Homepage of Wong Wing-Cheong

Professional appointments

2017-present	Principal Investigator (Joint appointment) Institute of Precision Medicine (PRISM) Singhealth Duke-NUS
2017-present	Principal Investigator Analytics of Biological Data Sequence (ABSD) Bioinformatics Institute (BII) Agency for Science Technology and Research (A*STAR), Singapore
2014-2016	Assistant Principal Investigator Analytics of Biological Data Sequence (ABSD) Bioinformatics Institute (BII) Agency for Science Technology and Research (A*STAR), Singapore
2012-2013	Postdoctoral Research Fellow Bioinformatics Institute (BII) Agency for Science Technology and Research (A*STAR), Singapore
2008-2011	Senior Research Associate Bioinformatics Institute (BII) Agency for Science Technology and Research (A*STAR), Singapore
2005-2007	Research Associate Bioinformatics Institute (BII) Agency for Science Technology and Research (A*STAR), Singapore

Education

2008-2011	Ph.D in Computer Science (summa cum laude) Faculty of Mathematics & Computer Science University of Leipzig, Germany Towards a complete sequence homology concept: Limitations and applications
2003-2004	M.Sc in Bioinformatics Faculty of Medicine National University of Singapore (NUS), Singapore
2001-2002	B.Sc (Honours) in Computer Engineering School of Computer Engineering Nanyang Technological University (NTU), Singapore
1998-2001	B.Sc (Merit) in Computer Engineering School of Computer Engineering Nanyang Technological University (NTU), Singapore

Summary of Bioinformatics practice

i) Biological function prediction of novel protein sequences for subsequent wet-lab validation (see publications 4, 8, 17, 20, 23). Current focus on the completeness of the sequence homology concept and therein the development of novel computational approaches to improve existing sequence searches of both globular and alpha-helical transmembrane membrane proteins, which leads to a series of key publications (see publications 3, 5, 7, 10, 11, 16, 19).

ii) Statistical analysis of omics-based high-throughput datasets for wet-lab collaborators to support downstream validation. This includes the biological pathway analysis of collaborators array-based/NGS‑based genomic or proteomic data to make sense of the specific biological context of the experiments (see publications 6, 9, 12, 13, 14, 15, 18, 22).

iii) Development of statistical method to elucidate target genes that were previously obscured by standard methods (see publication 24) with successful application on collaborators datasets. Furthermore, the customization of existing and self-developed methodologies into a task-specific computational workflow. These activities have led to several co-authored high impact publications, particularly in the field of immunology.

iv) Development of machine learning based methodology for improved pattern recognition (see publication 19).

Invited reviewer for manuscripts of scientific journals

BMC Bioinformatics, Oxford Bioinformatics, Biology Direct, Gene, PLoS ONE, Drug Discovery Today, Journal of Bioinformatics and Computational Biology, Transactions on Computational Biology & Bioinformatics

Invited lectures

BI6193 Current Computational Methods & Databases for Protein Sequence & Structure Analysis

(for the MSc in Bioinformatics, NTU)

Gene set enrichment analysis with DAVID

MGD5220 Array and Omics (for the Department of Biochemistry, NUS)

Enrichment analysis : From statistical significance to biological interpretation

Programming skills

C/C++, Java, Perl, MatLab, R

Book Chapter

Eisenhaber B, Kuchibhatla D, Sherman W, Sirota F, Berezovsky I, Wong WC, Eisenhaber F. The recipe for protein sequence-based function prediction and its implementation in the ANNOTATOR software environment., Methods in Molecular Biology [In press]

Publications

1. Wong WC*, Ng HK, Tantoso E, Soong R, Eisenhaber F 2017, Finite size effects in miRNA transcript sequencing count distribution : its necessary power law correction and implications for downstream normalization and comparative analysis [Submitted]

2. Baker J, Wong WC, Eisenhaber E, Warwicker J, Eisenhaber F, 2017, Charged residues next to transmembrane regions revisited: "Positive-inside rule" is complemented by the "negative inside depletion/outside enrichment rule". BMC Biology. In press

3. Yap CK, Eisenhaber B, Eisenhaber F, Wong WC*, 2016, Utilizing HMMER3's speed and HMMER2's sensitivity and specificity in the glocal alignment mode for improved large-scale protein domain annotation. Biol Direct. 2016 Nov 29;11(1):63. PubMed PMID: 27894340; PubMed Central PMCID: PMC5126834.

4. Wu G, Zhao H, Li C, Rajapakse MP, Wong WC, Xu J, Saunders CW, Reeder NL, Reilman RA, Scheynius A, Sun S, Billmyre BR, Li W, Averette AF, Mieczkowski P, Heitman J, Theelen B, Schroder MS, De Sessions PF, Butler G, Maurer-Stroh S, Boekhout T, Nagarajan N, Dawson TL Jr. Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PLoS Genet. 2015 Nov 5;11(11):e1005614. doi: 10.1371/journal.pgen.1005614. eCollection 2015 Nov.

5. Wong WC*, Yap CK, Eisenhaber B, Eisenhaber F. dissectHMMER: a HMMER based score dissection framework that statistically evaluates fold critical sequence segments for domain fold similarity; a pragmatic step towards homology inference., Biology Direct. 2015 10:39, doi: 10.1186/s13062-015-0068-3

6. MT Dang, Wong WC, SM Ong; Josephine Lum, JM Chen, M Poidinger, F Zolezzi, SC Wong. Micro-RNA expression profiling of human blood monocyte subsets highlights functional differences., Immunology, 2015, doi: 10.1111/imm.12456

7. 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

8. Maurer-Stroh S, Gunalan V, Wong WC, Eisenhaber F. A simple shortcut to unsupervised alignment-free phylogenetic genome groupings, even from unassembled sequencing reads. J Bioinform Comput Biol. 2013 Dec;11(6):1343005. doi: 10.1142/S0219720013430051. Epub 2013 Dec 2. PubMed PMID: 24372034.

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

10. 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

11. 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.

12. 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.

13. 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.

14. 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.

15. 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.

16. 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.

17. 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.

18. 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, 2010, The CD14+/lowCD16+ monocyte subset is more susceptible to spontaneous and oxidant-induced apoptosis than the CD14highCD16-subset., Cell Death and Disease, v1, e95, doi:10.1038/cddis.2010.69

19. 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.

20. 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 PPARγ. Cell Mol Life Sci. 2010 Dec;67(23):4049-64. Epub 2010 Jun 15. PubMed PMID: 20552250.

21. 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.

22. 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.

23. Ooi HS, Kwo CY, Wildpaner M, Sirota FL, Eisenhaber B, Maurer-Stroh S, Wong WC, Schleiffer A, Eisenhaber F, Schneider G. ANNIE: integrated de novo protein sequence annotation. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W435-40. Epub 2009 Apr 23. PubMed PMID: 19389726; PubMed Central PMCID: PMC2703921.

24. 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.

* corresponding author

Contact

30 Biopolis Street, #07-01, Matrix, Singapore 138671

Email: wongwc@bii.a-star.edu.sg