Razib Othman: Difference between revisions

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===Education===
===Education===
[[Image:Razib2.jpg|right]]
[[Image:razib3.png|right]]
* 2008, PhD (Computer Science), Universiti Teknologi Malaysia.
* 2008, PhD (Computer Science), Universiti Teknologi Malaysia.
* 2003, MSc (Computer Science), Universiti Teknologi Malaysia.
* 2003, MSc (Computer Science), Universiti Teknologi Malaysia.
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===Research Interests===
===Prospective Students===
# Research in [http://en.wikipedia.org/wiki/Computational_biology Computational Biology]:
# If you are interested in pursuing a PhD in CLOUD COMPUTING (not limited to software engineering, artificial intelligence, security, networking, software architecture) or AGILE UNIFIED PROCESS (AUP), please contact [mailto:razib@utm.my '''Razib M. Othman ''']
#* Protein Domain Detection.
# Sponsorship is provided (for Malaysian only) - [http://www.gates.my/ GATES Scholar Foundation]
#* Remote Protein Homology Detection.
#* Protein Structure Prediction.
#* Protein-Protein Interaction Prediction.
#* Gene Expression Analysis.
# Research in [http://en.wikipedia.org/wiki/Computational_intelligence Computational Intelligence]:
#* Multi-Agent System.
#* Ontology.
#* Fuzzy Logic.
#* Genetic Algorithm.
#* Support Vector Machines.
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===Awards (2003-present)===
===Publications===
# Gold Medal, 34th International Exhibition of Invention New Techniques and Products (2006), Geneva, Switzerland.
# Hassan R., Othman R.M., Saad P., and Kasim S. (2011). A Compact Hybrid Feature Vector for an Accurate Secondary Structure Prediction. Information Sciences [Elsevier; impact factor 2011: 2.833] 181(23): 5267-5277.
# The Best Invention of the Pacific Rim Award, 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
# Muda H.M., Saad P., and Othman R.M. (2011). Remote Protein Homology Detection and Fold Recognition Using Two-Layer Support Vector Machine Classifiers. Computers in Biology & Medicine [Elsevier; impact factor 2011: 1.089] 41(8): 687-699.  
# Silver Medal (Engineering Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
# Roslan R., Othman R.M., Shah Z.A, Kasim S., Asmuni H., Taliba J., Hassan R., and Zakaria Z. (2010). Incorporating Multiple Genomics Features with the Utilization of Interacting Domain Patterns to Improve Protein-Protein Interactions Prediction. Information Sciences [Elsevier; impact factor 2010: 2.833] 180(20): 3955-3973.
# Silver Medal (Design Technical Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
# 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 & Medicine [Elsevier; impact factor 2010: 1.112] 40(6): 555-564.
# Bronze Medal (Automotive Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
# Hassan U.K., Shah Z.A., Othman R.M., Hassan R., Rahim M.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 & Medicine [Elsevier; impact factor 2009: 1.269] 39(11): 1013-1019.
# Bronze Medal (Computer Software Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
# Othman R.M., Deris S., and Illias R.M. (2008). A Genetic Similarity Algorithm for Searching the Gene Ontology Terms and Annotation of Anonymous Protein Sequences. Journal Biomedical Informatics [Elsevier; impact factor 2008: 1.924] 41(1): 65-81.
# Bronze Medal, 6th Malaysia Technology Expo (2007), Kuala Lumpur, Malaysia.
# Taliba J., Othman R.M., Hassan U.K., and Roslan R. (2011). A Hybrid Ranking Method for Constructing Negative Datasets of Protein-Protein Interactions. Journal of Computing 3(11): 3(11): 48-55.
# Gold Medal, 5th Malaysia Technology Expo (2006), Kuala Lumpur, Malaysia.
# Ismail A.M., Asmuni H., and Othman R.M. (2011). The Fuzzy Cooperative Genetic Algorithm (FCoGA): The Optimisation of a Fuzzy Model Through Incorporation of a Cooperative Coevolutionary Method. Journal of Computing 3(11): 81-90.
# Gold Medal, 3rd Public Institutions of Higher Learning Research and Development Expo (2005), Kuala Lumpur, Malaysia.
# Ismail S., Othman R.M., Kasim S., Hassan R, Asmuni H., and Taliba J. (2011). Pairwise Protein Substring Alignment with Latent Semantic Analysis and Support Vector Machines to Detect Remote Protein Homology. International Journal of Bio-Science and Bio-Technology 3(3): 17-34.
# The Best Invention, 8th Industrial Art and Technology Exhibition (2005), Skudai, Malaysia.
# Abdullah F.M., Othman R.M., Kasim S., Hashim R., Hassan R, Asmuni H., and Taliba J. (2011). An Optimal Mesh Algorithm for Remote Protein Homology Detection. International Journal of Bio-Science and Bio-Technology 3(2): 13-38.
# Gold Medal, 8th Industrial Art and Technology Exhibition (2005), Skudai, Malaysia.
# Kasim S., Deris S., Othman R.M,, and Hashim R. (2011). Biological-Based Semi-Supervised Clustering Algorithm to Improve Gene Function Prediction. Journal of Computing 3(4): 1-11.
# Finalist of Malaysian Innovation Award 2006 by Malaysian Ministry of Science, Technology, and Innovation.
# Mohamad N.N., Amin I.M., Othman R.M., Asmuni H., Hassan R., and Kasim S. (2012). Design and Implementation of Product Structure Ontology. In Nazir M.A., Colomb R.M., and Syazwan M.A. (eds), Ontology-Based Applications for Enterprise Systems and Knowledge Management, pp 246-260.
# Excellence Scientist Recognition Award 2006 bestowed by Malaysian Ministry of Higher Education.
# Ismail S., Othman R.M., and Kasim S. (2011). Pairwise Protein Substring Alignment with Latent Semantic Analysis and Support Vector Machines to Detect Remote Protein Homology. In Kim T.-h., Adeli H., Robles R.J., and Balitanas M. (eds), Communications in Computer and Information Science: Ubiquitous Computing and Multimedia Applications 151(Part 2): 526-546.
# Young Researcher 2005 bestowed by Malaysian Association of Research Scientists.
# Abdullah F.M., Othman R.M., Kasim S., and Hashim R. (2011). An Optimal Mesh Algorithm for Remote Protein Homology Detection. In Kim T.-h., Adeli H., Robles R.J., and Balitanas M. (eds), Communications in Computer and Information Science: Ubiquitous Computing and Multimedia Applications 151(Part 2): 471-497.
# Excellence Scientist Recognition Award 2005 bestowed by Malaysian Ministry of Higher Education.
# Kasim S., Deris S., and Othman R.M. (2010). A New Computational Framework for Gene Expression Clustering. In Cao L., Feng Y., and Zhong J. (eds), Lecture Notes in Computer Science: Advanced Data Mining and Applications 6440(2010): 603-610.
# The Best Research Group Award 2006 bestowed by Universiti Teknologi Malaysia.
# Zafar F.M., Mohamad D., and Othman R.M. (2010). Performance Analysis of a Proposed Smoothing Algorithm for Isolated Handwritten Characters. International Journal of Artificial Intelligence and Soft Computing 2(3): 186-198.
# The Best Fundamental Research Award 2005 bestowed by Universiti Teknologi Malaysia.
# Zafar F.M., Mohamad D., Rab A., and Othman R.M. (2009). Application of a Proposed Efficient Smoothing Algorithm on Directional Vectors for Isolated Handwritten Characters. In Hussain D.M.A., Rajput A.Q.K., Chowdhry B.S., and Gee Q. (eds), Communications in Computer and Information Science: Wireless Networks, Information Processing and Systems 20(1): 52-63.
