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This document provides a summary of Chung-Chau Hon's background and qualifications. It includes his current position as a postdoctoral fellow at the Pasteur Institute in Paris, his education history which includes a BSc, MPhil, and PhD from the University of Hong Kong, as well as an internship at IBM. It also outlines his areas of expertise including genomics, transcriptomics, phylogenetics, and population genetics. Finally, it lists his publications in these areas and relevant technical skills.

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A. Basic Information NAME, SURNAME (EMAIL) CURRENT POSITION Chung-Chau, HON Transcriptome and Epigenome Platform of Genopole, & Cellular Biology of Parasitism Unit, BIRTH INFOMATION Postdoctoral Fellow, (chung-chau.hon@pasteur.fr) 22/04/1979 (Age: 34, male) Hong Kong Pasteur Institute, Paris EDUCATION and TRANING INSTITUTION AND LOCATION DEGREE/POSITION YEAR FIELD OF STUDY The University of Hong Kong (Hong Kong) Bachelor of Science 1998-2001 Molecular Biotechnology, General Bioinformatics Supervisor: Prof. Frederick Chi-Ching Leung fcleung@hkucc.hku.hk The University of Hong Kong (Hong Kong) Master of Philosophy 2001-2003 Molecular Virology Supervisor: Prof. Frederick Chi-Ching Leung fcleung@hkucc.hku.hk IBM Computational Biology Center (New York, USA) Computational biologist (Intern) 2005 Massively parallel molecular dynamics simulations Supervisor: Dr. Ruhong Zhou ruhongz@us.ibm.com The University of Hong Kong (Hong Kong) Doctor of Philosophy 2003-2008 Population Genetics of Viruses Supervisor: Prof. Frederick Chi-Ching Leung fcleung@hkucc.hku.hk EXPERTISE by TOPICS (DURATION: long, medium and short) • • • • • • • • Genomics and transcriptomics of protozoan parasites (3 years); Designing and analyzing RNA-Seq experiments (3 years); Gene regulation by small RNA and long non-coding RNA in protozoan parasites (2 years); Comparative genomics of closely related species (3 years); Gene expression analyses using microarray and RNA-Seq (5 years); Phylogenetics and population genetics of viruses (8 years); Origins of emerging viral diseases (8 years); Massively parallel molecular dynamics simulations (1 year); EXPERTISE by TECHNIQUES (LEVEL: proficient, semi-proficient and amateur) • • • • • • • • • • • • • • Development of custom scripts (mainly Perl) for analyses of next generation sequencing data (proficient); Genome-wide mapping of transcription start sites and polyadenylation sites of Pol II transcripts (proficient); Discovery of cis-regulatory motifs for transcription initiation and polyadenylation (semi-proficient); Revision of gene models and annotation of antisense transcripts using RNA-Seq (proficient); Annotation of alternative splicing transcript isoforms using RNA-Seq (proficient); Characterization of endogenous small RNA populations using RNA-Seq (proficient); Differential expression and functional enrichment analyses based on next generation sequencing data (semi-proficient); Weighted gene correlation network analyses using microarray expression data (semi-proficient); Identification of orthological and syntenic genes between closely related species (proficient); Identification and annotation of genes in orthologous protein families (proficient); Application of Bayesian, parsimony and likelihood methods in population genetics (semi-proficient); Large scale screening for viral recombination (proficient); Large scale genotyping of viruses (proficient); Massively parallel molecular dynamics simulations (amateur);
B. Postdoctoral Employment I. Senior Postdoctoral Fellow, Transcriptome and Epigenome Platform of Genopole, & Cellular Biology of Parasitism Unit, Institute of Pasteur (Paris) 2011-Now • Topic: Application of Next Generation Sequencing on Comparative genomics and Transcriptomics of Entamoeba; • Supervisor: Dr Nancy Guillen; email: nguillen@pasteur.fr and Dr Jean-Yves Coppee; email: jycoppee@pasteur.fr II. Postdoctoral Fellow, Cellular Biology of Parasitism Unit, Institute of Pasteur (Paris) • Topic: Genomics of Entamoeba; • Supervisor: Dr Nancy Guillen; email: nguillen@pasteur.fr 2008-2011 C. Competitive External Funds I. Agence Nationale Recherche Genomic Grant 2010 2010-2013 • Title: Understating the Pathogenicity of Entamoeba Using Comparative Transcriptomics and Phylogenomics • Amount: €641,744 (US$869,258), in total for 3 years; • Role: Proposal writing, project management, corresponding author, high throughput sequencing data analysis D. Specific Skill Sets (level: proficient, semi-Proficient and amateur) I. Computational Skills • • • • • • Perl scripting (proficient); Unix command line, system maintenance and software compiling and installation (proficient); Shell scripting (semi-proficient); Remote working on a server farm (semi-proficient); Python scripting (amateur); MySQL database (amateur); II. Next Generation Sequencing Data Analysis Skills • • • • • • • • Basic read data mapping using bowtie, tophat, eXpress, SOAP etc (proficient); Basic read data format handling using samtools, picard, bamtools, fastqc etc (proficient); Creating custom analysis pipelines using shell and Perl scripts (proficient); Discovery of transcription start sites and polyadenylation sites using custom scripts (proficient); Transcriptome assembly using cufflinks and custom scripts (proficient); Genome-wide discovery of cis-regulatory motifs using MEME suite and