Bioinformatics

L.S. Yi, T.L. Chin, M.S. Mohamad, S. Deris, S. Subair, Z. Ibrahim, A Review on Metabolic Pathway Analysis in Biological Production, Mini-Reviews in Organic Chemistry, In Press, Bentham Science. (IF: 1.042)

W.H. Chan, M.S. Mohamad, S. Deris, J.M. Corchado, S. Omatu, Z. Ibrahim, S. Kasim. An Improved gSVM-SCADL2 with Firefly Algorihtm for Identification of Informative Genes and Pathways, International Journal of Bioinformatics Research and Applications, In Press, Inderscience. Indexed by Scopus.

P.W. Tang, P.S. Chua, S.K. Chong, M.S. Mohamad, S. Deris, Z. Ibrahim, S. Kasim, M.S. Shamsir, Z.A. Shah, H.M. Jamil. Software for Genomic DNA Sequence Alignment, International Journal of Bio-Sciences and Bio-Technology (IJBSBT), In Press, Science and Engineering Research Support Society. Indexed by Scopus.

W.S. Tham, S.K. Wong, M.S. Mohamad, K. Moorthy, S. Deris, M.F. Sjaugi, S. Omatu, J.M. Corchado, S. Kasim, A Review of Gene Selection Tools in Classifying Cancer Microarray Data, Current Bioinformatics, Vol. 10, (2015), In Press, Bentham Science. (IF: 0.921)

Hassan, R., Othman, R. M., & Shah, Z. A. (2015). Granular support vector machine to identify unknown structural classes of protein. International journal of data mining and bioinformatics, 12(4), 451-467.

Ibrahim, K.S. Lim, S. Buyamin, S.N. Satiman, M.H. Suib, B. Muhammad, M.R. Ghazali, M.S. Mohamad, J. Watada, MLPSO: Multi-Leader Particle Swarm Optimization for Multi-Objective Optimization Problems, ARPN Journal of Engineering and Applied Sciences, Vol. 10, No. 23, (2015), pp. 17533-17538, Asian Research Publishing Network (ARPN). Indexed by Scopus.

Ibrahim, M.I. Shapiai, S.N. Satiman, M.S. Mohamad, N.W. Arshad, A Complete Investigation of Using Weighted Kernel Regression for the Case of Small Sample Problem with Noise, ARPN Journal of Engineering and Applied Sciences, Vol. 10, No. 23, (2015), pp. 17514-17520, Asian Research Publishing Network (ARPN). Indexed by Scopus.

Muhammad, Z. Ibrahim, K.H. Ghazali, K.Z.M. Azmi, N.A.A. Aziz, N.H.A. Aziz, M.S. Mohamad, A New Hybrid Simulated Kalman Filter and Particle Swarm Optimization for Continuous Numerical Optimization Problems, ARPN Journal of Engineering and Applied Sciences, Vol. 10, No. 22, (2015), pp. 17171-17176, Asian Research Publishing Network (ARPN). Indexed by Scopus.

Ibrahim, N.H.A. Aziz, N.A.A. Aziz, S. Razali, M.I. Shapiai, S.W. Nawawi, M.S. Mohamad. A Kalman filter approach for solving unimodal optimization problems, ICIC Express Letters, Vol. 9, No.12, (2015), pp. 3415-3422, ICIC Express Letters Office. Indexed by Scopus.

M.Y. Man, M.S. Ong, M.S. Mohamad, S. Deris, G. Sulong, J. Yunus, F.K. Che Harun. A Review on the Bioinformatics Tools for Neuroimaging, Malaysian Journal of Medical Sciences, Vol. 22, (2015), pp. 8-18, Malaysian Journal of Medical Sciences. Indexed by Scopus.

M.A. Ismail, S. Deris, M.S. Mohamad, A. Abdullah, M.A. Remli, S.M. Mohi-Aldeen. A Hybrid of Optimization Method for Multi-Objective Constraint Optimization of Biochemical System Production, Journal of Theoretical and Applied Information Technology, Vol. 81, No. 3, (2015), pp. 502-513, Asian Research Publishing Network (ARPN). Indexed by Scopus.