# Researcher Recognition Award 2005 bestowed by Universiti Teknologi Malaysia.
# Alashwal H.T., Deris S., and Othman R.M. (2009). A Bayesian Kernel for the Prediction of Protein-Protein Interactions. International Journal of Information and Mathematical Sciences 5(2): 119-124.
# Excellence Service Award 2007 bestowed by Universiti Teknologi Malaysia.
# Othman R.M., Hassan U.K., Hassan R., Asmuni H., Taliba J., and Kasim S. (2012). BRNN-SVM: Increasing the Strength of Domain Signal to Improve Protein Domain Prediction Accuracy. Recurrent Neural Network. Eds Elhefnawi M. and Mysara M. InTech. Rijeka, Croatia, pp. 133-150.
# Excellence Service Award 2005 bestowed by Universiti Teknologi Malaysia.
# Abdullah F.M. and Othman R.M. (2012). Multiple Alignments, Hidden Markov Models and SVMs: Development of a Computational Framework for Protein Homology Detection by Incorporating Realignment Algorithm. LAP LAMBERT Academic Publishing. Saarbrücken, Germany.
# Excellence Service Award 2003 bestowed by Universiti Teknologi Malaysia.
# Mohamad N.N. and Othman R.M. (2012). Knowledge Formalization and Information Retrieval: Product Structure Ontology to Support Semantic Search in Manufacturing Requirements Management. LAP LAMBERT Academic Publishing. Saarbrücken, Germany.
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===Publications (2006-present)===
===Reviewer of Scientific Journals===
# Kasim S., Deris S., Othman R.M., Shah Z.A., and Hassan R. (under review). Gene Ontology Based Biclustering in Gene Expression Data.
# [http://www.springer.com/springerwiennewyork/life+sciences/journal/726 Amino Acids] (Springer; impact factor 2009: 3.877; no of paper reviewed: 1; last reviewed: 2009)
# Kasim S., Deris S., Othman R.M., and Shah Z.A. (under review). Guidelines to Select Gene Ontology Data Formats and Traversal Methods.
# [http://www.elsevier.com/wps/find/journaldescription.cws_home/505627/description#description Artificial Intelligence in Medicine] (Elsevier; impact factor 2010: 1.568; no of paper reviewed: 1; last reviewed: 2010)
# Hassan K.U., Othman R.M., Shah Z.A., and Hassan R. (under review). Predict Protein Domain from Secondary Structure Information Based on Support Vector Machines.
# [http://www.journals.elsevier.com/computers-in-biology-and-medicine Computers in Biology and Medicine] (Elsevier; impact factor 2011: 1.089; no of paper reviewed: 6; last reviewed: 2012)
# Ismail S., Othman R.M., Zaki N.M., Yatim S.M., and Taliba J. (under review). Pairwise Substring with Latent Semantic Analysis and Support Vector Machines to Detect Remote Protein Homology. 
# [http://www.elsevier.com/wps/find/journaldescription.cws_home/622857/description#description Journal of Biomedical Informatics] (Elsevier; impact factor 2010: 1.719; no of paper reviewed: 3; last reviewed: 2010)
# Othman R.M., Deris S., and Illias R.M. (2008). A Genetic Similarity Algorithm for Searching the Gene Ontology Terms and Annotation of Anonymous Protein Sequences. Journal Biomedical Informatics [impact factor 2007: 2.000] 41(1): 65-81.
# [http://www.ploscompbiol.org/ PLoS Computational Biology] (PLoS.org; impact factor 2011: 5.215; no of paper reviewed: 3; last reviewed: 2012)
# Othman R.M. (2007). Genetic Algorithms for Gene Ontology-Based Protein Sequence Annotation. PhD Thesis: Universiti Teknologi Malaysia.
# [http://onlinelibrary.wiley.com/journal/10.1002/(ISSN)1097-0134/ Proteins: Structure, Function, and Bioinformatics] (Wiley; impact factor 2011: 3.392; no of paper reviewed: 1; last reviewed: 2011)
# Othman R.M., Deris S., and Illias R.M. (2006). Computational Method for Annotation of Protein Sequence According to Gene Ontology Terms. Int'l Journal Biomedical Sciences 1(3): 186-199 [a [http://www.geneontology.org/cgi-bin/biblio.cgi GO Bibliography]].
# [http://www.benthamscience.com/cbio/ Current Bioinformatics] (Bentham Science; impact factor 2011: 0.898; no of paper reviewed: 2; last reviewed: 2012)
# Othman R.M., Deris S., and Illias R.M. (2006). UTMGO: A Tool for Searching a Group of Semantically Related Gene Ontology Terms and Application to Annotation of Anonymous Protein Sequence. Int'l Journal Biomedical Sciences 1(2): 111-119 [a [http://www.geneontology.org/cgi-bin/biblio.cgi GO Bibliography]].
# [http://www.benthamscience.com/ppl/ Protein & Peptide Letters] (Bentham Science; impact factor 2011: 1.942; no of paper reviewed: 1; last reviewed: 2012)
# Alashwal H.T., Deris S., and Othman R.M. (2006). One-Class Support Vector Machines for Protein-Protein Interactions Prediction. Int'l Journal Biomedical Sciences 1(2): 120-127.
# Ahmed M.M., Ahmad A.M., Othman R.M., and Khan S. (2006). Speech Signal Endpoint Detection Using Hidden Markov Models. Journal Quality and Technology Management 2: 35-39.
# Othman R.M., Deris S., Illias R.M., Alashwal H.T., Hassan R., and Mohamed F. (2006). Incorporating Semantic Similarity Measure in Genetic Algorithm: An Approach for Searching the Gene Ontology Terms. Int'l Journal Computational Intelligence 3(3): 257-266 [a [http://www.geneontology.org/cgi-bin/biblio.cgi GO Bibliography]].
# Othman R.M., Deris S., Illias R.M., Zakaria Z., and Mohamad S.M. (2006). Automatic Clustering of Gene Ontology by Genetic Algorithm. Int'l Journal Information Technology 3(1): 37-46 [a [http://www.geneontology.org/cgi-bin/biblio.cgi GO Bibliography]].
# Alashwal H.T., Deris S., and Othman R.M. (2006). Comparison of Domain and Hydrophobicity Features for the Prediction of Protein-Protein Interactions Using Support Vector Machines. Int'l Journal Information Technology 3(1): 18-24.
# Zafar M.F., Mohamad Z., and Othman R.M. (2006). Writer Independent Online Handwritten Character Recognition Using a Simple Approach. Information Technology Journal 5(3): 476-484.
# Zafar M.F., Mohamad Z., and Othman R.M. (2005). Online Handwritten Character Recognition: An Implementation of Counterpropagation Neural Net. Trans Engineering, Computing, and Technology 10(1): 232-237.
# Alashwal H.T., Deris S., Othman R.M., and Mohamad S.M. (2006). One-Class Classifier to Predict Protein-Protein Interactions Based on Hydrophobicity Properties. In Proc 2nd Int'l Symp. Biomedical Engineering (ISBME'06), Bangkok, Thailand. pp 63-66.
# Alashwal H.T., Deris S., and Othman R.M. (2006). Proteins Interactions from Protein Sequence Features Using Support Vector Machines. Accepted at the Int'l Conf Bioinformatics & Computational Biology (BIOCOMP'06), Las Vegas, USA.
# Alashwal H.T., Deris S., and Othman R.M. (2006). Support Vector Machines for Predicting Protein-Protein Interactions Using Domains and Hydrophobicity Features. In Abstract Book Int'l Conf Computing & Informatics (ICOCI'06), Kuala Lumpur, Malaysia, pp. 31.
# Zafar M.F., Mohamad Z., and Othman R.M. (2006). Neural Nets for On-line Isolated Handwritten Character  Recognition: A Comparative Study. In Proc IEEE  Int'l  Conf Engineering of Intelligent Systems (ICEIS'2006), Islamabad, Pakistan. pp 1-6.
# Mohamad Z., Zafar M.F., and Othman R.M. (2006). On-Line Cursive Handwriting Recognition: A Survey of Methods and Performances. In Proc 4th Int'l Multiconf Computer Science & Information Technology (CSIT'06), Amman, Jordan. pp 70-84.
# Zakaria Z., Deris S., Othman R.M., and Yatim S.M. (2008). The Development of Integrated Planning and Scheduling Framework for Dynamic and Reactive Environment of Complex Manufacturing Problem. Technical Report 01-01-06-SF0004: Universiti Teknologi Malaysia.
# Othman R.M., Deris S., Illias R.M., and Yatim S.M. (2007). The Development of Machine Learning Based Software for Predicting Protein-Protein Interactions and Protein Function from Protein Primary Structure. Technical Report 04-02-06-10049-EAR: Universiti Teknologi Malaysia.
# Samsudin R., Deris S., Othman R.M., Illias R.M., and Yatim S.M. (2007). The Development of Semantic Meta-Database: An Ontology Based Semantic Integration of Biological Databases. Technical Report 04-02-06-10050-EAR: Universiti Teknologi Malaysia.
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===Grants (2003-present)===