custom scripts (proficient); Annotation of long non-coding and antisense transcripts using custom scripts (proficient); Annotation of endogenous small RNA populations using custom scripts (proficient); III. Gene Expression Data and System Biology Analysis Skills • Differential expression analyses using DESeq, Cuffdiff, EdgeR etc (proficient); • Functional enrichment analyses using GSEA, GOSeq, FUNC_hyper, etc (proficient); • Gene co-expression network analyses using WGCNA, Cytoscape and custom scripts (semi-proficient); IV. Comparative Genomic Analysis Skills • Identification of orthological genes using orthoMCL and inparanoid (proficient); • Identification of syntenic genes using DAGChainer etc (semi-proficient); • Genome-wide protein family clustering and classification using spectral clustering (SCPS) (proficient); V. Phylogenetic and Population Genetics Analysis Skills • • • • • Automatic retrieval of viral sequences from NCBI using custom scripts (proficient); Bayesian based molecular clock and coalescent analyses using BEAST (proficient); Likelihood based selection pressure analyses using PAML and HyPhy (semi-proficient); Large scale phylogeny reconstruction using PAML, PAUP*, mrBayes, BEAST etc (proficient); Semi-automatic viral genotyping base on large phylogenies using custom scripts (proficient);
D. Publications I. Genomics and Transcriptomics (13 journal articles & 3 book chapters) 1. Hon,C.-C., Weber, C., Sismeiro, O., Proux, C., Koutero, M., Deloger, M., Das, S., Agrahari, M., Dillies, M.-A., Jagla, B., Coppee, J.Y., Bhattacharya, A. and Guillen, N. (2012) Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica. Nucleic Acids Res, 10.1093/nar/gks1271. (Corresponding and first author). 2. Vasquez,J.-J., Hon,C.-C., Vanselow J.T., Schlosser A. and Siegel, T.N (2013). Comparative ribosome-profiling reveals extensive translational complexity in different Trypanosoma brucei life-cycle stages. Nucleic Acids Res accepted. 3. Thibeaux, R., Weber. C., Hon. C.-C., Dillies, M.-A., Copee, J.Y., Labruye, E. and Guillen, N. (2013). Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon. PLoS Pathogens accepted. 4. Njoya, E.M., Weber. C., Hernandez-Cuevas. N.A., Hon. C.-C., Janin, Y, Kamini, M.F.G, Moundipa, P.F and Guillén, N (2013). Bioassay-guided fractionation of Codiaeum variegatum’s aqueous extract killing Entamoeba histolytica target ceramide biosynthesis. PLoS Negl Trop Dis in press. 5. Hon,C.-C., Weber,C., Koutero,M., Coppée,J.-Y., Deloger,M and Guillen,N. Surveying Entamoeba histolytica transcriptome using massively parallel cDNA sequencing. In ‘Amebiasis: Biology and Pathogenesis of Entamoeba’ by SPRINGER In Press. (Corresponding and first author) 6. Janbon, G., Ormerod, K. L., Paulet , D., Byrnes, E., Chatterjee, G., Yadav, V., Hon, C.-C., A., Cuomo, C. A., Dietrich, F. S., Billmyre, Brunel, F, Bahn Y.-S., Chen, W., Chen, Y., Chow E. W. L., Coppée, J.Y., FloydAverette, A., Gaillardin C., Gerik, K. J., Goebels, C., Goldberg, J., Gonzalez-Hilarion S., Gujja, S., Hamlin, J. L., Hsueh, Y.-P., Ianiri, G., Jones, S., Kodira, C. D., Lam, W., Marra, M., Mesner, L. D., Mieczkowski, P.A., Moyrand, F., Nielsen, K., Proux, C., Rossignol, T., Schein1, J. E., Sun, S., Wood, I. A., Zeng, Q., Neuvéglise, C., Newlon, C. S., Perfect, J. R., Lodge, J. K., Idnurm. A., Stajich, J. E., Kronstad, J. W., Sanya, K. Heitman, J., Fraser, J., Cuomo C. A. and Dietrich F. (2013). The genome sequence of Cryptococcus neoformans var. grubii reveals complex mechanisms of RNA expression and virulence plasticity. PLoS Genetics in 1st revision. 7. Siegel, N, Hon,C.-C., Zhang,Q., Lopez-Rubio,J.J., Coppée,J.-Y., Sismeiro,O and Scherf,A . Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum. BMC Genomics in 2nd revision. 8. Santi-Rocca,J., Smith,S., Weber,C., Pineda,E., Hon,C.-C., Saavedra,E., Olivos-García,A., Rousseau,S., Dillies,M.-A., Coppée,J.-Y., et al. (2012) Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide. PLoS ONE, 7, e31777. 9. Marquay Markiewicz,J., Syan,S., Hon,C.-C., Weber,C., Faust,D. and Guillen,N. (2011) A proteomic and cellular analysis of uropods in the pathogen Entamoeba histolytica. PLoS Negl Trop Dis, 5, e1002. 10. Hon,C.-C., Nakada-Tsukui,K., Nozaki,T. and Guillen,N. (2009) Dissecting the actin cytoskeleton of Entamoeba histolytica from a genomic perspective. In Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. Edited by G. C. Clark, P. J. Johnson & A. R.D. Tucson AZ, USA: Caister Academic Press. (First author) 11. Yeung,Y.S., Yip,C.W., Hon,C.-C., Chow,K.Y.C., Ma,I.C.M., Zeng,F. and Leung,F.C.C. (2008) Transcriptional profiling of Vero E6 cells over-expressing SARS-CoV S2 subunit: insights on viral regulation of apoptosis and proliferation. Virology, 371, 32–43. 12. Wang,Y., Zeng,F., Hon,C.-C., Zhang,Y. and Leung,F.C.C. (2008) The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). FEMS Microbiol Lett, 280, 34–41. 13. Wong,R.T.-Y., Hon,C.-C., Zeng,F. and Leung,F.C.C. (2007) Screening of differentially expressed transcripts in infectious bursal disease virus-induced apoptotic chicken embryonic fibroblasts by using cDNA microarrays. J Gen Virol, 88, 1785–1796. 14. Zeng,F., Hon,C.-C., Sit,W.-H., Chow,K.Y.-C., Hui,R.K.-H., Law,I.K.-M., Ng,V.W.-L., Yang,X.-T., Leung,F.C.C. and Wan,J.M.-F. (2005) Molecular characterization of Coriolus versicolor PSP-induced apoptosis in human promyelotic leukemic HL-60 cells using cDNA microarray. Int J Oncol, 27, 513–523.
