Prof CHAN Man Lok Andrew

Professor and Director, School of Biomedical Sciences

407A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

Research Interests

  1. Cancer cell signaling
  2. PTEN tumor suppressor
  3. Ras-related small GTPases
  4. Tumor microenvironment
  5. Tumor Immunity
  6. Neurodevelopmental and Neurodegenerative disorders
  7. Mouse models of human diseases

Selected Publications

  1. Liu, T., Wang, Y., Wang, Y., & Chan, A.M. (2019). Multifaceted regulation of PTEN subcellular distributions and biological functions. Cancers, In Press.
  2. Sanchez-Puelles, C., Calleja-Felipe, M., Ouro, A., Bougamra, G., Arroyo, A., Diez, I., Erramuzpe Aliaga, A., Cortes, J.M., Martinez-Hernandez, J., Lujan, R., Navarrete, M., Venero, C., Chan, A.M., Morales, M., Esteban, J., & Knafo, S. (2019). PTEN activity defines an axis for plasticity at cortico-amygdala synapses and determines social behaviour. Cerebral Cortex, In Press.
  3. Dukhinova, M., Veremeyko, T., Yung, A.W.Y., Kuznetsova, I.S., Lau, T.Y.B., Kopeikina, E., Chan, A.M.L., & Ponomarev, E.D. (2019). Fresh evidence for major brain gangliosides as a target for the treatment of Alzheimer's disease. Neurobiol Aging, 77, 128-143.
  4. Yan, M., Wang, Y., Wong, C.W., Or, P.M., Wong, K.L., Li, L., Many, A.M., Guan, H., Khoo, U.S., & Chan, A.M. (2018). PTEN PDZ-binding domain suppresses mammary carcinogenesis in the MMTV-PyMT breast cancer model. Cancer Lett, 430, 67-78.
  5. Zhang, C., He, X., Kwok, Y.K., Wang, F., Xue, J., Zhao, H., Suen, K.W., Wang, C.C., Ren, J., Chen, G.G., Lai, P.B.S., Li, J., Xia, Y., Chan, A.M., Chan, W.Y., & Feng, B. (2018). Homology-independent multiallelic disruption via CRISPR/Cas9-based knock-in yields distinct functional outcomes in human cells. BMC Biol., 16, 151.
  6. Lee, Y.Y., Mok, M.T., Kang, W., Yang,W., Tang, W., Wu, F., Xu, L., Yan, M., Yu, Z., Lee, S.D., Tong, J.H.M., Cheung, Y.S., Lai, P.B.S., Yu, D. Y., Wang, Q., Wong, G.L. H., Chan, A.M., Yip, K.Y., To, K.F., & Cheng, A.S.L. (2018). Loss of tumor suppressor IGFBP4 drives epigenetic reprogramming in hepatic carcinogenesis. Nucleic Acids Res, 46, 8832-8847.
  7. Wang, Y., Wong, C.W., Yan, M., Li, L., Liu, T., Or, P.M., Tsui, S.K., Waye, M.M., & Chan, A.M. (2018). Differential regulation of the pro-inflammatory biomarker, YKL-40/CHI3L1, by PTEN/Phosphoinositide 3-kinase and JAK2/STAT3 pathways in glioblastoma. Cancer Lett, 429, 54-65.
  8. Wong, C.W., Or, P.M.-Y., Wang, Y., Li, L., Li, J., Yan, M., Cao, Y., Luk, H.M., Tong, T.M.F., Leslie, N.R., Lo, I.F.-M., Choy, R.K.W., & Chan, A.M. (2018). Identification of a PTEN mutation with reduced protein stability, phosphatase activity, and nuclear localization in Hong Kong patients with autistic features, neurodevelopmental delays and macrocephaly. Autism Research, 11, 1098-1109.
  9. Knafo, S., Sanchez-Puelles, C., Palomer, E., Delgado, I., Draffin, J.E., Mingo, J., Wahle, T., Kaleka, K., Mou, L., Pereda-Perez, I., Klosi, E., Faber, E.B., Chapman, H.M., Lozano-Montes, L., Ortega-Molina, A., Ordonez-Guiterrez, L., Wandosell, F., Vina, J., Dotti, C.G., Hall, R.A., Pulido, R., Gerges, N.Z., Chan, A.M., Spaller, M.R., Serrano, M., Venero, C., & Esteban, J.A. (2016). PTEN recruitment controls synaptic and cognitive function in Alzheimer's models. Nature Neuroscience, 19, 443-453.
  10. Yan, X., He, Y., Chen, Y., Yu, M., Singh, G., Wang, D., Hillery, C.A., & Chan, A.M. (2015). R-Ras regulates Murine T cell migration to peripheral lymph nodes and chemokine-induced activation of lymphocyte function-associated antigen-1. Plos One, 10, e0145218.

