Ph.D. in Electrical and Computer Engineering

- National University of Singapore, Singapore (2001-2004) - .

• Research title: Design, Analysis and Application of Divisible Load Scheduling Strategies in Linear Daisy Chain Networks With System Constraints

Bachelor of Engineering (1st class Honours) in Electronic Engineering

- University of Nottingham, United Kingdom (1997-2000) - .

• Comprehensive engineering courses with cross faculty subjects, including management accounting, engineering laws, quality control management, etc.

• 2001: The National University of Singapore PhD Scholarship (3 years)

• 1998: Certificates of Merit for academic excellence (1st year, BEng in Electronic Engineering, Inti College Malaysia and the University of Nottingham)

• 1996: 4th prize in SOFTCOM, a national secondary school software writing competition (school representative and team leader)

• 1996: School sports - 3rd in 4 x 100m relay and finalist in school 100m sprint

• 2008-present: Member, Scientific Computing in Cambridge (SciComp@Cam)

• 2008-present: Science, Technology, Engineering, and Math (STEM) Ambassador for (STEMNET)

• 1998-2000: IT group member, Student Community Action, University of Nottingham

• 1996: President, Computer Club, former secondary school

• 1996: Secretary, School Magazine Board, former secondary school

University of Cambridge, UK (2008 - present)

• Analyse the association of G-quadruplex motifs against important genomic features

• Identify G-quadruplex motifs that can potentially be used for drug design in cancer therapy

• Develop and maintain web portal quadruplex.org with database and web service for the G-quadruplex research community

• Utilize computational Grid for computationally intensive analyses

University of Exeter, UK (2005 - 2007)

• Research and development of an object orientated bioinformatics data warehouse database system (Versant FastObjects) that integrates multiple fungal genomes (from multiple data sources) into a logical model to facilitate genetic and functional data analyses

• Designed and developed loading infrastructure for automated uploading of data from multiple data sources

• Designed and developed a web service generator (in Java) to include web service capability to the data warehouse (and other compatible database systems) for bioinformatics analyses

• In-silico computational prediction of microRNA (miRNA) in fungal genomes

• Designed, developed and implemented visualisation tools (in Java) that integrates with bioinformatics database to facilitates biological pathway analyses

• Set up and maintained RAID enabled Linux system for computational intensive bioinformatics data processing, data backup, and act as the cvs server for the database system software version control

Data Storage Institute, A*STAR, Singapore (2004-2005)

• Studied and designed a dynamic Grid (web service) enabled storage resource allocation infrastructure, in line with the Storage Management Initiative Specifications (SMI-S) for high degree of compatibility with existing products in the market

• Designed and evaluated storage resource management strategies would adapt to data storage conditions and usage pattern, for maximum utilisation efficiency without compromising quality of service (QoS)

• Set up, configured, and maintained a storage system consisting 14 nodes cluster, 4 TeraBytes EMC network storage system, and a Brocade fibre channel switch

National University of Singapore, Singapore (2001-2004)

• Mathematically designed, evaluated and simulated (using Matlab) distribution strategy for large scale data processing in parallel and distributed systems with under various real life system constraints (large data to memory ratio, heterogeneous system components, multiple computational load, etc.)

• Developed vigorous simulations (Matlab) to verify mathematical findings

• Implemented and evaluated distribution strategy in biological sequence analysis

University of Nottingham, United Kingdom (1997-2000)

• Implemented (in assembly language) signal processing function with pulse width modulation on Digital Signal Processor for the electrical motor controlling

• Developed (C++) PC-DSP interface programs with graphical user interface and data visualisation (Matlab)

Research Associate

- University of Cambridge, UK (2008 - present)

• Analysis of quadruplex sequences in human genome

Research Associate

- University of Exeter, UK (2005 - 2007)

• Worked in the e-fungi project group (http://www.e-fungi.org.uk) that develops and utilises a data warehouse with genomic and functional data from multiple bioinformatics database sources

• Participated in team based software developments with project members and other related software developers

• Funded by the Biotechnology and Biological Sciences Research Council (BBSRC) Bioinformatics and E-science Programme II

• Joint research project between the University of Manchester (School of Computer Science and Faculty of Life Sciences) and University of Exeter (School of Biological Sciences)

Research Scientist

- Data Storage Institute, A*STAR, Singapore (2004 - 2005)

• Worked in the Network Storage group for pilot projects on of a dynamic Grid storage resource infrastructure

• A*STAR (Agency for Science, Technology And Research) is the key Singaporean government agency for the development of scientific research

Class teaching

• National University of Singapore, Singapore (2001-2003): Conducted tutorial classes (approximately 30 students per class) and marking of examinations on Electronic Circuits (undergraduate 1st year and 2nd year). Received outstanding score and good comments from students in the teaching feedback assessment (copies of the feedback available upon request)

