Address	(Office): Rm 177, Science Centre South Block (Lab): Rm 113, Run Run Shaw Science Building
Phone	(Office): (852) 3943 6876 (Lab): (852) 3943 1216
Fax	(852) 2603 7246
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Web	http://www.hkbic.cuhk.edu.hk/

Education

Position

• Professor, School of Life Sciences
• Co-director, Hong Kong Bioinformatics Centre
• Associate Director, Molecular Biotechnology Programme, CUHK
• Deputy Director, SKL Center for Soybean Research, CUHK
• Deputy Director, RGC Area of Excellence (AoE) Center for Genomic Studies on Plant-Environment Interaction
• Adjust Associate Professor, Hong Kong Institute of Diabetes and Obesity
• Investigator, State Key Laboratory for Agrobiotechnology, CUHK

Research Interests

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

Representative Publications   * denotes corresponding author

• Zhang J, Lin X, Chen Y, Li TH, Lee AC, Chow EY, Cho WC, Chan TF*. (2023) LAFITE reveals the complexity of transcript isoforms in subcellular fractions. Adv Sci. 10 (3), 2203480.
• Zhao J, Chow EY, Yeung PY, Zhang QC, Chan TF*, Kwok CK*. (2022) Enhanced transcriptome-wide RNA G-quadruplex sequencing for low RNA input samples with rG4-seq 2.0. BMC Biol. 20(1):257.
• Chen Y, Wang Y, Chen Y, Cheng Y, Wei Y, Li Y, Wang J, Wei YY, Chan TF*, Li Y*. (2022) Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis. Nat Commun 13 (1), 1-17.
• Yuan Y, Scheben A, Edwards D, Chan TF*. (2021) Towards haplotype studies in polyploid plants to assist breeding. Mol Plant 14 (12), 1969-1972.
• Dumetz F, Chow EY, Harris LM, Umar MI, Jensen A, Chung B, Chan TF*, Merrick CJ*, Kwok CK*. (2021) G-quadruplex RNA motifs influence gene expression in the malaria parasite Plasmodium falciparum. Nucleic Acids Res. 49 (21), 12486-12501.
• Jin N, Lee HM, Hou Y, Yu ACS, Li JW, Kong, AP, Lam CC, Wong SK, Ng EK, Ma RC, Chan JC*, Chan TF*. (2021) Integratome analysis of adipose tissues reveals abnormal epigenetic regulation of adipogenesis, inflammation and insulin signaling in obese individuals with type 2 diabetes. Clin Transl Med. 11(12): e596.
• Lyu K, Chow EY, Mou X, Chan TF*, Kwok CK*. (2021) RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res. 49 (10), 5426-5450.
• Lin X, Lin W, Ku YS, Wong FL, Li MW, Lam HM*, Ngai SM*, Chan TF* (2020) Analysis of soybean long non-coding RNAs reveals a subset of novel small peptide-coding transcripts. Plant Physiol 182(3):1359-74.
• Xie M, Chung CY, Li MW, Wong FL, Wang X, Liu A, Wang Z, Leung AK, Wong TH, Tong SW, Xiao Z, Fan K, Ng MS, Qi X, Yang L, Deng T, He L, Chen L, Fu A, Ding Q, He JX, Chung G, Isobe S, Tanabata T, Valliyodan B, Nguyen HT, Cannon SB, Foyer CH, Chan TF*, Lam HM* (2019) A reference grade wild soybean genome. Nat Commun 10(1):1216.
• 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 10(1):1025. (# Co-senior authors)

Research Grants

• 2022-2026, NSFC/RGC Joint Research Scheme N_CUHK488/22, Unravelling fusarium wilt resistant gene(s) in Cavendish banana and exploring the underlying resistance mechanisms, $1,244,471.
• 2022-2025, GRF14100422, A novel integrative method for the experimental identification and computational deconvolution of modifications at single RNA molecule resolution, $1,176,284.
• 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 for Heliyon (Section Biochemistry, Molecular, and Cell Biology)
• Associate Editor for The Plant Genome
• Associate Editor for Frontiers in Genetics
• Associate Editor for Frontiers in Ecology and Evolution
• Member, The RNA Society
• Member, The International Society for Computational Biology