Omatu S., Safaai D., Misman M.F. and Yoshioka M., A Multi-objective Strategy in Genetic Algorithm for Gene Selection of Gene Expression Data. Artificial Life and Robotics, Vol. 13, No. 2. 2009, 410-413. Springer.
8. Mohamad M.S., Omatu S., Safaai D., Misman M.F. and Yoshioka M., Selecting Informative Genes from Microarray Data by using Hybrid Methods for Cancer Classification. Artificial Life and Robotics, Vol. 13, No. 2. 2009, 414-417. Springer.
9. Mohamad M.S., Omatu S., Safaai D., and Yoshioka M., Particle swarm optimization for gene selection in classifying cancer classes. Artificial Life and Robotics, Vol. 14, No. 1. 2009, 16-19. Springer.
10. Mohamad, M.S., Omatu, S., Deris, S., Yoshioka, M., Gene subset selection using an iterative approach based on genetic algorithms. Artificial Life and Robotics, Vol. 14, No. 1. 2009, 12-15. Springer.
11. Mohamad, M.S., Omatu, S., Deris, S., Yoshioka, M., A recursive genetic algorithm to automatically select genes for cancer classification, Advances in Soft Computing 49. 2009, 166-174. Springer-Verlage.
12. Hany T. Alashwal, Safaai Deris, Razib M. Othman, Bayesian kernel for the prediction of protein-protein interactions, International Journal of Computational Intelligence. 2009, 5(2), 119-124.
13. Othman,M.R., Deris,S. and Illias,R.M. A genetic similarity algorithm for searching the gene ontology terms and     annotation     of anonymous protein sequences, Journal of Biomedical Informatics. 2008. 41(1): 65-81.
14. Mohamad R., Deris S., and Ammar H.H. Pattern-Oriented Design for Multi-Agent System: A Conceptual Model. Journal of     Object Technology. 2007. 6(3): 55-75.
15. Othman M.R., Deris S., and Illias R.M. A Genetic Similarity Algorithm for Searching the Gene Ontology Terms and     Annotating the Anonymous Protein Sequences. Journal of Biomedical Informatics. Accepted.
16. Razib M. Othman, Safaai Deris, Rosli M. Ilias, Hany T. Alashwal, Rohayanti Hassan, and Farhan Mohamed, Incorparation     semantic similarity measure in genetic algorithm: An approach for searching the gene ontology terms, Int. J.     of Computational Intelligence, Vol 3, No. 3, 2006.
17. Hany Alashwal, Safaai Deris, Razib M. Othman, One-class support vector machines for protein-protein interaction     prediction, International journal of biomedical sciences, Vol 1, No 2, 2006.
18. Abdalla, S. O. and Deris, S. (2005). Combining Artificial Neural Networks and GOR V Information Theory to Predict Protein     Secondary Structure from Amino Acid Sequences. International Journal of Intelligent Information Technologies,     1(4), 53-72, 2005.
19. NM Zaki, S Deris, R Illias, Application of string kernels in protein sequence classification, Applied Bioinformatics, 4(1), 45-52,   2005.
20. Mohd Saberi Mohamad, Safaai Deris, Rosli Md Illias, A hybrid of genetic algorithm and support vector machine for feature selection and classification of gene expression microarray, International Journal of Computational Intelligence and Applications, Vol. 5, No. 1, 91-107, 2005. Imperial College Press.
21. Saad Osman Abdalla, Safaai Deris, Predicting secondary structure using artificial neural networks: current status and     future directions, Information Technology Journal, 4(2), 189-196, 2005
22. Saad Osman Abdalla, Safaai Deris, Mohamed Saberi, A hybrid classifier for protein secondary structure prediction,     Information Technology Journal 4(4), 433-438, 2005.
23. Zaki, N.M., Deris, S., Illias, R.M. and Arjunan, S.N.V., Feature extraction for protein homologies detection using Markov     Model combining scores, Int. J. of Computatational Intelligence (IJCIA), Vol 4, No. 1, pp 1-12, 2004.
24. Zaki, N.M., Deris, S., Illias, R.M. and Arjunan, S.N.V., Assignment of Protein Sequence to Functional Family Using Neural     Network and Dempster-Shafer Theory,  Journal of Theoretics, Vol 5, No. 1, 2003.
25. Zaki, N.M., Deris, S., Illias, R.M. and Arjunan, S.N.V., Comparative analysis of multi-class support vector machine     approaches, Journal of Theoretics, Vol 5, No. 4, 2003.
26. Satya Nanda Vel Arjunan, Safaai Deris, Rosli Md Illias, Prediction of Protein Secondary Structure, Jurnal Teknologi,  35(C), 81-90,     2001.
27. Satya Nanda vel Arjunan, Safaai Deris, Rosli Md Illias, Literature survey of protien structure prediction, Jurnal Teknologi, 2002.
28. Zaki, N.M., Deris, S., Illias, R.M. and Chin,  K.K., Composition of quadratic programming solvers in support vector machines     training, Jurnal Teknologi, Vol 39 (D), pp 45-56, 2003.