===Graduate Students===
# Manufacturing Requirements Management System. Funded by ZILUN Systems Sdn Bhd. Grant no: 63681. Amount: MYR168,000. Duration: 12 months (Apr 2008 - Mar 2009).
# [mailto:jumail@cs.utm.my '''Jumail Taliba '''], PhD - Protein-Protein Interaction Prediction
# Vessel Chartering Management System. Funded by ZILUN Systems Sdn Bhd. Grant no: 63680. Amount: MYR33,000. Duration: 12 months (May 2008 - Apr 2009).
# [mailto:candy_shm@hotmail.com '''Sim Hiew Moi '''], PhD - Off-Angle Method in Iris Recognition
# Manufacturing Process Structure. Funded by ZILUN Systems Sdn Bhd. Grant no: 63673. Amount: MYR48,000. Duration: 12 months (Apr 2008 - Mar 2009).
# [mailto:asyrafacabz@yahoo.com '''Muhamad Asyraf Mohd Pouzi '''], MSc - Vegetation Classification in Mixed-Land Zones
# The Development of Clustering System for Protein Tertiary Structure Prediction Using Machine Learning Algorithms. Funded by Malaysian Ministry of Science, Technology, and Innovation under ScienceFund. Grant no: 01-01-06-SF0436. Amount: MYR294,600. Duration: 18 months (Jan 2008 - Jun 2009).
# [mailto:mardhiahaliasmsfint@yahoo.com '''Mardhiah Alias '''], MSc - Building Classification in Dense Urban Areas
# Computational Method for Protein Sequence Annotation Using Gene Ontology and Intelligent Techniques. Funded by Malaysian Ministry of Science, Technology, and Innovation under ScienceFund. Grant no: 01-01-06-SF0435. Amount: MYR123,800. Duration: 18 months (Jan 2008 - Jun 2009).
# [mailto:gsharon87@gmail.com '''Sharon Kaur Guramad Singh '''], MSc - Enzyme Sub-Family Class Prediction
# The Development of Automata Learning and Stochastic Modeling for Biosequence Analysis. Funded by Malaysian Ministry of Science, Technology, and Innovation under ScienceFund. Grant no: 02-01-06-SF0230. Amount: MYR122,000. Duration: 18 months (Oct 2007 - Mar 2009).
# [mailto:shiningstar0206@yahoo.com '''Noor Hidayah Zakaria '''], MSc - Herbs Ontology for Semantic Searching
# Heterogeneous Ontology Mapping by Semantic Enrichment. Funded by Malaysian Ministry of Higher Education under Fundamental Research Grant Scheme. Grant no: 78186. Amount: MYR100,000. Duration: 24 months (Sep 2007 - Aug 2009).
# [mailto:laradiana88@gmail.com '''Anis Farihan Mat Raffei '''], MSc - Reflection Removal Method in Iris Recognition
# Symbolic Data Structures and Lumping Techniques Representation of Large Markov Models. Funded by Malaysian Ministry of Higher Education under Fundamental Research Grant Scheme. Grant no: 78185. Amount: MYR120,000. Duration: 24 months (Sep 2007 - Aug 2009).
# [mailto:greenish_sarah@yahoo.com '''D'yia Sarah Md Shukri '''], MSc - Deblurring Method in Iris Recognition
# Remote Protein Homology Detection Using Artificial Intelligence Algorithm. Funded by Malaysian Ministry of Science, Technology, and Innovation under ScienceFund. Grant no: 01-01-06-SF0228. Amount: MYR199,400. Duration: 18 months (Sep 2007 - Feb 2009).
# [mailto:rohayanti@utm.my '''Rohayanti Hassan '''], PhD - Protein Structural Class Prediction, status: graduated 2011 (6 semesters)
# The Development of Feature Selection Tool for Classification of Microarrays Gene Expression Data Using Statistical and Machine Learning Techniques. Funded by Malaysian Ministry of Science, Technology, and Innovation under ScienceFund. Grant no: 02-01-06-SF0068. Amount: MYR197,998. Duration: 24 months (Dec 2006 - Nov 2008).
# [mailto:shahreen.kasim@gmail.com '''Shahreen Kasim '''], PhD - Gene Function Prediction, status: graduated 2011 (6 semesters)
# The Development of Integrated Planning and Scheduling Framework for Dynamic and Reactive Environment of Complex Manufacturing Problem. Funded by Malaysian Ministry of Science, Technology, and Innovation under ScienceFund. Grant no: 01-01-06-SF0004. Amount: MYR98,994. Duration: 18 months (Dec 2006 - May 2008).
# [mailto:nuu.nurul@gmail.com '''Nurul Akmal Muhd Shukri '''], MSc - Protein Subcellular Localization Prediction, status: graduated 2011 (4 semesters)
# Learning Classifiers from Distributed, Semantically Heterogeneous, and Autonomous Data Sources. Funded by Malaysian Ministry of Higher Education under Fundamental Research Grant Scheme. Grant no: 78092. Amount: MYR40,000. Duration: 24 months (Jan 2007 - Dec 2008).
# [mailto:firyarn84@gmail.com '''Mohamad Firdaus Abdullah '''], MSc - Protein Remote Homology Detection; status: graduated 2010 (3 semesters)
# The Development of Semantic Meta-Database: An Ontology Based Semantic Integration of Biological Databases. Funded by Malaysian Ministry of Science, Technology, and Innovation under Intensification of Research in Priority Areas. Grant no: 04-02-06-10050-EAR. Amount: MYR86,000. Duration: 23 months (Aug 2005 - Jun 2007).
# [mailto:surayatiismail@gmail.com '''Surayati Ismail '''], MSc - Protein Remote Homology Detection; status: graduated 2010 (3 semesters)
# The Development of Machine Learning Based Software for Predicting Protein-Protein Interactions and Protein Function from Protein Primary Structure. Funded by Malaysian Ministry of Science, Technology, and Innovation under Intensification of Research in Priority Areas. Grant no: 04-02-06-10049-EAR. Amount: MYR76,000. Duration: 23 months (Aug 2005 - Jun 2007).
# [mailto:mrhilmi@gmail.com '''Mohd Hilmi Muda '''], MSc - Protein Remote Homology Detection & Fold Recognition; status: graduated 2009 (2 semesters)
# The Development of Hybrid Cell Ontology for Storing and Exchanging Computer-Based Biological Models. Funded by Malaysian Ministry of Science, Technology, and Innovation under Intensification of Research in Priority Areas. Grant no: 04-02-06-0072-EA001. Amount: MYR125,000. Duration: 24 months (Jan 2003 - Dec 2004).
# [mailto:nadhiyamohammad@gmail.com '''Noor Nadhiya Mohammad '''], MSc - Product Structure Ontology; status: graduated 2009 (2 semesters)
# The Development of Collaborative Environment with Privacy and Conference Control for 3D Protein Structure Visualization. Funded by Malaysian Ministry of Science, Technology, and Innovation under Intensification of Research in Priority Areas. Grant no: 04-02-06-0063-EA001. Amount: MYR144,000. Duration: 24 months (Jan 2003 - Dec 2004).
# [mailto:rosexquisite@gmail.com '''Rosfuzah Roslan '''], MSc - Protein-Protein Interaction Prediction; status: graduated 2009 (2 semesters)
# The Development of Multi-Agent Systems for Biological Information Retrieval from Heterogeneous Distributed Data and Knowledge Sources. Funded by Malaysian Ministry of Science, Technology, and Innovation under Intensification of Research in Priority Areas. Grant no: 04-02-06-0057-EA001. Amount: MYR260,000. Duration: 36 months (Jan 2003 - Dec 2005).