15. Cheung,K.H., Hon,C.-C. and Leung,F.C.C. (2003) Illustration of Enhanced Features of Visual Genome Explorer Beta 2.1 by Comparative Analysis of Helicobacter pylori Strains 26695 and J99 Genomes. Biocomputing: Computer Tools for Biologists. 16. Hon,C.-C., Chow,Y.C., Zeng,F.Y. and Leung,F.C.C. (2003) Genetic authentication of ginseng and other traditional Chinese medicine. Acta Pharmacol Sin, 24, 841–846. (First author) II. Phylogenetics and Population Genetics (18 journal articles) 17. Lam,T.T.-Y., Chong,Y.L., Shi,M., Hon,C.-C., Li,J., Martin,D.P., Tang,J.W.-T., Mok,C.-K., Shih,S.-R., Yip,C.W., et al. (2013) Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infect Genet Evol, 10.1016/j.meegid.2013.03.015. 18. Lam,T.T.-Y., Hon,C.-C., Lemey,P., Pybus,O.G., Shi,M., Tun,H.M., Li,J., Jiang,J., Holmes,E.C. and Leung,F.C.C. (2012) Phylodynamics of H5N1 avian influenza virus in Indonesia. Mol Ecol, 21, 3062–3077. 19. Shi,M., Lam,T.T.-Y., Hon,C.-C., Hui,R.K.-H., Faaberg,K.S., Wennblom,T., Murtaugh,M.P., Stadejek,T. and Leung,F.C.C. (2010) Molecular epidemiology of PRRSV: a phylogenetic perspective. Virus Res, 154, 7–17. 20. Li,Y., Ge,X., Hon,C.-C., Zhang,H., Zhou,P., Zhang,Y., Wu,Y., Wang,L.-F. and Shi,Z. (2010) Prevalence and genetic diversity of adeno-associated viruses in bats from China. J Gen Virol 91, 2601–2609. 21. Shi,M., Lam,T.T.-Y., Hon,C.-C., Murtaugh,M.P., Davies,P.R., Hui,R.K.-H., Li,J., Wong,L.T.-W., Yip,C.W., Jiang,J.-W., et al. (2010) Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. J Virol, 84, 8700–8711. 22. Yuan,J., Hon,C.-C., Li,Y., Wang,D., Xu,G., Zhang,H., Zhou,P., Poon,L.L.M., Lam,T.T.-Y., Leung,F.C.C., et al. (2010) Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J Gen Virol, 91, 1058–1062. (Equally contributed first author) 23. Lam,T.T.-Y., Hon,C.-C. and Tang,J.W. (2010) Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Critical Reviews in Clinical Laboratory Sciences, 47, 5–49. 24. Yip,C.W., Hon,C.-C., Shi,M., Lam,T.T.-Y., Chow,K.Y.-C., Zeng,F. and Leung,F.C.C. (2009) Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses. Infect Genet Evol, 9, 1185–1196. 25. Hon,C.-C., Lam,T.T.-Y., Yip,C.W., Wong,R.T.-Y., Shi,M., Jiang,J., Zeng,F. and Leung,F.C.C. (2008) Phylogenetic evidence for homologous recombination within the family Birnaviridae. J Gen Virol, 89, 3156– 3164. (First author) 26. Hon,C.-C., Lam,T.-Y., Shi,Z.-L., Drummond,A.J., Yip,C.W., Zeng,F., Lam,P.-Y. and Leung,F.C.C. (2008) Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol, 82, 1819–1826. (First author) 27. Lam,T.-Y., Hon,C.-C., Wang,Z., Hui,R.K.-H., Zeng,F. and Leung,F.C.C. (2008) Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events. Virus Res, 131, 271–278. 28. Lam,T.T.-Y., Hon,C.-C., Lam,P.-Y., Yip,C.W., Zeng,F. and Leung,F.C.C. (2008) Comments to the predecessor of human SARS coronavirus in 2003-2004 epidemic. Vet Microbiol, 126, 390–393. 29. Lam,T.T.-Y., Hon,C.-C., Pybus,O.G., Kosakovsky Pond,S.L., Wong,R.T.-Y., Yip,C.W., Zeng,F. and Leung,F.C.C. (2008) Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathog, 4, e1000130. 30. Ma,C.M., Hon,C.-C., Lam,T.-Y., Li,V.Y.-Y., Wong,C.K.-W., de Oliveira,T. and Leung,F.C.C. (2007) Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China. J Gen Virol, 88, 1733–1737. 31. Hon,C.-C., Lam,T.-Y., Drummond,A., Rambaut,A., Lee,Y.-F., Yip,C.W., Zeng,F., Lam,P.-Y., Ng,P.T.W. and Leung,F.C.C. (2006) Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B. J Virol, 80, 8503–8509. (First author)