M.A. Remli, S. Deris, M. Jamous, M.S. Mohamad, A. Abdullah, Service Composition Optimization Using Differential Evolution and Opposition-based Learning, Research Journal of Applied Sciences, Engineering and Technology, Vol. 11, No. 2, pp. 229-234, (2015). Indexed by Scopus.

C.S. Tan, W.S. Ting, S. Kasim, M.S. Mohamad, W.H. Chan, S. Deris, Z. Zakaria, Z.A Shah, Z. Ibrahim. A Review of Cancer Classification Software for Gene Expression Data, International Journal of Bio-Sciences and Bio-Technology (IJBSBT), Vol. 7, No. 4, (2015), pp. 89-108, Science and Engineering Research Support Society. Indexed by Scopus.

C.L. Koo, M.J. Liew, M.S. Mohamad, A.H.M. Salleh, S. Deris, Z. Ibrahim, B. Susilo, Y. Hendrawan, A.K. Wardani, Software for Detecting Gene-Gene Interactions in Genome Wide Association Studies, Biotechnology and Bioprocess Engineering, Vol. 20, No. 4, pp. 662-676, (2015), Springer. (IF: 1.113).

A.H.M. Salleh, M.S. Mohamad, S. Deris, S. Omatu, F. Fdez-Riverola, J.M. Corchado, Gene Knockout Identification for Metabolite Production Improvement Using a Hybrid of Genetic Ant Colony Optimization and Flux Balance Analysis, Biotechnology and Bioprocess Engineering, Vol. 20, No. 4, pp. 685-693, (2015), Springer. (IF: 1.113).

M.A. Remli, S. Deris, M. Jamous, M.S. Mohamad, A. Abdullah. Web Services Composition for Concurrent Plan Using Artificial Intelligence Planning, Journal of Theoretical and Applied Information Technology, Vol. 78, No. 2, (2015), pp. 228-235. Indexed by Scopus.

P.S. Chua, A.H.M. Salleh, M.S. Mohamad, S. Deris, S. Omatu, M. Yoshioka, Identifying a Gene Knockout Strategy Using a Hybrid of Bat Algorithm and Flux Balance Analysis to Enhance the Production of Succinate and Lactate in Escherichia Coli, Biotechnology and Bioprocess Engineering, Vol. 20, No. 2, pp. 349-357, Springer. (IF: 1.113).

M.A. Ismail, S. Deris, M.S. Mohamad, A. Abdullah, A Newton cooperative genetic algorithm method for in silico optimization of metabolic pathway production, PLoS ONE, Vol. 10. No. 5, (2015), ID e0126199, Public Library of Science. Indexed by ISI & Scopus.

S.K. Loh, S.T. Low, M.S. Mohamad, S. Deris, S. Kasim, Y.W. Choon, Z. Ibrahim, B. Susilo, Y. Hendrawan, A.K. Wardani. A Review of Software for Predicting Gene Function, International Journal of Bio-Sciences and Bio-Technology (IJBSBT), Vol. 7, No. 2, pp. 57-70, (2015), Science and Engineering Research Support Society. Indexed by Scopus.

S.J. Lu, F.F.M. Shah, M.S. Mohamad, K. Moorthy, S. Deris, Z. Zakaria, S. Napis, A Review on Bioinformatics Enrichment Analysis Tools towards Functional Analysis of High Throughput Gene Set Data, Current Proteomics, Vol. 12, No. 1, pp. 14-27, (2015), Bentham Science. Indexed by ISI & Scopus.

A.H.M. Salleh, M.S. Mohamad, S. Deris, R.M. Illias, Metabolites Production Improvement by Identifying Minimal Genomes and Essential Genes Using Flux Balance Analysis, International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 12, No. 1, pp. 85-99, (2015), Inderscience. Indexed by ISI & Scopus.

S.K. Wong, K. Moorthy, M.S. Mohamad, Biological Analysis of Microarray Data Using Orthogonal Forward Selection with a Clustering Approach, Journal of Biological Systems, Vol. 23, No. 2, pp. 275-288, (2015), World Scientific Publishing. Indexed by ISI & Scopus.