Small group teaching

• University of Exeter, UK (2006) for the Marie Curie Research (Signalpath) Training Network: Designed and conducted bioinformatics class (general bioinformatics, Perl in bioinformatics, and web service access) to approximately 10 participating biologists from all over the world

Small group supervision

• University of Cambridge, UK (2008 - present): Designed and conducted supervision on final year subjects (Digital Communication Part 2, and Distributed Systems) in Computer Laboratory (the Computer Science Department)

One-to-One supervision

• University of Cambridge, UK (2008): Helped in supervising a summer student

• National University of Singapore, Singapore (2003-2004): Supervised 2 final year students on bioinformatics research projects

Teaching related course attended

• University of Cambridge, UK (2008): "Supervising Undergraduates and Small Group Teaching: A Course for Graduate Students", Centre for Personal and Professional Development

Administrative

• Quadruplex.org (2008 - present): (Webpage) Managing the G-quadruplex publication list, conference events calendars, discussion forum, etc., for the G-quadruplex research community

• Podtdocs Of Cambridge (Postdocs society), University of Cambridge (2008): Applied for the university representative URL for the society

• Talbot Lab Webpage, University of Exeter (2005 - 2007): (Webpage) Managed the group details, contacts, and publications list

• e-fungi project, University of Exeter and University of Manchester (2005 - 2007): Managed the research group server for analyses as well as for data and code synchronizations

Course Design

• Marie Curie Research (Signalpath) Training Network (2006): Designed the course syllabus and materials for approximately 10 participating biologist.

Organization

• Science, Technology, Engineering and Mathematics Network (STEM-NET) (2009): Explained and guided groups of 14 years old students in science related activities

Assessment

• National University of Singapore (2001-2003) as graduate facilitator (teaching assistant): Markings of mid-term examination papers (2nd year students)

Volunteers demonstrators

• Cambridge Science Festival(2008,2009) Helped to promote science to the general public with fun experiments

STEM Ambassador

• Science, Technology, Engineering and Mathematics Network (STEM-NET)(2008 - present) Demonstrate and explain STEM related issues, subjects, and opportunities in a fun and informative way to young learners to promote STEM interest in the younger generations

IT/Computer

• Programming: Assembly, Visual Basic, C/C++, Java, Perl, SQL

• Analysis software: Matlab, RATS (Regression Analysis of Time Series), R

• Others: Photoshop, GIMPS, Inkscape

Others

• Guitar

• Juggle

• Solve the Rubik's cube

• Sept 2008 - Quadruplex Nucleic Acids Discussion Meeting, London. "Quaruple Triage" (Quadruplex in oncogenes)

• Sept 2007 - All Hands Meeting 2007, Nottingham. "e-Fungi: An e-Science Infrastructure for Comparative Functional Genomics in Fungal Species"

• Wong, H.M., Payet, L., and Huppert, J., "Quadruple triage - selecting biologically important G-quadruplex targets" (in progress)

• Wong, H.M., Soanes, D.M., and Talbot, N.J., "A bioinformatic investigation to determine if miRNAs are encoded by the genomes of filamentous fungi" (in progress)

• Wong, H.M., Hedeler, C., and Paton, N., "Web services from user interface models" (in progress - to be submitted to Bioinformatics)

• Wong, H.M., and Huppert, J., "Stable G-quadruplexes are found outside nucleosome-bound regions", Molecular BioSystems, 2009. (accepted)

• Wong, H.M., and Bharadwaj Veeravalli, "Handling Biological Sequence Alignments on Networked-Computing Systems: A Divide-and-Conquer Approach", Journal of Parallel and Distributed Computing, 2009. (accepted)

• Wong, H.M., Payet, L., Huppert, J., "Function and targeting of G-quadruplexes", Current opinion in molecular therapeutics, 11(2):146-55, Apr 2009.

• Soanes, D.M., Alam, I., Cornell M., Wong, H.M., Hedeler, C., Paton, N., Rattray, M., Hubbard, S.J., Oliver, S.G., Talbot, N.J., "Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis", PLoS ONE 3(6), 2008. [Full paper]

[Citation] Jung K et al., "SNUGB: a versatile genome browser supporting comparative and functional fungal genomics", BMC Genomics, 9, 2008

[Citation] Marthey S et al., "FUNYBASE: a FUNgal phYlogenomic dataBASE", BMC Bioinformatics, 9, 2008

• Alam, I., Cornell, M. , Soanes, D.M., Hedeler, C., Wong, H. M., Rattray, M., Hubbard, S.J., Talbot, N.J., Oliver, S.G. and Paton, N.W., "A Methodology for Comparative Functional Genomics", J. Integrative Bioinformatics. 4(3)69. [Full paper]

• Hedeler, C., Wong, H.M., Cornell, M., Alam, I., Soanes, D.M., Rattray, M., Hubbard S.J., Talbot N.J., Oliver S.G., and Paton, N., "e-Fungi DB: Comparative analysis of fungal genomes", BMC Genomics 8:426, 2007 [Full paper]

