Razib Othman

Education

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

Research Interests

1. Current high-priority research: Neuroinformatics in the Blue Brain Project.
2. Research in Bioinformatics:
   • Protein Sequence Analysis.
   • Protein-Protein Interaction Prediction.
   • Protein Structure Prediction.
   • Gene Expression Analysis.
   • Biological Ontologies, Data Mining, and Data Integration.

Awards (2003-present)

1. Gold Medal, 34th International Exhibition of Invention New Techniques and Products (2006), Geneva, Switzerland.
2. The Best Invention of the Pacific Rim Award, 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
3. Silver Medal (Engineering Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
4. Silver Medal (Design Technical Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
5. Bronze Medal (Automotive Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
6. Bronze Medal (Computer Software Category), 22nd Invention and New Product Exposition (2005), Pittsburgh, USA.
7. Bronze Medal, 6th Malaysia Technology Expo (2007), Kuala Lumpur, Malaysia.
8. Gold Medal, 5th Malaysia Technology Expo (2006), Kuala Lumpur, Malaysia.
9. Gold Medal, 3rd Public Institutions of Higher Learning Research and Development Expo (2005), Kuala Lumpur, Malaysia.
10. The Best Invention, 8th Industrial Art and Technology Exhibition (2005), Skudai, Malaysia.
11. Gold Medal, 8th Industrial Art and Technology Exhibition (2005), Skudai, Malaysia.
12. Finalist of Malaysian Innovation Award 2006 by Malaysian Ministry of Science, Technology, and Innovation.
13. Excellence Scientist Recognition Award 2006 bestowed by Malaysian Ministry of Higher Education.
14. Young Researcher 2005 bestowed by Malaysian Association of Research Scientists.
15. Excellence Scientist Recognition Award 2005 bestowed by Malaysian Ministry of Higher Education.
16. The Best Fundamental Research Award 2005 bestowed by Universiti Teknologi Malaysia.
17. Researcher Recognition Award 2005 bestowed by Universiti Teknologi Malaysia.
18. Excellence Service Award 2005 bestowed by Universiti Teknologi Malaysia.
19. Excellence Service Award 2003 bestowed by Universiti Teknologi Malaysia.

Publications (2006-present)

1. Othman R.M. Computational Method for Protein Sequence Annotation Using Gene Ontology and Intelligent Techniques. PhD Thesis: Universiti Teknologi Malaysia. (draft).
2. Othman R.M., Deris S., and Illias R.M. A Genetic Split-Merge Algorithm for Splitting the Monolithic Gene Ontology RDF/XML File. Journal Biomedical Informatics. (accepted).
3. Othman R.M., Deris S., and Illias R.M. A Genetic Similarity Algorithm for Searching the Gene Ontology Terms and Annotation of Anonymous Protein Sequences. Journal Biomedical Informatics. (DOI: 10.1016/j.jbi.2007.05.010 ).
4. 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 GO Bibliography].
5. 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 GO Bibliography].
6. 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.
7. 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.
8. 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 GO Bibliography].
9. 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 GO Bibliography].
10. 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.
11. 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.
12. 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.
13. 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.
14. 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.
15. 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.
16. 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.
17. 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.
18. 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.
19. 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.

Grants (2003-present)

1. Heterogeneous Ontology Mapping by Semantic Enrichment. Submitted to Malaysian Ministry of Higher Education under Fundamental Research Grant Scheme.
2. Symbolic Data Structures and Lumping Techniques Representation of Large Markov Models. Submitted to Malaysian Ministry of Higher Education under Fundamental Research Grant Scheme.
3. Parallel Molecular Modelling Framework to Assess DNA Sequence Effects on Nucleosome Stability. Under evaluation by Malaysian Ministry of Science, Technology, and Innovation Internal Committee. Application under ScienceFund.
4. Framework of Conditional Graphical Models for Protein Quaternary Structure Prediction. Under evaluation by Malaysian Ministry of Science, Technology, and Innovation Approval Committee. Application under ScienceFund.
5. The Development of Intelligent Tool for Discovering Protein Sequence-Structure Motifs Using Machine Learning Techniques. Under evaluation by Malaysian Ministry of Science, Technology, and Innovation Approval Committee. Application under ScienceFund.
6. The Development of Automata Learning and Stochastic Modeling for Biosequence Analysis. Under evaluation by Malaysian Ministry of Science, Technology, and Innovation Approval Committee. Application under ScienceFund.
7. Remote Protein Homology Detection Using Artificial Intelligence Algorithm. Under evaluation by Malaysian Ministry of Science, Technology, and Innovation Approval Committee. Application under ScienceFund.
8. 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).
9. 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).
10. 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).
11. 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).
12. 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).
13. 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).
14. 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).
15. 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).
16. 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).
17. 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).
18. 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).

Software

1. AIBIL-UTMGO: A Tool for Searching the Gene Ontology Terms and Annotating the Anonymous Protein Sequence.
2. UTMost-EDEx: A Tool for Extraction of 2D Engineering Drawing in Production Engineering.
3. UTMost-DSR: A Tool for Recognition of Design Structure in Production Engineering.
4. UTMost-CAPP: A Software for Generation of Process Plans in Production Engineering.
5. Qsystem-PlantSys: A Software for Multi-Entrprise, Multi-Level, and Distributed Plantation Management.
6. Qsystem-MillSys: A Software for Palm Oil Mill Management.
7. Qsystem-HRSys: A Software for Human Resource Management.
8. Metabone-ERMS: A Software for Product Lifecycle Management.
9. Metabone-ECMMS: A Software for Preventive Maintenance and Asset Management.

Group Members

1. Hany Taher Alashwal, PhD Student (Protein-Protein Interaction Prediction).
2. Muhammad Firdaus Mustapha, MSc Student (Scheduling in Agile Manufacturing System).
3. Hashimah Samion, Research Officer.
4. Norlelawati Abdul Manap, Research Officer.
5. Sairee Sainel, Research Officer.
6. Zilfaharinah Hashim, Research Officer.
7. Norlina Deraman, Assistant Research Officer.
8. Mohd Asri Pahorudin, Analyst Programmer.

Collaborators

1. Hishamuddin Lab.
2. Rohayanti Lab.
3. Shafry Lab.
4. Zalmiyah Lab.
5. Zuraini Lab.
6. Laboratory of Molecular Neurobiology and Functional Neuroproteomics, Swiss Federal Institute for Technology.
7. ZILUN Systems Sdn Bhd.
8. APM Automotive Holdings Bhd.
9. LKPP Corporation Sdn Bhd.
10. Strategi Tegas (M) Sdn Bhd.

Contact Info

Razib M. Othman (Razib Lab)
Laboratory of Artificial Intelligence and Bioinformatics
Department of Software Engineering
Faculty of Computer Science and Information Systems
Universiti Teknologi Malaysia
81310 UTM Skudai, MALAYSIA
Tel: +607-55-32358
Fax: +607-55-65044
E-mail: razib@utm.my