Y.W. Choon, M.S. Mohamad, S. Deris, C.K. Chong, S. Omatu, J.M. Corchado, Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis, BioMed Research International, Vol. 2015, ID 124537, 10 pages, (2015), Hindawi. Indexed by ISI & Scopus.

I.J. Aliaga, V. Vera, J.F. De Paz, A.E. Garcia, M.S. Mohamad, Modelling the Longevity of Dental Restorations by Means of a CBR System, BioMed Research International, Vol. 2015, ID 540306, 10 pages, (2015), Hindawi. Indexed by ISI & Scopus.

P.W. Tang, Y.W. Choon, M.S. Mohamad, S. Deris, S. Napis, Optimising the Production of Succinate and Lactate in Escherichia Coli Using a Hybrid of Artificial Bee Colony (ABC) Algorithm and Minimization of Metabolic Adjustment, Journal of  Bioscience and Bioengineering, Vol. 119, No. 3, pp. 363-368, (2015), Elsevier. Indexed by ISI & Scopus.

J.X. Yeoh, C.K. Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S. Mohamad. Parameter Estimation Using Improved Differential Evolution (IDE) and Bacterial Foraging Algorithm to Model Tyrosine Production in Mus Musculus (Mouse), Jurnal Teknologi, Vol. 72, No. 1, (2015), pp. 49-56. Indexed by Scopus.

C.K. Chong, M.S. Mohamad, S. Deris, M.S. Shamsir, Y.W. Choon, L.E. Chai, A Review on Modelling methods, Pathway Simulation Software and Recent Development on Differential Evolution Algorithms for Metabolic Pathways in Systems Biology, Current Bioinformatics, Vol. 9, No. 5, (2014), pp. 509-521. Indexed by ISI & Scopus.

Navarro, F. De La Prieta, G. Villarrubia, M.S. Mohamad,CronoClock: A Multiagent Mobile Model to Assist Drivers in Park Zones, ACCAIJ: Advances in Distributed Computing and Artificial Intelligence Journal, Vol. 3, No. 8, (2014), pp. 38-45.

S.J. Lu, A.H.M. Salleh, M.S. Mohamad, S. Deris, S. Omatu, M. Yoshioka, Identification of Gene Knockout Strategies using a Hybrid of an Ant Colony Optimization Algorithm and Flux Balance Analysis to Optimize Microbial Strains, Computational Biology and Chemistry, Vol. 53, Part B, Dec 2014, pp. 175-183. Indexed by ISI & Scopus.

C.S. Tan, W.S. Ting, M.S. Mohamad, W.H. Chan, S. Deris, Z.A. Shah, A Review of Feature Extraction Software for Microarray Gene Expression Data, BioMed Research International, Vol. 2014, ID 213656, 15 pages, (2014), doi: 10.1155/2014/213656. Indexed by ISI & Scopus.

Adam, M.I. Shapiai, M. Mubin, M.Z.M. Tumari, M.S. Mohamad, Feature Selection and Classifier Parameters Estimation for EEG Signals Peak Detection Using Particle Swarm Optimization, The Scientific World Journal, Vol. 2014, ID 973063, 13 pages, (2014), doi : 10.1155/2014/973063. Indexed by ISI & Scopus.

S.J. Lu, F.F.M. Shah, M.S. Mohamad, N.L. Hamran, A.H.M Salleh, S. Deris, H. Alashwal, Database and Tools for Metabolic Network Analysis, Biotechnology and Bioprocess Engineering, Vol. 19, No. 4, (2014), pp. 568-585. Indexed by ISI & Scopus.

L.E. Chai, M.S. Mohamad, S. Deris, C.K. Chong, Y.W. Choon, S. Omatu, Current Development and Review of Dynamic Bayesian Network-based Methods for Inferring Gene Regulatory Networks from Gene Expression Data, Current Bioinformatics, Vol. 9, No. 5, (2014), pp. 531-539. Indexed by ISI & Scopus.

