Analytics of Biological Sequence Data
 
Dr. WONG Wing Cheong
Principal Investigator
 
Group Members
 
NameTitle
Dr. WONG Wing CheongPrincipal Investigator
Mr. TANTOSO ErwinBioinformatics Specialist
Mr. TAY Wei HongSoftware Architect
 
Research Overview

Since the declared completion of the human genome sequence in 2003, high throughput omics based (array or sequence) technology has advanced considerably. The latter is exceptional in profiling which aims to elucidate highly expressed or strongly regulated genes/proteins but it does not address the problem of unraveling the biological functions of the elucidated proteins. Added to that, the biological functions of many proteins remain either elusive or inconclusive till today. Taken together, function prediction remains the only viable approach to provide the biologists with a first glance into the possible biological functions of their unknown proteins as a complimentary approach to profiling experiments.

With the above background as motivation, our group focuses on developing analytics methods (through computational and statistical methods) to improve the interpretation of biological sequence data that arises from these high throughput experimental platforms in a collective manner. Concurrently, we also exist to address both the technical and scientific needs of our external clinical collaborators as well.


 
Selected Publications
 

Methodology:

  1. Wong WC, Maurer-Stroh S, Eisenhaber B, Eisenhaber F.
    On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation.
    BMC Bioinformatics. 2014. 15:166. doi: 10.1186/1471-2105-15-166.

  2. Wong WC, Maurer-Stroh S, Schneider G, Eisenhaber F.
    TMSOC (Transmembrane helix: Simple Or Complex).
    Nucleic Acids Res. 2012 Jul (Web Server issue), doi: 10.1093/nar/GKS379

  3. Wong WC, Maurer-Stroh S, Eisenhaber F.
    Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins.
    Biol Direct. 2011 Oct 25;6(1):57. [Epub ahead of print]
    PubMed PMID:22024092.

  4. Wong WC, Maurer-Stroh S, Eisenhaber F.
    The Janus-faced E-values of HMMER2: extreme value distribution or logistic function?
    J Bioinform Comput Biol. 2011 Feb;9(1):179-206.
    PubMed PMID: 21328712.

  5. Wong WC, Maurer-Stroh S, Eisenhaber F.
    More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology.
    PLoS Comput Biol. 2010 Jul 29;6(7):e1000867.
    PubMed PMID: 20686689; PubMed Central PMCID: PMC2912341.

  6. Wong WC, Cho SY, Quek C.
    R-POPTVR: a novel reinforcement-based POPTVR fuzzy neural network for pattern classification.
    IEEE Trans Neural Netw. 2009 Nov;20(11):1740-55. Epub 2009 Sep 18.
    PubMed PMID: 19770091.

  7. Wong WC, Loh M, Eisenhaber F.
    On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation.
    Biol Direct. 2008 Jun 3;3:23.
    PubMed PMID: 18522715; PubMed Central PMCID: PMC2453111.


Application:

  1. Wong FY, Liem N, Xie C, Yan FL, Wong WC, Wang LZ, Yong WP.
    Combination Therapy with Gossypol Reveals Synergism against Gemcitabine Resistance in Cancer Cells with High BCL-2 Expression.
    PLoS One 2012, 7(12), e50786. doi: 10.1371/journal.pone.0050786.

  2. Ong SM, Tan YC, Beretta O, Jiang D, Yeap WH, Tai JJ, Wong WC, Yang H, Schwarz H, Lim KH, Koh PK, Ling KL, Wong SC.
    Macrophages in Human Colorectal Cancer are Pro-inflammatory and Prime T cells towards an Anti-Tumour Type-1 Inflammatory Response.
    Eur J Immunol. 2011 Oct 18. doi: 10.1002/eji.201141825. [Epub ahead of print]
    PubMed PMID: 22009685.

  3. Toh B, Wang X, Keeble J, Sim WJ, Khoo K, Wong WC, Kato M, Prevost-Blondel A, Thiery JP, Abastado JP.
    Mesenchymal transition and dissemination of cancer cells is driven by myeloid-derived suppressor cells infiltrating the primary tumor.
    PLoS Biol. 2011 Sep;9(9):e1001162. Epub 2011 Sep 27.
    PubMed PMID: 21980263; PubMed Central PMCID: PMC3181226.

  4. Nardin A, Wong WC, Tow C, Molina TJ, Tissier F, Audebourg A, Garcette M, Caignard A, Avril MF, Abastado JP, Provost-Blondel A.
    Dacarbazine promotes stromal remodeling and lymphocyte infiltration in cutaneous melanoma lesions.
    J Invest Dermatol. 2011 Sep;131(9):1896-905. doi: 10.1038/jid.2011.128. Epub 2011 Jun 9.
    PubMed PMID: 21654834.

  5. Wong KL, Tai JJ, Wong WC, Han H, Sem X, Yeap WH, Kourilsky P, Wong SC.
    Gene expression profiling reveals the defining features of the classical, intermediate, and nonclassical human monocyte subsets.
    Blood. 2011 Aug 4;118(5):e16-31. Epub 2011 Jun 7.
    PubMed PMID: 21653326.

  6. Prokesch A, Bogner-Strauss JG, Hackl H, Rieder D, Neuhold C, Walenta E, Krogsdam A, Scheideler M, Papak C, Wong WC, Vinson C, Eisenhaber F, Trajanoski Z.
    Arxes: retrotransposed genes required for adipogenesis.
    Nucleic Acids Res. 2011 Apr;39(8):3224-39. Epub 2010 Dec 21.
    PubMed PMID: 21177646; PubMed Central PMCID: PMC3082915.

  7. Changqing Zhao, Yann-Chong Tan, Wong WC, Xiaohui Sem, Huoming Zhang, Hao Han, Siew-Min Ong, Kok-Loon Wong, Wei-Hseun Yeap, Siu-Kwan Sze, Philippe Kourilsky and Siew-Cheng Wong.
    The CD14+/lowCD16+ monocyte subset is more susceptible to spontaneous and oxidant-induced apoptosis than the CD14highCD16-subset.
    Cell Death and Disease 2010, v1, e95, doi:10.1038/cddis.2010.69.

  8. Bogner-Strauss JG, Prokesch A, Sanchez-Cabo F, Rieder D, Hackl H, Duszka K, Krogsdam A, Di Camillo B, Walenta E, Klatzer A, Lass A, Pinent M, Wong WC, Eisenhaber F, Trajanoski Z.
    Reconstruction of gene association network reveals a transmembrane protein required for adipogenesis and targeted by PPAR?
    Cell Mol Life Sci. 2010 Dec;67(23):4049-64. Epub 2010 Jun 15.
    PubMed PMID: 20552250.

  9. Zhao C, Zhang H, Wong WC, Sem X, Han H, Ong SM, Tan YC, Yeap WH, Gan CS, Ng KQ, Koh MB, Kourilsky P, Sze SK, Wong SC.
    Identification of novel functional differences in monocyte subsets using proteomic and transcriptomic methods.
    J Proteome Res. 2009 Aug;8(8):4028-38.
    PubMed PMID: 19514703.


 
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