Professor CHAN Ting Fung

Address

(Office): Rm 177, Science Centre South Block
(Lab): Rm 113, Run Run Shaw Science Building

People TFC
 

Phone

(Office): (852) 3943 6876
(Lab): (852) 3943 1216

Fax (852) 2603 7246
Email This email address is being protected from spambots. You need JavaScript enabled to view it.
Web http://www.hkbic.cuhk.edu.hk/
 

 

Education

2003 Ph. D. Washington University School of Medicine
1997 B. Sc. University of Wisconsin-Madison

Position

  • Associate Professor, School of Life Sciences
  • Co-director, Hong Kong Bioinformatics Centre
  • Investigator, State Key Laboratory for Agrobiotechnology, CUHK
  • Associate Professor, Department of Computer Sciences and Engineering (by courtesy)
  • Associate Professor, CUHK-BGI Innovation Institute of Trans-omics
  • Associate Professor, Hong Kong Institute of Diabetes and Obesity

Research Interests

  • RNomics and bioinformatics in biological processes and diseases
  • Technology and algorithm development for genomics and transcriptomics

Representative Publications

  • Levy-Sakin M, Pastor S, Mostovoy Y, Li L, Leung AK, McCaffrey J, Young E, Lam ET, Hastie AR, Wong KH, Chung CY, Ma W, Sibert J, Rajagopalan R, Jin N, Chow EY, Chu C, Poon A, Lin C, Naguib A, Wang WP, Cao H, Chan TF#, Yip KY#, Xiao M#, Kwok PY#. (2019) Genome maps across 26 human populations reveal population-specific patterns of structural variation. Nat Commun (in press). (# co-senior authors)
  •  Li L, Leung AK, Kwok TP, Lai YYY, Pang IK, Chung GT, Mak ACY, Poon A, Chu C, Li M, Wu JJK, Lam ET, Cao H, Lin C, Sibert J, Yiu SM, Xiao M, Lo KW, Kwok PY, Chan TF*, Yip KY*. (2017) OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps. Genome Biol. 18(1):230. (*co-corresponding)
  •  Wang SY, Lau K, Lai KP, Zhang JW, Tse AC, Li JW, Tong Y, Chan TF, Wong CK, Chiu JM, Au DW, Wong AS, Kong RY, Wu RS. (2016) Hypoxia causes transgenerational impairments in reproduction of fish. Nat Commun. 7:12114.
  • Chan TF, Ji KM, Yim AK, Liu XY, Zhou JW, Li RQ, Yang KY, Li J, Li M, Law PT, Wu YL, Cai ZL, Qin H, Bao Y, Leung RK, Ng PK, Zou J, Zhong XJ, Ran PX, Zhong NS, Liu ZG, Tsui SK. (2015) The draft genome, transcriptome, and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens. J Allergy Clin Immunol. 135(2):539-48.
  • Tsoi H, Yu AC, Chen ZS, Ng NK, Chan AY, Yuen LY, Abrigo JM, Tsang SY, Tsui SK, Tong TM, Lo IF, Lam ST, Mok VC, Wong LK, Ngo JC, Lau KF, Chan TF, Chan HY. A novel missense mutation in CCDC88C activates the JNK pathway and causes a dominant form of spinocerebellar ataxia. J Med Genet. 2014 51(9):590-5. (*co-corresponding)
  • Lou S, Lee HM, Qin H, Li JW, Gao Z, Liu X, Chan LL, Kl Lam V, So WY, Wang Y, Lok S, Wang J, Ma RC, Tsui SK, Chan JC, Chan TF, Yip KY. (2014) Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. Genome Biol. 15(7):408. (*co-corresponding)
  • Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM. (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun. 5:4340.
  • Lau CC, Sun T, Ching AK, He M, Li JW, Wong AM, Co NN, Chan AW, Li PS, Lung RW, Tong JH, Lai PB, Chan HL, To KF, Chan TF, Wong N. (2014) Viral-human chimeric transcript predisposes risk to liver cancer development and progression. Cancer Cell. 2014 25(3):335-49. (*co-corresponding)
  • Law PT, Qin H, Ching AK, Lai KP, Co NN, He M, Lung RW, Chan AW, Chan TF, Wong N. (2013) Deep sequencing of small RNA transcriptome reveals novel non-coding RNAs in hepatocellular carcinoma. J Hepatol. 58(6):1165-73. (*co-corresponding)
  • Li JW, Wan R, Yu CS, Co NN, Wong N, Chan TF. (2013) ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution. Bioinformatics. 29(5):649-51.

Research Grants

  • 2019-2021, RGC Collaborative Research Fund C4057-18E, A nanochannel-based next-generation mapping system for the study of complex genomic feature and variation for biotechnological and biomedical applications (as PC), $2,173,431.
  • 2017-2025, UGC-Area of Excellence AoE/M-403/16, Center for Genomic Studies on Plant-Environment Interaction for Sustainable Agriculture and Food Security (as co-PI and Deputy Director), $75,591,000.
  • 2014-2017, GRF14102014, Integrative analyses of RNA-sequencing, bioinformatics and biological studies to define cancer-associated long intergenic noncoding RNAs in hepatocellular carcinoma, $749,433.
  • 2014-2018, RGC Theme-based research T12-401/13R, Systematic development of molecular targets for nasopharyngeal carcinoma (as co-PI), $55,610,000.
  • 2011-2016, RGC Theme-based research T12-403/11, The Liver Cancer Genome Project: translating genetic discoveries to clinical benefits (as co-PI), $45,000,000.
  • 2012-2015, GRF461712, In search of the missing heritability in complex diseases: whole transcriptome analysis of type 2 diabetes using a strand-specific RNA-sequencing approach, $784,020.
  • 2012-2014, HMRF 12110542, A single DNA molecule detection platform for pathogen typing and identification, $859,340.
  • 2011-2013, RFCID 11100512, Transcriptome analysis of the multidrug-resistant Acinetobacter baumannii by a strand-specific RNA-sequencing approach, $918,592.
  • 2011-2012, ITF UIM/206, A high performance computing solution to enable bioinformatics research, $1,142,180.
  • 2009-2011, GRF461809, Revisiting co-evolution theory of the genetic code from a whole-genome perspective: potential applications in synthetic biology, $709,264.
  • 2008-2011, GRF461708, Identification of genetic polymorphisms modulating natural variation in mRNA splicing in the human genome, $1,348,616.

Patents

  • Polynucleotide Barcoding; US Ser No. 10/976,546; USPTO Patent No. 7,829,278; Issued: Nov 09, 2010

Professional Activities

  • Associate Editor, Frontiers in Genetics
  • Associate Editor, Frontiers in Plant Science
  • Member, Human Genome Organisation (HUGO)
  • Member, The International Society for Computational Biology