32. Guan,Y., Peiris,J.S.M., Zheng,B., Poon,L.L.M., Chan,K.H., Zeng,F.Y., Chan,C.W.M., Chan,M.N., Chen,J.D., Chow,K.Y.C. Hon,C.-C, Hui, K.H., Li, J., Li, V.Y.Y., Wang, Y., Leung, S.W., Yuen, K.Y. and Leung F.C. (2004) Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome. Lancet, 363, 99–104. 33. Chow,K.Y.-C., Hon,C.-C., Hui,R.K.-H., Wong,R.T.-Y., Yip,C.W., Zeng,F. and Leung,F.C.C. (2003) Molecular advances in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). Genomics Proteomics Bioinformatics, 1, 247–262. 34. Zeng,F.Y., Chan,C.W.M., Chan,M.N., Chen,J.D., Chow,K.Y.C., Hon,C.-C, Hui,K.H., Li,J., Li,V.Y.Y., Wang, C.Y. Hui, K.H., Li, J., Li, V.Y.Y, Wang, C.Y., Wang, P.Y., Guan, Y., Zheng, B., Poon, L.L.M., Chan, K.H., Yuen, K.Y., Peiris, J.S.M., and Leung F.C. (2003) The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39). Exp. Biol. Med. (Maywood), 228, 866–873. III. Molecular Virology and Immunology (9 journal articles) 35. Li,K.K.B., Yip,C.W., Hon,C.C., Lam,C.Y., Zeng,F. and Leung,F.C.C. (2012) Characterisation of animal angiotensin-converting enzyme 2 receptors and use of pseudotyped virus to correlate receptor binding with susceptibility of SARS-CoV infection. Hong Kong Med J, 18 Suppl 3, 35–38. 36. Yip,C.W., Hon,C.-C., Zeng,F. and Leung,F.C.C. (2012) Cell culture-adapted IBDV uses endocytosis for entry in DF-1 chicken embryonic fibroblasts. Virus Res, 165, 9–16. 37. Chow,K.Y., Yeung,Y.S., Hon,C.C., Zeng,F., Law,K.M. and Leung,F.C. (2008) SARS coronavirus and apoptosis. Hong Kong Med J, 14 Suppl 4, 8–13. 38. Yip,C.W., Yeung,Y.S., Ma,C.M., Lam,P.-Y., Hon,C.-C., Zeng,F. and Leung,F.C.C. (2007) Demonstration of receptor binding properties of VP2 of very virulent strain infectious bursal disease virus on Vero cells. Virus Res, 123, 50–56. 39. Yip,C.W., Hon,C.-C., Zeng,F., Chow,K.Y.C., Chan,K.H., Peiris,J.S.M. and Leung,F.C.C. (2007) Naturally occurring anti-Escherichia coli protein antibodies in the sera of healthy humans cause analytical interference in a recombinant nucleocapsid protein-based enzyme-linked immunosorbent assay for serodiagnosis of severe acute respiratory syndrome. Clin. Vaccine Immunol., 14, 99–101. 40. Zeng,F., Hon,C.-C., Yip,C.W., Law,K.M., Yeung,Y.S., Chan,K.H., Malik Peiris,J.S. and Leung,F.C.C. (2006) Quantitative comparison of the efficiency of antibodies against S1 and S2 subunit of SARS coronavirus spike protein in virus neutralization and blocking of receptor binding: implications for the functional roles of S2 subunit. FEBS Lett, 580, 5612–5620. 41. Chow,K.Y.C., Yeung,Y.S., Hon,C.-C., Zeng,F., Law,K.M. and Leung,F.C.C. (2005) Adenovirus-mediated expression of the C-terminal domain of SARS-CoV spike protein is sufficient to induce apoptosis in Vero E6 cells. FEBS Lett, 579, 6699–6704. 42. Yip,C.W., Hon,C.-C., Zeng,F., Chow,K.Y.C. and Leung,F.C.C. (2004) Prevalence of non-pneumonic infections with SARS-correlated virus. Lancet, 363, 1825–author reply 1826–7. 43. Zeng,F., Chow,K.Y.-C., Hon,C.-C., Law,K.M., Yip,C.W., Chan,K.H., Peiris,J.S.M. and Leung,F.C.C. (2004) Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments. Biochem Biophys Res Commun, 315, 1134–1139. IV. Massively Parallel Molecular Dynamics Simulations (1 journal article) 44. Zhou,R., Eleftheriou,M., Hon,C.-C., Germain,R.S., Royyuru,A.K. and Berne,B.J. (2008) Massively parallel molecular dynamics simulations of lysozyme unfolding. Ibm J Res Dev, 52, 19–30.

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Cvnoheader

  • 1.