# [mailto:umiekalsum@gmail.com '''Umi Kalsum Hassan '''], MSc - Protein Domain Prediction; status: graduated 2009 (2 semesters)
# A Study on Information Extraction from Heterogeneous, Distributed, and Autonomous DNA Databases Using Ontology-Based Agent. Funded by Universiti Teknologi Malaysia under Short Term Grant. Grant no: 75162. Amount: MYR43,500. Duration: 12 months (Aug 2004 - Jul 2005).
# A Study on Biomolecular Sequence Alignment Using Machine Learning Techniques. Funded by Universiti Teknologi Malaysia under Short Term Grant. Grant no: 75079. Amount: MYR38,000. Duration: 12 months (Feb 2004 - Jan 2005).
# A Study on Component Based Technology for Development of Complex Bioinformatics Software. Funded by Universiti Teknologi Malaysia under Short Term Grant. Grant no: 75031. Amount: MYR19,500. Duration: 12 months (Sep 2003 - Aug 2004).
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===Software===
===Projects===
# LCIB-basic-UTMGO: A Tool for Browsing and Searching the Gene Ontology.
# 3D/2D Slope Stability Analysis: [http://www.jkr.gov.my/ Jabatan Kerja Raya Malaysia], [http://www.ikram.com.my/ Kumpulan IKRAM Sdn Bhd]
# LCIB-extended-UTMGO: A Tool for Annotation of Anonymous Protein Sequences.
# BooksOnline: [http://www.penerbit.utm.my/ Penerbit UTM Press, UTM]
# LCIB-AMS: A Software for Accounting Management.
# Graduate Studies Management System: [http://www.sps.utm.my/ School of Graduate Studies, UTM]
# UTMost-EDEx: A Tool for Extraction of 2D Engineering Drawing in Production Engineering.
# e-Biodiesel (Online Information for Production of Biodiesel): [http://www.mpob.gov.my/ Malaysian Palm Oil Board]
# UTMost-DSR: A Tool for Recognition of Design Structure in Production Engineering.
# e-Cost (Online Survey for Production Cost of Palm Oil): [http://www.mpob.gov.my/ Malaysian Palm Oil Board]
# UTMost-CAPP: A Tool for Generation of Process Plans in Production Engineering.
# ECOMAS (Estate Cost Management System): [http://www.mpob.gov.my/ Malaysian Palm Oil Board]
# LCSB-IPAMIS-HO/Estate: A Software for Oil Palm Plantation Management.
# EsyMOS (FFB Yield Performance Monitoring System): [http://www.mpob.gov.my/ Malaysian Palm Oil Board]
# LCSB-IPAMIS-Mill: A Software for Palm Oil Mill Management.
# e-Kampus: [http://www.kipsas.edu.my/ Kolej Islam Pahang Sultan Ahmad Shah] & [http://www.puspatri.edu.my/ Johor Skills Development Centre]
# LCSB-HCMS: A Software for Human Capital Management.
# Malaysia Coordinate System Transformation: [http://www.macgdi.gov.my/ Malaysian Center for Geospatial Data Infrastructure]
# Metabone-ERMS: A Software for Product Lifecycle Management.
# MS1759 Search Engine: [http://www.macgdi.gov.my/ Malaysian Center for Geospatial Data Infrastructure]
# Metabone-ECMMS: A Software for Preventive Maintenance and Asset Management.
# Malaysia National Oceanography Data Centre: [http://www.mosti.gov.my/ National Oceanography Directorate, MOSTI]
# [http://shareifyoucare.org Share If You Care].
# Malaysia National Spatial Data Infrastructure: [http://www.mosti.gov.my/ National Oceanography Directorate, MOSTI]
# Pipeline Corrosion Assessment System: [http://www.petronasgas.com/ Petronas Gas Bhd]
# SAP Premier Programme: [http://www.khazanah.com.my/ Khazanah Nasional Bhd], [http://www1.sap.com/malaysia/index.epx SAP Malaysia Sdn Bhd], [http://www.bcsynergy.com.my/ BC Synergy Sdn Bhd]
# The Study of ICT Capacity Enhancement: [http://www.lpj.gov.my/ Lembaga Pelabuhan Johor]
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===Group Members===
===Grants===
# [http://ac.utm.my/web/jumail Jumail Taliba], PhD Student (Protein-Protein Interaction Prediction).
# Othman R.M., Asmuni H., and Hassan R. (2011). Intelligent Mixed-Land Classifier for Change Detection in Coastal Zone Using LiDAR Point Cloud Data. GUP Grant: Universiti Teknologi Malaysia.
# [http://openwetware.org/wiki/User:Rohayanti_Hassan Rohayanti Hassan], PhD Student (Protein Local Structure Prediction).
# Asmuni H., Othman R.M., and Hassan R. (2011). Enhancement of the Accuracy and Privacy of Iris Biometrics Recognition System. GUP Grant: Universiti Teknologi Malaysia.
# [http://openwetware.org/wiki/User:Shahreen_Kasim Shahreen Kasim], PhD Student (Gene Expression Analysis).
# Hassan R., Othman R.M., and Asmuni H. (2011). A Web-Semantic Approach to Knowledge Management for Integration of Heterogeneous Herbs Data. GUP Grant: Universiti Teknologi Malaysia.
# [http://www.se.fsksm.utm.my/~zuraini Zuraini Ali Shah], PhD Student (Gene Expression Analysis).
# Asmuni H., Othman R.M., Zakaria Z., and Rahim M.S.M. (2010). Spatial Data Infrastructure for Heterogeneous Distributed Oceanography and Marine Sciences Data and Knowledge Sources. NODFund: Ministry of Science, Technology and Innovation.
# [http://openwetware.org/wiki/Mohamad_Firdaus_Abdullah Mohamad Firdaus Abdullah], MSc Student (Remote Protein Homology Detection).
# Othman R.M. and Asmuni H. (2010). The Development of Oceanographic Data and Marine Information Center. NODFund: Ministry of Science, Technology and Innovation.
# [http://openwetware.org/wiki/User:M_Hilmi_Muda Mohd Hilmi Muda], MSc Student (Remote Protein Homology Detection).
# Othman R.M., Shah Z.A., Rahim M.S.M., and Asmuni H. (2010). Computational Method to Predict Protein Domain Using Machine Learning Algorithms and Biological Knowledge. ScienceFund: Ministry of Science, Technology and Innovation.
# [http://openwetware.org/wiki/User:Rosfuzah_Roslan Rosfuzah Roslan], MSc Student (Protein-Protein Interaction Prediction).
# Othman R.M., Yatim S.M., Zakaria Z., Hassan R., and Shah Z.A. (2010). Improving Fuzzy C-Means Clustering Algorithm by Incorporating Functional Annotation Databases and Biological Knowledge. FRGS: Ministry of Higher Education.
# [http://openwetware.org/wiki/User:Surayati_Ismail Surayati Ismail], MSc Student (Remote Protein Homology Detection).
# Asmuni H., Othman R.M., Yatim S.M., Hassan R., and Shah Z.A. (2009). Two Layers Multi-Class Support Vector Machines (SVM) Classifiers. FRGS: Ministry of Higher Education.
# [http://openwetware.org/wiki/User:Umie_Kalsum Umi Kalsum Hassan], MSc Student (Protein Domain Detection).
# [http://www.se.fsksm.utm.my/~zalmiyah Zalmiyah Zakaria], PhD Student (Integrated Genetic Planning and Scheduling in Flexible Manufacturing System).
# Mohammad Khairuddin Ahmad, MSc Student (Multi-Agent System for 2D Engineering Drawing Extraction).  
# [http://openwetware.org/wiki/Noor_Nadhiya_Mohammad Noor Nadhiya Mohammad], MSc Student (Product Structure Ontology).
# [http://www.friendster.com/shimasamion Hashimah Samion], Senior System Analyst.
# Mohd Asri Pahorudin, System Analyst.
# Farah Ramly, Programmer.
# Maisarah Shaharuddin, Programmer.
# Noramira Mohd Lazim, Programmer.
# Nurulhuda Ismail@Wahid, Programmer.
# Nurul Saniah Mohd Shahlan, Programmer.
# Siti Noraishah Abdull Rahman, Programmer.
# Yussalina Mohd Yusop, Programmer.
# [http://profiles.friendster.com/24346088 Norazlin Mohd Agil], Secretariat.
<br>
 