Y.W.Choon, M.S. Mohamad,S.Deris,R.M. Illias,C.K.Chong, L.E. Chai, S. Omatu, J.M. Corchado, Differential Bees Flux Balance Analysis with OptKnock for in Silico Microbial Strains Optimization, PLoS ONE, Vol. 9, No. 7, Id e102744, (2014), doi: 10.1371. Indexed by ISI & Scopus.

M.A. Ismail, S. Deris, M.S. Mohamad, A. Abdullah, A Hybrid of Newton Method and Genetic Algorithm for Constrained Optimization Method of the Production of Metabolic Pathway, Life Science Journal, Vol. 11, No. 9s, (2014), pp. 409-414. Indexed by Scopus.

S.K. Chong, M.S. Mohamad, A.H.M. Salleh, Y.W. Choon, C.K. Chong, S. Deris, A Hybrid of Ant Colony Optimization and Minimization of Metabolic Adjustment to Improve the Production of Succinic Acid in Escherichia Coli, Computers in Biology and Medicine, Vol. 49, (2014). pp. 74-89. Indexed by ISI & Scopus.

C.K. Chong, M.S. Mohamad, S. Deris, M.S. Shamsir, A. Abdullah, An Improved Differential Evolution Algorithm for Enhancing Biochemical Pathways Simulation and Production, Int. J. Data Mining and Bioinformatics, Vol. 10, No. 4, (2014), pp. 424-439. Indexed by ISI & Scopus.

Fotoohifiroozabadi, S. Deris, M.S. Mohamad, J. Razmara, A Review on Linear Encoding Methods and Geometry Based Methods for Protein Structure Alignment, Life Science Journal, Vol. 11, No. 3s, (2014), pp. 202-206.Indexed by Scopus.

M.F. Misman, M.S. Mohamad, S. Deris, S.Z.M. Hashim, A Group-Specific Tuning Parameter for Hybrid of SVM and SCAD in Identification of Informative Genes and Pathways, International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 10, No. 2. (2014), pp. 146-160. Indexed by ISI & Scopus.

Y.W. Choon, M.S. Mohamad, S. Deris, R.M. Illias, A Hybrid of Bees Algorithm and Flux Balance Analysis (BAFBA) for the Optimization of Microbial Strains, International Journal of Data Mining and Bioinformatics (IJDMB), Vol. 10, No. 2. (2014), pp. 225-238. Indexed by ISI & Scopus.

L.E. Chai, S.K. Loh, S.T. Low,M.S. Mohamad, S. Deris, Z. Zakaria, A Review on the Computational Approaches for Gene Regulatory Network Construction, Computers in Biology and Medicine, Vol. 48, (2014), pp 55-65. Indexed by ISI & Scopus. Top 5 (No. 3) downloaded article in Computers in Biology and Medicine on 2014.

Moorthy, M.S. Mohamad, S. Deris, A Review on Missing Value Imputation Algorithms for Microarray Gene Expression Data, Current Bioinformatics, Vol. 9, No. 1, (2014), pp. 18-22. Indexed by ISI & Scopus.

C.K. Chong, M.S. Mohamad, S. Deris, M.S. Shamsir, L.E. Chai, Y.W. Choon, Parameter Estimation by Using an Improved Bee Memory Differential Evolution Algorithm (IBMDE) to Simulate Biochemical Pathways, Current Bioinformatics, Vol. 9, No. 1, (2014), pp. 65-75. Indexed by ISI & Scopus.

C.K.Chong, M.S. Mohamad, S. Deris, M.S. Shamsir, Y.W. Choon, L.E. Chai, Using An Improved Bee Memory Differential Evolution Algorithm for Parameter Estimation to Simulate Biochemical Pathways, Journal of Biological Systems, Vol. 22, No.1. (2014), pp. 101-121. Indexed by ISI & Scopus.

Y.W. Choon, M.S. Mohamad, S. Deris, R.M. Illias,C.K. Chong, L.E. Chai, A Hybrid of Bees Algorithm and Flux Balance Analysis with OptKnock as a Platform for in Silico Optimization of Microbial Strains, Bioprocess and Biosystems Engineering, Vol. 37, No. 3, (2014), pp. 521-532. Indexed by ISI & Scopus.