Prof CHAN Wood Yee

Head, Division of Biomedical Sciences

Professor, School of Biomedical Sciences

B.Sc., Ph.D.
Rm 621A, 6/F., Lo Kwee-Seong Integrated Biomedical
Sci. Bldg, Area 39, CUHK

Research Interests

  1. Formation, migration and differentiation of neural crest cells and neural crest stem cells
  2. Development of the nervous systems in experimental animals and human fetuses
  3. Genetic and epigenetic controls of cellular migration, proliferation and differentiation in embryos and cancers
  4. Early organogenesis in post-implantation embryos
  5. Embryotoxicity and teratogenicity of various bioactive compounds

Selected Publications

  1. Li YH, Tai WC, Khan I, Lu C, Lu Y, Wong WY, Chan WY, Hsiao WW, Lin G (2018) Toxicoproteomic assessment of liver responses to acute pyrrolizidine alkaloid intoxication in rats. Journal of Environmental Science and Health, Part C 36: 65-83.
  2. Burns, A. J., Goldstein, A. M., Newgreen, D. F., Stamp, L., Schafer, K. H., Metzger, M., Hotta, R., Young, H. M., Andrews, P. W., Thapar, N., Belkind-Gerson, J., Bondurand, N., Bornstein, J. C., Chan, W. Y., Cheah, K., Gershon, M. D., Heuckeroth, R. O., Hofstra, R. M., Just, L., Kapur, R. P., King, S. K., McCann, C. J., Nagy, N., Ngan, E., Obermayr, F., Pachnis, V., Pasricha, P. J., Sham, M. H., Tam, P., & Vanden Berghe, P. (2016). White paper on guidelines concerning enteric nervous system stem cell therapy for enteric neuropathies. Developmental Biology, 417(2), 229-251.
  3. Wang, B., Chen, Y. C., Jiang, G., Ning, Q., Ma, L., Chan, W. Y., Wu, S., Zhou, G. Q., Bao, R., Zheng, Z. C., Yang, X., Luo, J. X., Zheng, W., Guo, H. W., Zeng, C., Zeng, Q. Y., & Shu, S. Y. (2016). New learning and memory related pathways among the hippocampus, the amygdala and the ventromedial region of the striatum in rats. Journal of Chemical Neuroanatomy, 71, 13-19.
  4. Wang, C., Kam, R. K., Shi, W., Xia, Y., Chen, X., Cao, Y., Sun, J., Du, Y., Lu, G., Chen, Z., Chan, W. Y., Chan, S. O., Deng, Y., & Zhao, H. (2015). The proto-oncogene transcription factor Ets1 regulates neural crest development through histone deacetylase 1 to mediate output of bone morphogenetic protein signaling. The Journal of Biological Chemistry, 290(36), 21925-21938.
  5. Shu, S. Y., Jiang, G., Zeng, Q. Y., Wang, B., Li, H., Ma, L., Steinbusch, H., Song, C., Chan, W. Y., Chen, X. H., Wu, Y. M., Bao, R., Chen, Y. C., & Wu, J. Y. (2015). The marginal division of the striatum and hippocampus has different role and mechanism in learning and memory. Molecular Neurobiology, 51(2), 827-839.
  6. Chan, W. Y., Wong, J. H., & Ng, T. B. (2014). Embryotoxic and abortifacient activities of ribosome-inactivating proteins. In F. Stirpe, & D. A. Lappi (Eds.), Ribosome-inactivating proteins: Ricin and related proteins (pp. 270-280). Iowa USA: John Wiley & Sons.
  7. Wong, C. H., Nguyen, L., Peh, J., Luu, L. M., Sanchez, J. S., Richardson, S. L., Tuccinardi, T., Tsoi, H., Chan, W. Y., Chan, H. Y., Baranger, A. M., Hergenrother, P. J., & Zimmerman, S. C. (2014). Targeting toxic RNAs that cause myotonic dystrophy type 1 (DM1) with a bisamidinium inhibitor. Journal of the American Chemical Society, 136(17), 6355-6361.
  8. Kam, R. K., Shi, W., Chan, S. O., Chen, Y., Xu, G., Lau, C. B., Fung, K. P., Chan, W. Y., & Zhao, H. (2013). Dhrs3 protein attenuates retinoic acid signaling and is required for early embryonic patterning. The Journal of Biological Chemistry, 288(44), 31477-31487.
  9. Qu, Z. Q., Zhou, Y., Zeng, Y. S., Lin, Y. K., Li, Y., Zhong, Z. Q., & Chan, W. Y. (2012). Protective effects of a rhodiola crenulata extract and salidroside on hippocampal neurogenesis against streptozotocin-induced neural injury in the rat. PLoS One, 7(1), e29641.
  10. Wang, X., Chan, A. K., Sham, M. H., Burns, A. J., & Chan, W. Y. (2011). Analysis of the sacral neural crest cell contribution to the hindgut enteric nervous system in the mouse embryo. Gastroenterology, 141(3), 992-1002.e1-6.