===Collaborators===
# Bitech Enterprise.
#* [http://www.kpypj.edu.my/ Kumpulan Pendidikan YPJ].
#* [http://www.olicollectiononline.com/ Oli Collection Sdn Bhd].
# [http://bmi.epfl.ch/ Brain Mind Institute], Switzerland.
# [http://www.lcsb.com.my/ LKPP Corporation Sdn Bhd].
# Koperasi Pegawai-pegawai Kerajaan Negeri Pahang Bhd.
# Lunas Technology Sdn Bhd.
#* [http://www.agrobank.com.my/ AgroBank].
#* [http://www.felcra.com.my/ FELCRA Bhd].
# [http://www.pinelabs.com.my/ Pinelabs (M) Sdn Bhd].
#* [http://www.mara.gov.my/ Majlis Amanah Rakyat (MARA)].
#* Rukun Saksama Sdn Bhd.
# ROXYNET Technology Sdn Bhd.
# Strategi Tegas (M) Sdn Bhd.
# [http://www.zilun.com.my/ ZILUN Systems Sdn Bhd].
#* APM Spring Sdn Bhd.
#* Carigali-PTTEPI Operating Company Sdn Bhd.
#* Carigali-Triton Operating Company Sdn Bhd.
#* [http://www.gpdoors.com.my/ Golden Pharos Doors Sdn Bhd].
#* MajuPadu Development Sdn Bhd.
#* PT Bio Inti Agrindo, Indonesia.
#* Tuah Tankers Sdn Bhd.
<br>
<br>


