Who am I?
Hi, my name is Joshua (Wing Kei) Ho. I am currently a PhD candidate at the
School of Information Technologies,
University of Sydney and National ICT Australia.
I am jointly supervised by Dr. Michael Charleston, Prof. Cris dos Remedio and Prof. Albert Zomaya.
I can be contacted at  .
Brief Biography
I moved to Australia for tertiary studies after completing the school certificate in Hong Kong in 2002. After completing the first year of Bioinformatics/Science degree
at La Trobe University, I transferred to the University of Sydney where I completed my
Bachelor of Science (Advanced) in Biology, Biochemistry and Computer Science. I was awarded first class honours and a University Medal.
Now I am staying on for a PhD at the same university. I am a winner of the Australian Postgraduate Award and the
NICTA Research Project Award. My full CV is available here.
Research Interest
My current PhD research project focuses on the systems biology of gene expression. I ask questions like "What are the organization principles
of gene regulatory networks?", "How did GRN structures evolve?", "How do GRN structures affect gene expression dynamics?",
"How can we better infer GRN from various experimental data?", "How can we understand human diseases in terms of GRN structures
and expression dynamics?". I am always open to new collaboration opportunities in the general areas of systems biology and bioinformatics.
I have experience and interest in the following research areas:
- Systems biology of the human heart
- Evolutionary origin of complex gene regulatory network (GRN)
- Inference of GRN from microarray data
- Analysis and visualization of complex networks
- Microarray data analysis
- Graph drawing
- Visualization
- Proteomics
- Data mining in large biological databases
- Machine learning using graphical models
- Software Engineering
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Publications
- Jermiin LS, Ho JWK, Lau KW, Jayaswal V (2009) SeqVis: A tool for detecting compositional heterogeneity
among aligned nucleotide sequences. In Bioinformatics for DNA sequence analysis (Ed. Posada D), Humana Press, Totowa, NJ. (Invited, in press)
- Ho JWK, Koundinya R, Caetano TS, dos Remedios CG, Charleston MA (2008)
Inferring differential leukocyte activity from antibody microarrays using a latent variable model,
Genome Informatics (accepted)
- Ho JWK, Stefani M, dos Remedios CG, Charleston MA (2008) Differential variability analysis of gene expression
and its application to human diseases, Bioinformatics, 24, i390-i398
- Ho JWK, Charleston MA (2007) Modeling the Evolution of Gene Regulatory Networks
In Proceedings of The Eighth International Conference on Systems Biology (ICSB 2007), Long Beach, USA
- Ho JWK, Morrissey B, Downard KM (2007) A Computer Algorithm for the Identification of
Protein Interaction from the Spectra of Masses (PRISM). J. Am. Soc. Mass Spectrom., 18, 563-566
- Ho JWK, Adams CE, Lew JB, Matthews TJ, Ng CC, Shahabi-Sirjani A, Tan LH, Zhao Y,
Easteal S, Wilson SR, Jermiin LS (2006) SeqVis: Visualization of compositional heterogeneity
in large alignments of nucleotides. Bioinformatics, 22(17), 2162-2163
- Ho JWK, Manwaring T, Hong SH, Roehm U, Fung DCY, Xu K, Kraska T, Hart D (2006)
PathBank: Web-based Querying and Visualization of an Integrated Biological Pathway Database.
In Banissi E, Sarfraz M, Huang ML, Wu Q (Eds) Computer Graphics, Imaging and Visualization
- Techniques and Application (Proceedings of CGIV2006), IEEE Computer Society,84-89
- Ho J, Lukov L, Chawla S (2005) Sequential Pattern Mining with Constraints on Large Protein
Databases. In Chakrabarti S, Sudarshan S, Radha Krishnan P (Eds) Proceedings of the 12th
International Conference on Management of Data (COMAD 2005b), 89-100
- Ho J, Hong SH (2005) Drawing Clustered Graph in Three Dimensions. In Haely P, Nikolov NS
(Eds) Proceedings of the 13th International Symposium of Graph Drawing (GD2005). Lecture
Notes in Computer Science, Springer, 492-502
- Ahmed A, Dwyer T, Foster M, Fu X, Ho J, Hong SH, Koschutzki D, Murray C, Nikolov N, Taib
R, Tarassov A, Xu K, (2005) GEOMI:GEOmetry for Maximum Insight. In Haely P, Nikolov NS
(Eds) Proceedings of the 13th International Symposium of Graph Drawing (GD2005). Lecture
Notes in Computer Science, Springer,468-479
Poster
- Ho JWK (2008) Towards a Bayesian network approach for microarray gene set analysis.
The fourth ISCB Student Symposium, Toronto, Canada
- Ho JWK, Stefani M, dos Remedios C and Charleston MA (2007) Computational Genomics of The Failing Heart
ICE-EM Summer Symposium in Bioinformatics (BioinfoSummer 2007), Canberra, Australia Winner of the Hilary Booth Prize for the best poster
- Ho JWK, Charleston MA (2007) Modeling the Evolution of Gene Regulatory Networks
The Eighth International Conference on Systems Biology (ICSB 2007), Long Beach, USA
- Ho JWK, Charleston MA(2007) Assessing Limitations of Gene Regulatory Network Inference Methods
The Fifth Asia Pacific Bioinformatics Conference (APBC 2007), Hong Kong, China
- Ho JWK, Charleston MA (2006) Evolving and Simulating Gene Regulatory Networks
The First Bioinformatics Australia Conference, Sydney, Australia
Thesis
- Ho JWK (2006) Computational Analysis of Evolution and Inference of Gene Regulatory Networks. BSc (Advanced) (Honours) Thesis, School of Biological Sciences, University of Sydney
Software
- Heart Tissue Bank - A SQL database management system for a collection of human heart tissues (restricted access)
- SeqVis - A tool to visualize compositional heterogeneity in large alignmnet of
nucleotide sequences.
- GNLab - A tool of large-scale analysis of gene regulatory network
- PexSPAM - A tool for mining high-confident sequential features for protein secondary structure prediction
- GEOMI - A 3D visual analytic tool. It includes a few modules for clusterd graph drawing that I developed. A gallery of
3D clustered graph visualization is available here .
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