    A. Basic Information NAME,SURNAME (EMAIL) CURRENT POSITION Chung-Chau, HON Transcriptome and Epigenome Platform of Genopole, & Cellular Biology of Parasitism Unit, BIRTH INFOMATION Postdoctoral Fellow, (chung-chau.hon@pasteur.fr) 22/04/1979 (Age: 34, male) Hong Kong Pasteur Institute, Paris EDUCATION and TRANING INSTITUTION AND LOCATION DEGREE/POSITION YEAR FIELD OF STUDY The University of Hong Kong (Hong Kong) Bachelor of Science 1998-2001 Molecular Biotechnology, General Bioinformatics Supervisor: Prof. Frederick Chi-Ching Leung fcleung@hkucc.hku.hk The University of Hong Kong (Hong Kong) Master of Philosophy 2001-2003 Molecular Virology Supervisor: Prof. Frederick Chi-Ching Leung fcleung@hkucc.hku.hk IBM Computational Biology Center (New York, USA) Computational biologist (Intern) 2005 Massively parallel molecular dynamics simulations Supervisor: Dr. Ruhong Zhou ruhongz@us.ibm.com The University of Hong Kong (Hong Kong) Doctor of Philosophy 2003-2008 Population Genetics of Viruses Supervisor: Prof. Frederick Chi-Ching Leung fcleung@hkucc.hku.hk EXPERTISE by TOPICS (DURATION: long, medium and short) • • • • • • • • Genomics and transcriptomics of protozoan parasites (3 years); Designing and analyzing RNA-Seq experiments (3 years); Gene regulation by small RNA and long non-coding RNA in protozoan parasites (2 years); Comparative genomics of closely related species (3 years); Gene expression analyses using microarray and RNA-Seq (5 years); Phylogenetics and population genetics of viruses (8 years); Origins of emerging viral diseases (8 years); Massively parallel molecular dynamics simulations (1 year); EXPERTISE by TECHNIQUES (LEVEL: proficient, semi-proficient and amateur) • • • • • • • • • • • • • • Development of custom scripts (mainly Perl) for analyses of next generation sequencing data (proficient); Genome-wide mapping of transcription start sites and polyadenylation sites of Pol II transcripts (proficient); Discovery of cis-regulatory motifs for transcription initiation and polyadenylation (semi-proficient); Revision of gene models and annotation of antisense transcripts using RNA-Seq (proficient); Annotation of alternative splicing transcript isoforms using RNA-Seq (proficient); Characterization of endogenous small RNA populations using RNA-Seq (proficient); Differential expression and functional enrichment analyses based on next generation sequencing data (semi-proficient); Weighted gene correlation network analyses using microarray expression data (semi-proficient); Identification of orthological and syntenic genes between closely related species (proficient); Identification and annotation of genes in orthologous protein families (proficient); Application of Bayesian, parsimony and likelihood methods in population genetics (semi-proficient); Large scale screening for viral recombination (proficient); Large scale genotyping of viruses (proficient); Massively parallel molecular dynamics simulations (amateur);
  • 2.
    B. Postdoctoral Employment I.Senior Postdoctoral Fellow, Transcriptome and Epigenome Platform of Genopole, & Cellular Biology of Parasitism Unit, Institute of Pasteur (Paris) 2011-Now • Topic: Application of Next Generation Sequencing on Comparative genomics and Transcriptomics of Entamoeba; • Supervisor: Dr Nancy Guillen; email: nguillen@pasteur.fr and Dr Jean-Yves Coppee; email: jycoppee@pasteur.fr II. Postdoctoral Fellow, Cellular Biology of Parasitism Unit, Institute of Pasteur (Paris) • Topic: Genomics of Entamoeba; • Supervisor: Dr Nancy Guillen; email: nguillen@pasteur.fr 2008-2011 C. Competitive External Funds I. Agence Nationale Recherche Genomic Grant 2010 2010-2013 • Title: Understating the Pathogenicity of Entamoeba Using Comparative Transcriptomics and Phylogenomics • Amount: €641,744 (US$869,258), in total for 3 years; • Role: Proposal writing, project management, corresponding author, high throughput sequencing data analysis D. Specific Skill Sets (level: proficient, semi-Proficient and amateur) I. Computational Skills • • • • • • Perl scripting (proficient); Unix command line, system maintenance and software compiling and installation (proficient); Shell scripting (semi-proficient); Remote working on a server farm (semi-proficient); Python scripting (amateur); MySQL database (amateur); II. Next Generation Sequencing Data Analysis Skills • • • • • • • • Basic read data mapping using bowtie, tophat, eXpress, SOAP etc (proficient); Basic read data format handling using samtools, picard, bamtools, fastqc etc (proficient); Creating custom analysis pipelines using shell and Perl scripts (proficient); Discovery of transcription start sites and polyadenylation sites using custom scripts (proficient); Transcriptome assembly using cufflinks and custom scripts (proficient); Genome-wide discovery of cis-regulatory motifs using MEME suite and custom scripts (proficient); Annotation of long non-coding and antisense transcripts using custom scripts (proficient); Annotation of endogenous small RNA populations using custom scripts (proficient); III. Gene Expression Data and System Biology Analysis Skills • Differential expression analyses using DESeq, Cuffdiff, EdgeR etc (proficient); • Functional enrichment analyses using GSEA, GOSeq, FUNC_hyper, etc (proficient); • Gene co-expression network analyses using WGCNA, Cytoscape and custom scripts (semi-proficient); IV. Comparative Genomic Analysis Skills • Identification of orthological genes using orthoMCL and inparanoid (proficient); • Identification of syntenic genes using DAGChainer etc (semi-proficient); • Genome-wide protein family clustering and classification using spectral clustering (SCPS) (proficient); V. Phylogenetic and Population Genetics Analysis Skills • • • • • Automatic retrieval of viral sequences from NCBI using custom scripts (proficient); Bayesian based molecular clock and coalescent analyses using BEAST (proficient); Likelihood based selection pressure analyses using PAML and HyPhy (semi-proficient); Large scale phylogeny reconstruction using PAML, PAUP*, mrBayes, BEAST etc (proficient); Semi-automatic viral genotyping base on large phylogenies using custom scripts (proficient);
  • 3.