===Contact Info===
===Contact Info===
Razib M. Othman <br>
Razib M. Othman <br>
Laboratory of Computational Intelligence and Biology (LCIB) <br>
Laboratory of Computational Intelligence and Biotechnology<br>
No. 204, Level 2 <br>  
Lot 4, Kompleks Usahawan Teknologi MARA <br>  
Industry Centre, Technovation Park <br>
Industry Centre, Technovation Park <br>
[http://www.utm.my Universiti Teknologi Malaysia (UTM)] <br>
[http://www.utm.my Universiti Teknologi Malaysia (UTM)] <br>
Line 169: Line 105:
81300 Skudai, [http://www.tourismjohor.com/ Johor], [http://www.tourism.gov.my/ MALAYSIA]  <br>
81300 Skudai, [http://www.tourismjohor.com/ Johor], [http://www.tourism.gov.my/ MALAYSIA]  <br>
Mobile: +6016-736-0533 <br>
Mobile: +6016-736-0533 <br>
Tel/Fax: +607-559-9230 <br>
Tel: +607-520-4992 / 551-2684 <br>
E-mail: razib@utm.my <br>
Fax: +607-521-3023 <br>
<br>
E-mail: razib[@]utm.my <br>

Latest revision as of 06:56, 30 December 2012

Education

  • 2008, PhD (Computer Science), Universiti Teknologi Malaysia.
  • 2003, MSc (Computer Science), Universiti Teknologi Malaysia.
  • 1999, BSc (Computer Science), Universiti Teknologi Malaysia.
  • 2007, internship on the Blue Brain Project, Brain Mind Institute, Swiss Federal Institute for Technology.


Prospective Students

  1. If you are interested in pursuing a PhD in CLOUD COMPUTING (not limited to software engineering, artificial intelligence, security, networking, software architecture) or AGILE UNIFIED PROCESS (AUP), please contact Razib M. Othman
  2. Sponsorship is provided (for Malaysian only) - GATES Scholar Foundation