L.H. Yin, Y.W. Choon, M.S. Mohamad, L.E. Chai, C.K. Chong, A. Abdullah, S. Deris, R.M. Illias, Prediction of Vanillin and Glutamate Productions in Yeast Using a Hybrid of Continuous Bees Algorithm and Flux Balance Analysis (CBAFBA), Current Bioinformatics, Vol. 9, No. 3, (2014), pp. 284-294. Indexed by ISI & Scopus.

N.A.A. Aziz, M. Mubin, M.S. Mohamad, .K.A. Aziz, A Synchronous-Asynchronous Particle Swarm Optimisation Algorithm, The World Scientific Journal, Vol. 2014, 17 pages, (2014), doi : 10.1155/2014/123019. Indexed by ISI & Scopus.

L.E. Chai,  M.S. Mohamad,  S. Deris,  C. K. Chong,  Y. W. Choon,  S. Omatu, A Dynamic Bayesian Network-Based Model for Inferring Gene Regulatory Networks from Gene Expression Data, International Journal of BioSciences and Biotechnology (IJBSBT), Vol. 6, No. 1, (2014). pp. 41-52. Indexed by Scopus.

L.E. Chai,C.K. Law, M.S. Mohamad, C.K. Chong, Y.W. Choon, S. Deris, R.M. Illias, Investigating the Effects of Imputation Methods for Modelling Gene Networks Using a Dynamic Bayesian Network from Gene Expression Data, The Malaysian Journal of Medical Sciences : MJMS, Vol. 21, No. 2, (2014), pp. 20- 27. Indexed by Scopus.

C.L. Koo, M.J. Liew, M.S. Mohamad, A.H.M. Salleh, A Review for Detecting Gene-Gene Interactions using Machine Learning Methods in Genetic Epidemiology, BioMed Research International,Vol. 2013, (2013), pp. 1-13. Indexed by ISI & Scopus.

M.S. Mohamad, S. Omatu, S. Deris, Michifumi Yoshioka, A. Abdullah, Z. Ibrahim, An Enhancement of Binary Particle Swarm Optimization for Gene Selection in Classifying Cancer Classes, Algorithms for Molecular Biology, Vol. 8, (2013), No. 1, pp. 1-11. Indexed by ISI & Scopus.

Abdullah, S. Deris, M.S. Mohamad, S. Anwar, An Improved Swarm Optimization for Parameter Estimation and Biological Model Selection, PLoS ONE, Vol.8, No. 4, (2013), pp.e61258. Indexed by ISI & Scopus.

W.H. Chan, M.S. Mohamad, S. Deris and R. M. Illias, A Review of Computational Approaches for In Silico Metabolic Engineering for Microbial Fuel Production, Current Bioinformatics, Vol. 8, No. 2, (2013), pp. 253-258. Indexed by ISI & Scopus.

Abdullah, S. Deris, M.S. Mohamad, S.Z.M. Hashim, A New Particle Swarm Evolutionary Optimization for Parameter Estimation of Biological Models, International Journal of Computer Information Systems and Industrial Management Applications, Vol. 5, (2013),pp. 571-580. Indexed by  Scopus.

A.H.A. Rashid, Y.W. Choon, M.S. Mohamad, L.E. Chai, C.K. Chong, S. Deris, R.M. Illias, Producing Succinic Acid in Yeast using A Hybrid of Differential Evolution and Flux Balance Analysis, International Journal of Bio-Sciences and Bio-Technology (IJBSBT), Vol. 5, No. 6. (2013), pp. 91-100. Indexed by Scopus.

S.T. Ng, C.K. Chong, Y.W. Choon, L.E. Chai, S. Deris, R.M. Illias, M.S. Shamsir, M.S. Mohamad, Estimating Kinetic Parameters for Essential Amino Acid Production in ArabidopsisThaliana by Using Particle Swarm Optimization, Jurnal Teknologi (Sciences and Engineering), Vol. 64, No. 1. (2013), pp. 73-80. Indexed by Scopus.