    D. Publications I. Genomicsand Transcriptomics (13 journal articles & 3 book chapters) 1. Hon,C.-C., Weber, C., Sismeiro, O., Proux, C., Koutero, M., Deloger, M., Das, S., Agrahari, M., Dillies, M.-A., Jagla, B., Coppee, J.Y., Bhattacharya, A. and Guillen, N. (2012) Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica. Nucleic Acids Res, 10.1093/nar/gks1271. (Corresponding and first author). 2. Vasquez,J.-J., Hon,C.-C., Vanselow J.T., Schlosser A. and Siegel, T.N (2013). Comparative ribosome-profiling reveals extensive translational complexity in different Trypanosoma brucei life-cycle stages. Nucleic Acids Res accepted. 3. Thibeaux, R., Weber. C., Hon. C.-C., Dillies, M.-A., Copee, J.Y., Labruye, E. and Guillen, N. (2013). Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon. PLoS Pathogens accepted. 4. Njoya, E.M., Weber. C., Hernandez-Cuevas. N.A., Hon. C.-C., Janin, Y, Kamini, M.F.G, Moundipa, P.F and Guillén, N (2013). Bioassay-guided fractionation of Codiaeum variegatum’s aqueous extract killing Entamoeba histolytica target ceramide biosynthesis. PLoS Negl Trop Dis in press. 5. Hon,C.-C., Weber,C., Koutero,M., Coppée,J.-Y., Deloger,M and Guillen,N. Surveying Entamoeba histolytica transcriptome using massively parallel cDNA sequencing. In ‘Amebiasis: Biology and Pathogenesis of Entamoeba’ by SPRINGER In Press. (Corresponding and first author) 6. Janbon, G., Ormerod, K. L., Paulet , D., Byrnes, E., Chatterjee, G., Yadav, V., Hon, C.-C., A., Cuomo, C. A., Dietrich, F. S., Billmyre, Brunel, F, Bahn Y.-S., Chen, W., Chen, Y., Chow E. W. L., Coppée, J.Y., FloydAverette, A., Gaillardin C., Gerik, K. J., Goebels, C., Goldberg, J., Gonzalez-Hilarion S., Gujja, S., Hamlin, J. L., Hsueh, Y.-P., Ianiri, G., Jones, S., Kodira, C. D., Lam, W., Marra, M., Mesner, L. D., Mieczkowski, P.A., Moyrand, F., Nielsen, K., Proux, C., Rossignol, T., Schein1, J. E., Sun, S., Wood, I. A., Zeng, Q., Neuvéglise, C., Newlon, C. S., Perfect, J. R., Lodge, J. K., Idnurm. A., Stajich, J. E., Kronstad, J. W., Sanya, K. Heitman, J., Fraser, J., Cuomo C. A. and Dietrich F. (2013). The genome sequence of Cryptococcus neoformans var. grubii reveals complex mechanisms of RNA expression and virulence plasticity. PLoS Genetics in 1st revision. 7. Siegel, N, Hon,C.-C., Zhang,Q., Lopez-Rubio,J.J., Coppée,J.-Y., Sismeiro,O and Scherf,A . Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum. BMC Genomics in 2nd revision. 8. Santi-Rocca,J., Smith,S., Weber,C., Pineda,E., Hon,C.-C., Saavedra,E., Olivos-García,A., Rousseau,S., Dillies,M.-A., Coppée,J.-Y., et al. (2012) Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide. PLoS ONE, 7, e31777. 9. Marquay Markiewicz,J., Syan,S., Hon,C.-C., Weber,C., Faust,D. and Guillen,N. (2011) A proteomic and cellular analysis of uropods in the pathogen Entamoeba histolytica. PLoS Negl Trop Dis, 5, e1002. 10. Hon,C.-C., Nakada-Tsukui,K., Nozaki,T. and Guillen,N. (2009) Dissecting the actin cytoskeleton of Entamoeba histolytica from a genomic perspective. In Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. Edited by G. C. Clark, P. J. Johnson & A. R.D. Tucson AZ, USA: Caister Academic Press. (First author) 11. Yeung,Y.S., Yip,C.W., Hon,C.-C., Chow,K.Y.C., Ma,I.C.M., Zeng,F. and Leung,F.C.C. (2008) Transcriptional profiling of Vero E6 cells over-expressing SARS-CoV S2 subunit: insights on viral regulation of apoptosis and proliferation. Virology, 371, 32–43. 12. Wang,Y., Zeng,F., Hon,C.-C., Zhang,Y. and Leung,F.C.C. (2008) The mitochondrial genome of the Basidiomycete fungus Pleurotus ostreatus (oyster mushroom). FEMS Microbiol Lett, 280, 34–41. 13. Wong,R.T.-Y., Hon,C.-C., Zeng,F. and Leung,F.C.C. (2007) Screening of differentially expressed transcripts in infectious bursal disease virus-induced apoptotic chicken embryonic fibroblasts by using cDNA microarrays. J Gen Virol, 88, 1785–1796. 14. Zeng,F., Hon,C.-C., Sit,W.-H., Chow,K.Y.-C., Hui,R.K.-H., Law,I.K.-M., Ng,V.W.-L., Yang,X.-T., Leung,F.C.C. and Wan,J.M.-F. (2005) Molecular characterization of Coriolus versicolor PSP-induced apoptosis in human promyelotic leukemic HL-60 cells using cDNA microarray. Int J Oncol, 27, 513–523.