Publications

  1. Hassan R., Othman R.M., Saad P., and Kasim S. (2011). A Compact Hybrid Feature Vector for an Accurate Secondary Structure Prediction. Information Sciences [Elsevier; impact factor 2011: 2.833] 181(23): 5267-5277.
  2. Muda H.M., Saad P., and Othman R.M. (2011). Remote Protein Homology Detection and Fold Recognition Using Two-Layer Support Vector Machine Classifiers. Computers in Biology & Medicine [Elsevier; impact factor 2011: 1.089] 41(8): 687-699.
  3. Roslan R., Othman R.M., Shah Z.A, Kasim S., Asmuni H., Taliba J., Hassan R., and Zakaria Z. (2010). Incorporating Multiple Genomics Features with the Utilization of Interacting Domain Patterns to Improve Protein-Protein Interactions Prediction. Information Sciences [Elsevier; impact factor 2010: 2.833] 180(20): 3955-3973.
  4. 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 & Medicine [Elsevier; impact factor 2010: 1.112] 40(6): 555-564.
  5. Hassan U.K., Shah Z.A., Othman R.M., Hassan R., Rahim M.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 & Medicine [Elsevier; impact factor 2009: 1.269] 39(11): 1013-1019.
  6. Othman R.M., Deris S., and Illias R.M. (2008). A Genetic Similarity Algorithm for Searching the Gene Ontology Terms and Annotation of Anonymous Protein Sequences. Journal Biomedical Informatics [Elsevier; impact factor 2008: 1.924] 41(1): 65-81.
  7. Taliba J., Othman R.M., Hassan U.K., and Roslan R. (2011). A Hybrid Ranking Method for Constructing Negative Datasets of Protein-Protein Interactions. Journal of Computing 3(11): 3(11): 48-55.
  8. Ismail A.M., Asmuni H., and Othman R.M. (2011). The Fuzzy Cooperative Genetic Algorithm (FCoGA): The Optimisation of a Fuzzy Model Through Incorporation of a Cooperative Coevolutionary Method. Journal of Computing 3(11): 81-90.
  9. Ismail S., Othman R.M., Kasim S., Hassan R, Asmuni H., and Taliba J. (2011). Pairwise Protein Substring Alignment with Latent Semantic Analysis and Support Vector Machines to Detect Remote Protein Homology. International Journal of Bio-Science and Bio-Technology 3(3): 17-34.
  10. Abdullah F.M., Othman R.M., Kasim S., Hashim R., Hassan R, Asmuni H., and Taliba J. (2011). An Optimal Mesh Algorithm for Remote Protein Homology Detection. International Journal of Bio-Science and Bio-Technology 3(2): 13-38.
  11. Kasim S., Deris S., Othman R.M,, and Hashim R. (2011). Biological-Based Semi-Supervised Clustering Algorithm to Improve Gene Function Prediction. Journal of Computing 3(4): 1-11.
  12. Mohamad N.N., Amin I.M., Othman R.M., Asmuni H., Hassan R., and Kasim S. (2012). Design and Implementation of Product Structure Ontology. In Nazir M.A., Colomb R.M., and Syazwan M.A. (eds), Ontology-Based Applications for Enterprise Systems and Knowledge Management, pp 246-260.
  13. Ismail S., Othman R.M., and Kasim S. (2011). Pairwise Protein Substring Alignment with Latent Semantic Analysis and Support Vector Machines to Detect Remote Protein Homology. In Kim T.-h., Adeli H., Robles R.J., and Balitanas M. (eds), Communications in Computer and Information Science: Ubiquitous Computing and Multimedia Applications 151(Part 2): 526-546.
  14. Abdullah F.M., Othman R.M., Kasim S., and Hashim R. (2011). An Optimal Mesh Algorithm for Remote Protein Homology Detection. In Kim T.-h., Adeli H., Robles R.J., and Balitanas M. (eds), Communications in Computer and Information Science: Ubiquitous Computing and Multimedia Applications 151(Part 2): 471-497.
  15. Kasim S., Deris S., and Othman R.M. (2010). A New Computational Framework for Gene Expression Clustering. In Cao L., Feng Y., and Zhong J. (eds), Lecture Notes in Computer Science: Advanced Data Mining and Applications 6440(2010): 603-610.
  16. Zafar F.M., Mohamad D., and Othman R.M. (2010). Performance Analysis of a Proposed Smoothing Algorithm for Isolated Handwritten Characters. International Journal of Artificial Intelligence and Soft Computing 2(3): 186-198.
  17. Zafar F.M., Mohamad D., Rab A., and Othman R.M. (2009). Application of a Proposed Efficient Smoothing Algorithm on Directional Vectors for Isolated Handwritten Characters. In Hussain D.M.A., Rajput A.Q.K., Chowdhry B.S., and Gee Q. (eds), Communications in Computer and Information Science: Wireless Networks, Information Processing and Systems 20(1): 52-63.
  18. Alashwal H.T., Deris S., and Othman R.M. (2009). A Bayesian Kernel for the Prediction of Protein-Protein Interactions. International Journal of Information and Mathematical Sciences 5(2): 119-124.
  19. Othman R.M., Hassan U.K., Hassan R., Asmuni H., Taliba J., and Kasim S. (2012). BRNN-SVM: Increasing the Strength of Domain Signal to Improve Protein Domain Prediction Accuracy. Recurrent Neural Network. Eds Elhefnawi M. and Mysara M. InTech. Rijeka, Croatia, pp. 133-150.
  20. Abdullah F.M. and Othman R.M. (2012). Multiple Alignments, Hidden Markov Models and SVMs: Development of a Computational Framework for Protein Homology Detection by Incorporating Realignment Algorithm. LAP LAMBERT Academic Publishing. Saarbrücken, Germany.
  21. Mohamad N.N. and Othman R.M. (2012). Knowledge Formalization and Information Retrieval: Product Structure Ontology to Support Semantic Search in Manufacturing Requirements Management. LAP LAMBERT Academic Publishing. Saarbrücken, Germany.