A.H.M. Salleh, M.S. Mohamad, S. Deris, R.M. Illias, A Review on Pathway Analysis Software Based On Microarray Data Interpretation, International Journal of BioSciences and BioTechnology (IJBSBT),Vol. 5, No. 4. (2013), pp. 149-157. Indexed by Scopus.

Abdullah, S. Deris, M.S. Mohamad, A New Hybrid Bee Evolution Algorithm for parameter Estimation in Biological Model, ICIC Express Letter Part B: Application, Vol. 4, No. 1, (2013), pp. 1-6. Indexed by Scopus.

L.F. Tee, M.S. Mohamad, S. Deris, A.A.M. Faudzi, M.S.A. Latiff, R. Sallehuddin, Validation of Hierarchical Gene Clusters Using Repeated Measurements, Jurnal Teknologi, Vol. 61. No. 1, (2013), pp. 7-12. Indexed by Scopus.

S.P. Chai, M.S. Mohamad, A Method To Construct Gene Regulatory Networks To Estimate and Calculate Time Delay, Jurnal Teknologi, Vol. 62, No. 1, (2013), pp. 25-31. Indexed by Scopus.

Y.Y. Leong, C.K. Chong, L.E. Chai, S. Deris, R. Illias, S. Omatu, M.S. Mohamad, Simulation of Fermentation Pathway Using Bees Algorithm, ADCAIJ: Advances in Distributed Computing and Artificial Intelligence Journal, Vol. 1, No. 2, (2013), pp. 13-19.

M.F.M. Saaid, S. Sudin, I. Ibrahim, Z.M. Yusof, K. Khalil, J.A.A. Mukred, M.S. Mohamad, N. Mokhtar, Z. Ibrahim, J. Watada, Automation of DNA Computing Readout Method Based on Real-Time PCR Implemented on DNA Engine Opticon 2 System, International Journal of Innovative Computing, Information and Control, Vol. 8, No. 3(A), (2012), pp. 1907-1916. Indexed by Scopus.

H. M. Salleh, M.S. Mohamad, Metabolic Pathway Extraction Using Combined Probabilistic Models, International Journal of BioSciences and BioTechnology (IJBSBT), Vol. 4, No. 2, (2012), pp. 1–10. Indexed by Scopus.

A.K. Tan, M.S. Mohamad, Using Bayesian Networks to Construct Gene Regulatory Networks From Microarray Data, Jurnal Teknologi, Vol. 58, (2012), pp. 1-6. Indexed by Scopus.

C.Y. Fai, R. Hassan, M.S. Mohamad, Protein Secondary Structure Prediction Using Optimal Local Protein Structure Based SVM, International Journal of BioSciences and BioTechnology (IJBSBT), Vol. 4, No. 2, (2012), pp. 35–44. Indexed by Scopus.

M.S. Mohamad, S. Omatu, S. Deris, M. Yoshioka, Z. Ibrahim, Selecting a Small Subset of Informative Genes from Gene Expression Data by Using a Modified Binary Particle Swarm Optimization, International Journal of Innovative Computing, Information and Control, Vol. 8, No. 6, (2012), pp. 4285-4297. Indexed by ISI & Scopus.

Ibrahim, N.K. Khalid, S. Buyamin, J. Abdulla, A. Mukred, Z.M. Yusof, M.S. Mohamad, K. Khalil, M.F.M. Saaid, N. Mokhtar, J. Watada, A. Engelbrecht, DNA Sequence Design for DNA Computation based on Binary Particle Swarm Optimization, International Journal of Innovative Computing, Information and Control, Vol. 8, No. 5(B), (2012), pp. 3341-3450. Indexed by Scopus.

M.F. Misman, M.S. Mohamad, S. Deris, S.Z.M. Hashim, N. Leham, Z. Ibrahim, A Tuning Parameter Selector Method for the gSVM-SCAD in Determining Significant Genes and Biological Pathways, ICIC Express Letters, Vol 6, No.4, (2012), pp. 851-856. Indexed by Scopus.

C.H. Shi, M.S. Mohamad, S. Deris, Z. Ibrahim, A Pathway-Based Approach for Analyzing Microarray Data using Random Forests, ICIC Express Letters (ICIC-EL), Vol 6, No.5, (2012), pp. 1253-1257. Indexed by Scopus.