  • 4.
    15. Cheung,K.H., Hon,C.-C.and Leung,F.C.C. (2003) Illustration of Enhanced Features of Visual Genome Explorer Beta 2.1 by Comparative Analysis of Helicobacter pylori Strains 26695 and J99 Genomes. Biocomputing: Computer Tools for Biologists. 16. Hon,C.-C., Chow,Y.C., Zeng,F.Y. and Leung,F.C.C. (2003) Genetic authentication of ginseng and other traditional Chinese medicine. Acta Pharmacol Sin, 24, 841–846. (First author) II. Phylogenetics and Population Genetics (18 journal articles) 17. Lam,T.T.-Y., Chong,Y.L., Shi,M., Hon,C.-C., Li,J., Martin,D.P., Tang,J.W.-T., Mok,C.-K., Shih,S.-R., Yip,C.W., et al. (2013) Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infect Genet Evol, 10.1016/j.meegid.2013.03.015. 18. Lam,T.T.-Y., Hon,C.-C., Lemey,P., Pybus,O.G., Shi,M., Tun,H.M., Li,J., Jiang,J., Holmes,E.C. and Leung,F.C.C. (2012) Phylodynamics of H5N1 avian influenza virus in Indonesia. Mol Ecol, 21, 3062–3077. 19. Shi,M., Lam,T.T.-Y., Hon,C.-C., Hui,R.K.-H., Faaberg,K.S., Wennblom,T., Murtaugh,M.P., Stadejek,T. and Leung,F.C.C. (2010) Molecular epidemiology of PRRSV: a phylogenetic perspective. Virus Res, 154, 7–17. 20. Li,Y., Ge,X., Hon,C.-C., Zhang,H., Zhou,P., Zhang,Y., Wu,Y., Wang,L.-F. and Shi,Z. (2010) Prevalence and genetic diversity of adeno-associated viruses in bats from China. J Gen Virol 91, 2601–2609. 21. Shi,M., Lam,T.T.-Y., Hon,C.-C., Murtaugh,M.P., Davies,P.R., Hui,R.K.-H., Li,J., Wong,L.T.-W., Yip,C.W., Jiang,J.-W., et al. (2010) Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. J Virol, 84, 8700–8711. 22. Yuan,J., Hon,C.-C., Li,Y., Wang,D., Xu,G., Zhang,H., Zhou,P., Poon,L.L.M., Lam,T.T.-Y., Leung,F.C.C., et al. (2010) Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J Gen Virol, 91, 1058–1062. (Equally contributed first author) 23. Lam,T.T.-Y., Hon,C.-C. and Tang,J.W. (2010) Use of phylogenetics in the molecular epidemiology and evolutionary studies of viral infections. Critical Reviews in Clinical Laboratory Sciences, 47, 5–49. 24. Yip,C.W., Hon,C.-C., Shi,M., Lam,T.T.-Y., Chow,K.Y.-C., Zeng,F. and Leung,F.C.C. (2009) Phylogenetic perspectives on the epidemiology and origins of SARS and SARS-like coronaviruses. Infect Genet Evol, 9, 1185–1196. 25. Hon,C.-C., Lam,T.T.-Y., Yip,C.W., Wong,R.T.-Y., Shi,M., Jiang,J., Zeng,F. and Leung,F.C.C. (2008) Phylogenetic evidence for homologous recombination within the family Birnaviridae. J Gen Virol, 89, 3156– 3164. (First author) 26. Hon,C.-C., Lam,T.-Y., Shi,Z.-L., Drummond,A.J., Yip,C.W., Zeng,F., Lam,P.-Y. and Leung,F.C.C. (2008) Evidence of the recombinant origin of a bat severe acute respiratory syndrome (SARS)-like coronavirus and its implications on the direct ancestor of SARS coronavirus. J Virol, 82, 1819–1826. (First author) 27. Lam,T.-Y., Hon,C.-C., Wang,Z., Hui,R.K.-H., Zeng,F. and Leung,F.C.C. (2008) Evolutionary analyses of European H1N2 swine influenza A virus by placing timestamps on the multiple reassortment events. Virus Res, 131, 271–278. 28. Lam,T.T.-Y., Hon,C.-C., Lam,P.-Y., Yip,C.W., Zeng,F. and Leung,F.C.C. (2008) Comments to the predecessor of human SARS coronavirus in 2003-2004 epidemic. Vet Microbiol, 126, 390–393. 29. Lam,T.T.-Y., Hon,C.-C., Pybus,O.G., Kosakovsky Pond,S.L., Wong,R.T.-Y., Yip,C.W., Zeng,F. and Leung,F.C.C. (2008) Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathog, 4, e1000130. 30. Ma,C.M., Hon,C.-C., Lam,T.-Y., Li,V.Y.-Y., Wong,C.K.-W., de Oliveira,T. and Leung,F.C.C. (2007) Evidence for recombination in natural populations of porcine circovirus type 2 in Hong Kong and mainland China. J Gen Virol, 88, 1733–1737. 31. Hon,C.-C., Lam,T.-Y., Drummond,A., Rambaut,A., Lee,Y.-F., Yip,C.W., Zeng,F., Lam,P.-Y., Ng,P.T.W. and Leung,F.C.C. (2006) Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B. J Virol, 80, 8503–8509. (First author)
  • 5.