Planning and Scheduling

1. Asmuni, H., Burke, E.K., Garibaldi, J.M., McCollum, B. and Parkes, A. J., An Investigation of Fuzzy Multiple Heuristic Orderings in the Construction of University Examination Timetables. Computers & Operations Research, 36 (4). 2009, 981-1001. [2008 Impact Factor: 1.366]
2. Zalmiyah Zakaria, Safaai Deris, Penyelesaian masalah penjadualan yang dinamik dengan menggunakan pendekatan taakulan     berasaskan kes, Jurnal Teknologi, 2002.
3. Safaai Deris, Omatu, S., Ohta, H., Pathiah Abd Samat, University timetable planning by constraint-based reasoning - A case     study, J. of Operational Research Society, Vol. 48, No. 12, pp. 1178-1190, 1997.
4. Safaai Deris, Omatu, S., Ohta, H., and Pathiah Abd Samat, Ship maintenance scheduling by genetic algorithms and constraint-    based reasoning, European Journal of Operational Research, Vol.112, pp. 489-502, 1999.
5. Safaai Deris, Omatu, S., Ohta, and Puteh Saad, Incorporating constraint propagation in genetic algorithm for university     timetable planning, International Journal of Engineering Applications of Artificial Intelligence, Vol. 12, pp.241-253,     1999.
6. Safaai Deris, Omatu, S., Ohta, H., Timetable planning using the constraint-based reasoning, Computers and Operations     Research, Vol. 27, pp. 819-840, 2000.
7. Safaai Deris, and Ohta, H., A machine scheduling model for large scale rice production in Malaysia, Journal of Operational     Research Society, Vol. 14, No. 8, pp. 713 - 723, 1990.
8. Safaai Deris, Omatu, S., Ohta, H., and Pathiah Abd Samat, An object oriented constraint logic programming for timetable     planning, International Journal of System Science, Vol. 28, No. 10, pp. 987-999, 1997.
9. Safaai Deris, Omatu, S., and Ohta, H., Course scheduling and timetabling by constraint-based reasoning, Bulletin of the     University of Osaka Prefecture, Series A, Vol 44, No. 2, 1996.
10. Deris, S. and Ohta, H., On building an intelligent decision support system for agriculture production planning, Bulletin of the     University of Osaka Prefecture, Series A, Vol. 36, No. 1, 1987.
11. Deris, S. and Ohta, H., A computer assisted soil-crop suitability identification and classification (CASSIC), Bulletin of the     University of Osaka Prefecture, Series A, Vol. 36, No. 2, 1987.

Software Engineering

1. Radziah Mohamed, Safaai Deris, Hany H. Ammar, MaSE2Jadex: A Roadmap to engineer JADEX agents from MaSE     methodology, Int. Journal of Intelligent Technology, Vol 1, No. 3, 2006.
2. Radziah Mohamed, Safaai Deris, Hanny H. Ammar, Pattern-oriented design for multiagent system: A conceptual model, Journal     of Object Technology, 2006
3. Dayang Norhayati Abang Jawawi, Safaai Deris, Rosbi Mamat, Software reuse for mobile robot applications through analysis     pattern, The Int. Arab J. of of Information Technology, Vol. x No. x, 2006.
4. Dyg. Norhayati Abg. Jawawi, Safaai Deris,, Rosbi Mamat, A review of real-time software engineering methodologies for     developing a     wall-climbing robot control firmware, Elektrika, Vol. 3, No.1, pp.54-60, 2000
5. Dyg Norhayati Abg Jawawi, Safaai Deris, Rosbi Mamat,  A review of real-time software engineering methologies for developing     a wall-climbing robot control firmware, Elektrika, Journal of Electrical Engineering, Vol 3, No. 1, pp. 54-60
6. Mohd Razib Othman, Safaai Deris, Nur Azura Saleh, Formal method for distributed concurrent intelligent mobile agent system:     A survey of Belief-Desire-Intention model and logic-based representation and reasoning, Jurnal Teknologi     Maklumat, 2002.

Image Processing

1. Saad, P., Shamsuddin, S.M., Deris, S., and Mohamad, D, Rough Set on Trademark Images for Neural Network Classifier, Int. J.     of Computer Mathematics., Vol. 79, No 7, pp. 789-796, 2002.
2. Puteh Saad, Safaai Deris, Dzulkefli Mohamed, Siti Sakira Kamarudin, Habsah Abdullah, Trademark image registration – A review     of the current systems. Jurnal Teknologi Maklumat, Vol. 11, Bil. 1, pp. 81-95, 1999.