[Citation] Marthey S et al., "FUNYBASE: a FUNgal phYlogenomic dataBASE", BMC Bioinformatics, 9, 2008

[Citation] Craddock T et al., "e-Science: relieving bottlenecks in large-scale genome analyses", Nat. Rev. Microbiol., 6(12), 2008

[Citation] Jung K et al., "SNUGB: a versatile genome browser supporting comparative and functional fungal genomics", BMC Genomics, 9, 2008

• Cornell MJ, Alam I, Soanes DM, Wong H.M., Hedeler C, Paton NW, Rattray M, Hubbard SJ, Talbot NJ, Oliver SG, "Comparative genome analysis across a kingdom of eukaryotic organisms: Specialization and diversification in the Fungi.", Genome Research, 2007 [Full Paper]

[Citation] Park J et al., "Fungal cytochrome P450 database", BMC Genomics, 9, 2009

[Citation] Shen YQ, and Burger G, "Plasticity of a key metabolic pathway in fungi", Funct. Integr. Genomics, 9(2), 2009

[Citation] Marcet-Houben and Gabaldo, "The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome", PLoS ONE, 4(2), 2009

[Citation] Jung K et al., "SNUGB: a versatile genome browser supporting comparative and functional fungal genomics", BMC Genomics, 9, 2008

• Cornell M., Alam I., Soanes D.M., Wong H.M., Rattray M., Hubbard S., Talbot N.J., Lings B., Hoyle D., Oliver S.G. and Paton N.W., "e-Fungi: An e-Science Infrastructure for Comparative Functional Genomics in Fungal Species", Proceedings of UK e-Science Programme All Hands Meeting 2005, Nottingham, September 2005 [Full paper]

• Wong H.M., Wang Y, Yeo H.N., Wang D., Li Z., Leong K.H., and Yong K.L., "Dynamic Storage Resource Management Framework for the Grid", Proceedings of the IEEE/NASA Mass Storage Systems and Technologies (MSST'05), April 2005.

[Citation] Yuhui Deng, et al. "Dynamic and scalable storage management architecture for Grid Oriented Storage devices", Parallel Computing, v.34 n.1, p.17-31, 2008

[Citation] Yuhui Deng, and Frank Wang, "A Heterogeneous Storage Grid Enabled by Grid Service", ACM Operating Systems Review, Volume 41 , Issue 1, January 2007.

• Wong, H.M., and Veeravalli, B., "Aligning Biological Sequences on Distributed Bus Networks: A Divisible Load Scheduling Approach", IEEE Transactions on Information Technology in Biomedicine, 9(4), 489-501, 2005.

• Wong H.M., Veeravalli, B., and Barlas, G., "Design and Performance Evaluation of Load Distribution Strategies for Multiple Divisible Loads on Heterogenous Linear Daisy Chain Networks", Journal of Parallel and Distributed Computing, 65 (12), 2005.

• Wong, Han Min, "Design, Analysis and Application of Divisible Load Scheduling Strategies in Linear Daisy Chain Networks with System Constraints", PhD Dissertation, Department of Electrical and Computer Engineering, National University of Singapore, 2004. [Download full thesis (755KB) ZIP]

• Veeravalli, B., and Wong, H.M., "Scheduling Divisible Loads on Heterogeneous Linear Daisy Chain Networks with Arbitrary Processor Release Times", IEEE Transactions on Parallel and Distributed Systems, Vol 15, 3, pp.273-288, March 2004. [Abstract][Full draft paper]

[Citation] Yeim-Kuan Chang et al., "Improved Methods for Divisible Load Distribution on k-Dimensional Meshes Using Multi-Installment," IEEE Transactions on Parallel and Distributed Systems, vol. 18, no. 11, pp. 1618-1629, November, 2007.

• Wong H.M., Veeravalli, B., Yu, D., and Robertazzi, T. G., "Data Intensive Grid Scheduling: Multiple Sources with Capacity Constraints", Proceedings of the International Conference on Parallel and Distributed Computing Systems, (PDCS) 2003, Marina del Rey, USA, 2003.PDF

[Citation] Yudith Cardinale, "An evaluation of job scheduling strategies for divisible loads on grid platforms", Proceedings of the High Performance Computing and Simulation Conference, 2006.

[Citation] Seonho Kim and Jon B. Weissman, "A Genetic Algorithm Based Approach for Scheduling Decomposable Data Grid Applications", Proceedings of the International Conference on Parallel Processing (ICPP), August 15 - 18, 2004.

• Wong H.M., Veeravalli, B., and Barlas, G., "Scheduling Multiple Divisible Loads on Heterogeneous Linear Daisy Chain Networks", Proceedings of the International Conference on Parallel and Distributed Computing and Systems (PDCS) 2002, Cambridge, USA, 2002.