Moorthy, M.S. Mohamad, S. Deris, Z. Ibrahim, Multivariate Analysis of Gene Expression Data and Missing Value Imputation Based On LLSimpute Algorithms, ICIC Express Letters (ICIC-EL), Vol 6, No.5, (2012), pp.1335-1339. Indexed by Scopus.

Z.M. Yusof, A.F.Z. Abidin, A. Adam, K. Khalil, J.A.A Mukred, M.S. Mohamad, Z. Ibrahim, A Two-Step Binary Particle Swarm Optimization Approach for Routing in VLSI, ICIC Express Letters (ICIC-EL), Vol 6, No.3, (2012), pp.771-776. Indexed by Scopus.

Ibrahim, S.A.R.S.A Bakar, M.M. Mokji, K. Khalil, Z.M. Yusof, J.A.A. Mukred, M.S. Mohamad, Z. Ibrahim, An Image Registration Technique to Enhance PCB Inspection Algorithm with Real Images, ICIC Express Letters (ICIC-EL), Vol 6, No.3, (2012), pp. 717-722. Indexed by Scopus.

M.I. Shapiai, Z. Ibrahim, S. Sudin, M.S. Mohamad, M. Khalid, Investigation on Different Learning Techniques for Weighted Kernel Regression in Solving Small Sample Problem, ICIC Express Letters (ICIC-EL), Vol 6, No.3, (2012), pp. 705-710. Indexed by Scopus.

Roslan, R., Othman, R.M., Shah, Z.A., Kasim, S., Asmuni, H., Taliba, J., Hassan, R. and Zakaria, Z., 2010. Incorporating multiple genomic features with the utilization of interacting domain patterns to improve the prediction of protein–protein interactions. Information Sciences, 180(20), pp.3955-3973.

Roslan, R., Othman, R.M., Shah, Z.A., Kasim, S., Asmuni, H., Taliba, J., Hassan, R. and Zakaria, Z., 2010. Utilizing shared interacting domain patterns and Gene Ontology information to improve protein–protein interaction prediction. Computers in biology and medicine, 40(6), pp.555-564.

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.

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.

Roslan, R., Othman, R.M., Shah, Z.A., Kasim, S., Asmuni, H., Taliba, J., Hassan, R. and Zakaria, Z., 2010. Incorporating multiple genomic features with the utilization of interacting domain patterns to improve the prediction of protein–protein interactions. Information Sciences, 180(20), pp.3955-3973.

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.

Kalsum, H.U., Shah, Z.A., Othman, R.M., Hassan, R., Rahim, S.M., Asmuni, H., Taliba, J. and Zakaria, Z., 2009. SPlitSSI-SVM: An algorithm to reduce the misleading and increase the strength of domain signal. Computers in biology and medicine, 39(11), pp.1013-1019.

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]

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.

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]

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.

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.

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.

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.

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.

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.

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.

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.

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.

Razib M. Othman, Safaai Deris, Rosli M. Ilias, Hany T. Alashwal, Rohayanti Hassan, and Farhan Mohamed, Incorporation     semantic similarity measure in genetic algorithm: An approach for searching the gene ontology terms, Int. J.     of Computational Intelligence, Vol 3, No. 3, 2006.

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.

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.

NM Zaki, S Deris, R Illias, Application of string kernels in protein sequence classification, Applied Bioinformatics, 4(1), 45-52, 2005.

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.

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

Saad Osman Abdalla, Safaai Deris, Mohamed Saberi, A hybrid classifier for protein secondary structure prediction, Information Technology Journal 4(4), 433-438, 2005.

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 Computational Intelligence (IJCIA), Vol 4, No. 1, pp 1-12, 2004.

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.

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.

Satya Nanda Vel Arjunan, Safaai Deris, Rosli Md Illias, Prediction of Protein Secondary Structure, Jurnal Teknologi, 35(C), 81-90, 2001.

Satya Nanda vel Arjunan, Safaai Deris, Rosli Md Illias, Literature survey of protein structure prediction, Jurnal Teknologi, 2002.

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.