    32. Guan,Y., Peiris,J.S.M.,Zheng,B., Poon,L.L.M., Chan,K.H., Zeng,F.Y., Chan,C.W.M., Chan,M.N., Chen,J.D., Chow,K.Y.C. Hon,C.-C, Hui, K.H., Li, J., Li, V.Y.Y., Wang, Y., Leung, S.W., Yuen, K.Y. and Leung F.C. (2004) Molecular epidemiology of the novel coronavirus that causes severe acute respiratory syndrome. Lancet, 363, 99–104. 33. Chow,K.Y.-C., Hon,C.-C., Hui,R.K.-H., Wong,R.T.-Y., Yip,C.W., Zeng,F. and Leung,F.C.C. (2003) Molecular advances in severe acute respiratory syndrome-associated coronavirus (SARS-CoV). Genomics Proteomics Bioinformatics, 1, 247–262. 34. Zeng,F.Y., Chan,C.W.M., Chan,M.N., Chen,J.D., Chow,K.Y.C., Hon,C.-C, Hui,K.H., Li,J., Li,V.Y.Y., Wang, C.Y. Hui, K.H., Li, J., Li, V.Y.Y, Wang, C.Y., Wang, P.Y., Guan, Y., Zheng, B., Poon, L.L.M., Chan, K.H., Yuen, K.Y., Peiris, J.S.M., and Leung F.C. (2003) The complete genome sequence of severe acute respiratory syndrome coronavirus strain HKU-39849 (HK-39). Exp. Biol. Med. (Maywood), 228, 866–873. III. Molecular Virology and Immunology (9 journal articles) 35. Li,K.K.B., Yip,C.W., Hon,C.C., Lam,C.Y., Zeng,F. and Leung,F.C.C. (2012) Characterisation of animal angiotensin-converting enzyme 2 receptors and use of pseudotyped virus to correlate receptor binding with susceptibility of SARS-CoV infection. Hong Kong Med J, 18 Suppl 3, 35–38. 36. Yip,C.W., Hon,C.-C., Zeng,F. and Leung,F.C.C. (2012) Cell culture-adapted IBDV uses endocytosis for entry in DF-1 chicken embryonic fibroblasts. Virus Res, 165, 9–16. 37. Chow,K.Y., Yeung,Y.S., Hon,C.C., Zeng,F., Law,K.M. and Leung,F.C. (2008) SARS coronavirus and apoptosis. Hong Kong Med J, 14 Suppl 4, 8–13. 38. Yip,C.W., Yeung,Y.S., Ma,C.M., Lam,P.-Y., Hon,C.-C., Zeng,F. and Leung,F.C.C. (2007) Demonstration of receptor binding properties of VP2 of very virulent strain infectious bursal disease virus on Vero cells. Virus Res, 123, 50–56. 39. Yip,C.W., Hon,C.-C., Zeng,F., Chow,K.Y.C., Chan,K.H., Peiris,J.S.M. and Leung,F.C.C. (2007) Naturally occurring anti-Escherichia coli protein antibodies in the sera of healthy humans cause analytical interference in a recombinant nucleocapsid protein-based enzyme-linked immunosorbent assay for serodiagnosis of severe acute respiratory syndrome. Clin. Vaccine Immunol., 14, 99–101. 40. Zeng,F., Hon,C.-C., Yip,C.W., Law,K.M., Yeung,Y.S., Chan,K.H., Malik Peiris,J.S. and Leung,F.C.C. (2006) Quantitative comparison of the efficiency of antibodies against S1 and S2 subunit of SARS coronavirus spike protein in virus neutralization and blocking of receptor binding: implications for the functional roles of S2 subunit. FEBS Lett, 580, 5612–5620. 41. Chow,K.Y.C., Yeung,Y.S., Hon,C.-C., Zeng,F., Law,K.M. and Leung,F.C.C. (2005) Adenovirus-mediated expression of the C-terminal domain of SARS-CoV spike protein is sufficient to induce apoptosis in Vero E6 cells. FEBS Lett, 579, 6699–6704. 42. Yip,C.W., Hon,C.-C., Zeng,F., Chow,K.Y.C. and Leung,F.C.C. (2004) Prevalence of non-pneumonic infections with SARS-correlated virus. Lancet, 363, 1825–author reply 1826–7. 43. Zeng,F., Chow,K.Y.-C., Hon,C.-C., Law,K.M., Yip,C.W., Chan,K.H., Peiris,J.S.M. and Leung,F.C.C. (2004) Characterization of humoral responses in mice immunized with plasmid DNAs encoding SARS-CoV spike gene fragments. Biochem Biophys Res Commun, 315, 1134–1139. IV. Massively Parallel Molecular Dynamics Simulations (1 journal article) 44. Zhou,R., Eleftheriou,M., Hon,C.-C., Germain,R.S., Royyuru,A.K. and Berne,B.J. (2008) Massively parallel molecular dynamics simulations of lysozyme unfolding. Ibm J Res Dev, 52, 19–30.