Reviewer of Scientific Journals

  1. Amino Acids (Springer; impact factor 2009: 3.877; no of paper reviewed: 1; last reviewed: 2009)
  2. Artificial Intelligence in Medicine (Elsevier; impact factor 2010: 1.568; no of paper reviewed: 1; last reviewed: 2010)
  3. Computers in Biology and Medicine (Elsevier; impact factor 2011: 1.089; no of paper reviewed: 6; last reviewed: 2012)
  4. Journal of Biomedical Informatics (Elsevier; impact factor 2010: 1.719; no of paper reviewed: 3; last reviewed: 2010)
  5. PLoS Computational Biology (PLoS.org; impact factor 2011: 5.215; no of paper reviewed: 3; last reviewed: 2012)
  6. Proteins: Structure, Function, and Bioinformatics (Wiley; impact factor 2011: 3.392; no of paper reviewed: 1; last reviewed: 2011)
  7. Current Bioinformatics (Bentham Science; impact factor 2011: 0.898; no of paper reviewed: 2; last reviewed: 2012)
  8. Protein & Peptide Letters (Bentham Science; impact factor 2011: 1.942; no of paper reviewed: 1; last reviewed: 2012)


Graduate Students

  1. Jumail Taliba , PhD - Protein-Protein Interaction Prediction
  2. Sim Hiew Moi , PhD - Off-Angle Method in Iris Recognition
  3. Muhamad Asyraf Mohd Pouzi , MSc - Vegetation Classification in Mixed-Land Zones
  4. Mardhiah Alias , MSc - Building Classification in Dense Urban Areas
  5. Sharon Kaur Guramad Singh , MSc - Enzyme Sub-Family Class Prediction
  6. Noor Hidayah Zakaria , MSc - Herbs Ontology for Semantic Searching
  7. Anis Farihan Mat Raffei , MSc - Reflection Removal Method in Iris Recognition
  8. D'yia Sarah Md Shukri , MSc - Deblurring Method in Iris Recognition
  9. Rohayanti Hassan , PhD - Protein Structural Class Prediction, status: graduated 2011 (6 semesters)
  10. Shahreen Kasim , PhD - Gene Function Prediction, status: graduated 2011 (6 semesters)
  11. Nurul Akmal Muhd Shukri , MSc - Protein Subcellular Localization Prediction, status: graduated 2011 (4 semesters)
  12. Mohamad Firdaus Abdullah , MSc - Protein Remote Homology Detection; status: graduated 2010 (3 semesters)
  13. Surayati Ismail , MSc - Protein Remote Homology Detection; status: graduated 2010 (3 semesters)
  14. Mohd Hilmi Muda , MSc - Protein Remote Homology Detection & Fold Recognition; status: graduated 2009 (2 semesters)
  15. Noor Nadhiya Mohammad , MSc - Product Structure Ontology; status: graduated 2009 (2 semesters)
  16. Rosfuzah Roslan , MSc - Protein-Protein Interaction Prediction; status: graduated 2009 (2 semesters)
  17. Umi Kalsum Hassan , MSc - Protein Domain Prediction; status: graduated 2009 (2 semesters)


Projects

  1. 3D/2D Slope Stability Analysis: Jabatan Kerja Raya Malaysia, Kumpulan IKRAM Sdn Bhd
  2. BooksOnline: Penerbit UTM Press, UTM
  3. Graduate Studies Management System: School of Graduate Studies, UTM
  4. e-Biodiesel (Online Information for Production of Biodiesel): Malaysian Palm Oil Board
  5. e-Cost (Online Survey for Production Cost of Palm Oil): Malaysian Palm Oil Board
  6. ECOMAS (Estate Cost Management System): Malaysian Palm Oil Board
  7. EsyMOS (FFB Yield Performance Monitoring System): Malaysian Palm Oil Board
  8. e-Kampus: Kolej Islam Pahang Sultan Ahmad Shah & Johor Skills Development Centre
  9. Malaysia Coordinate System Transformation: Malaysian Center for Geospatial Data Infrastructure
  10. MS1759 Search Engine: Malaysian Center for Geospatial Data Infrastructure
  11. Malaysia National Oceanography Data Centre: National Oceanography Directorate, MOSTI
  12. Malaysia National Spatial Data Infrastructure: National Oceanography Directorate, MOSTI
  13. Pipeline Corrosion Assessment System: Petronas Gas Bhd
  14. SAP Premier Programme: Khazanah Nasional Bhd, SAP Malaysia Sdn Bhd, BC Synergy Sdn Bhd
  15. The Study of ICT Capacity Enhancement: Lembaga Pelabuhan Johor


Grants

  1. Othman R.M., Asmuni H., and Hassan R. (2011). Intelligent Mixed-Land Classifier for Change Detection in Coastal Zone Using LiDAR Point Cloud Data. GUP Grant: Universiti Teknologi Malaysia.
  2. Asmuni H., Othman R.M., and Hassan R. (2011). Enhancement of the Accuracy and Privacy of Iris Biometrics Recognition System. GUP Grant: Universiti Teknologi Malaysia.
  3. Hassan R., Othman R.M., and Asmuni H. (2011). A Web-Semantic Approach to Knowledge Management for Integration of Heterogeneous Herbs Data. GUP Grant: Universiti Teknologi Malaysia.
  4. Asmuni H., Othman R.M., Zakaria Z., and Rahim M.S.M. (2010). Spatial Data Infrastructure for Heterogeneous Distributed Oceanography and Marine Sciences Data and Knowledge Sources. NODFund: Ministry of Science, Technology and Innovation.
  5. Othman R.M. and Asmuni H. (2010). The Development of Oceanographic Data and Marine Information Center. NODFund: Ministry of Science, Technology and Innovation.
  6. Othman R.M., Shah Z.A., Rahim M.S.M., and Asmuni H. (2010). Computational Method to Predict Protein Domain Using Machine Learning Algorithms and Biological Knowledge. ScienceFund: Ministry of Science, Technology and Innovation.
  7. Othman R.M., Yatim S.M., Zakaria Z., Hassan R., and Shah Z.A. (2010). Improving Fuzzy C-Means Clustering Algorithm by Incorporating Functional Annotation Databases and Biological Knowledge. FRGS: Ministry of Higher Education.
  8. Asmuni H., Othman R.M., Yatim S.M., Hassan R., and Shah Z.A. (2009). Two Layers Multi-Class Support Vector Machines (SVM) Classifiers. FRGS: Ministry of Higher Education.


Contact Info

Razib M. Othman
Laboratory of Computational Intelligence and Biotechnology
Lot 4, Kompleks Usahawan Teknologi MARA
Industry Centre, Technovation Park
Universiti Teknologi Malaysia (UTM)
Jalan Pontian Lama
81300 Skudai, Johor, MALAYSIA
Mobile: +6016-736-0533
Tel: +607-520-4992 / 551-2684
Fax: +607-521-3023
E-mail: razib[@]utm.my

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