Prof TSUI Kwok Wing Stephen

Professor and Associate Director of Research, School of Biomedical Sciences

Programme Director, Master of Science in Genomics and Bioinformatics

BSc, DipEd, PhD
524A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK

Research Interests

  1. Gene regulation in human cancers.
  2. Drug resistance of Mycobacterium tuberculosis.
  3. Molecular biology and epidemiology of HIV.
  4. Changes in microbiota in human diseases.
  5. Bioinformatics.

Selected Publications

  1. Yang, KY, Chen, Y, Ng, PKS, Zhou, WJ, Chen, JY, Mao, BY & Tsui, SKW (2016) Transcriptome analysis of different developmental stages of amphioxus reveals dynamic changes of distinct classes of genes during development. Sci. Rep., 6, 23195.
  2. 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 SKW (2015) The draft genome, transcriptome and microbiome of Dermatophagoides farinae reveal a broad spectrum of dust mite allergens. J. Allergy Clin. Immunol., 135, 539-548.
  3. Leung KK, Zhou, JW, Guan, W, Li SK, Yang, ZF, Tsui, SKW. (2013). Differences of respiratory microbiota in influenza virus-infected and non-influenza virus-infected pneumonia patients. Clin Microbiol Infect, 19, 930-935.
  4. Chan TM, Leung KS, Lee KH, Wong MH, Lau CK, Tsui SKW (2012) Subtypes of associated Protein-DNA (TF-TFBS) patterns. Nucleic Acid Res 40:9392-9403.
  5. Ng CF, Ng PKS, Lui VWY, Li J, Chan JYW, Fung KP, Ng YK, Lai PBS, Tsui SKW (2011) FHL2 exhibits anti-proliferative and anti-apoptotic activity in liver cancer cells. Cancer Letter 304:97-106.
  6. Leung KS, Wong KC, Chan TM, Wong MH, Lee KH, Lau CK, Tsui SKW (2010) Discovering protein-DNA binding sequence patterns using association rule mining. Nucleic Acids Res 38: 6324-6337.
  7. The International HapMap Consortium (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851-861.
  8. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437:1299-1320.
  9. Chim SSC*, Tsui SKW*, Chan KCA, Au TCC, Hung ECW, Tong YK, Chiu RWK, Ng EKO, Chan PKS, Chu CM, Sung JJY, Tam JS, Fung KP, Waye MMY, Lee CY, Yuen KY, Lo YMD (2003) Genomic characterization of the SARS-coronavirus of the Amoy Gardens outbreak in Hong Kong. Lancet 362:1807-1808 (*equal contribution).
  10. Tsui SKW, Chim SSC, Lo YMD and the Chinese University of Hong Kong Molecular SARS Research Group. (2003) Coronavirus genomic-sequence variations and the epidemiology of the severe acute respiratory syndrome. N Engl J Med 349:187-188.

Prof SUN Hao


Professor Hao Sun is currently a professor and a bioinformatics specialist in the Department of Chemical Pathology. He received his Ph.D. in the field of Environmental Chemistry from Nanjing University, China in 1998 and a M.S. degree in Computer Science from the University of Akron, USA in 2002. Before he joined The Chinese University of Hong Kong in 2009, he worked as a Co-Director of the Bioinformatics Core Facility in Wistar Institute at Philadelphia, USA during 2008 to 2009 and as a Research Scientist/Adjunct Assistant Professor in the Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine and Public Health, at the Ohio State University, USA from 2001 to 2008.

Research Interests

Professor Sun Hao's research interests focus on:

  1. Understanding the fundamental aspects of transcriptional regulation of both coding and noncoding genes;
  2. Developing bioinformatics software for Next Generation Sequencing (NGS) data analysis;
  3. Developing of new computational algorithms and tools for identifying novel biomarkers, particularly for non-invasive prenatal diagnosis using high-throughput DNA sequencing.

His research is computationally driven and interdisciplinary in nature with a complement of collaborative experimental investigation with bench scientists.

Selected Publications

  1. Yao M, Zhou X, Zhou J, Gong S, Hu G, Li J, Huang K, Lai P, Shi G, Hutchins AP, Sun H, Wang H and Yao H. (2018). PCGF5 is required for neural differentiation of embryonic stem cells. Nat Commun. 2018 May 15;9(1):1463. (IF2017: 12.124)
  2. Bao X, Guo X, Yin M, Tariq M, Lai Y, Kanwal S, Zhou J, Li N, Lv Y, Pulido-Quetglas C, Wang X, Ji L, Khan MJ, Zhu X, Luo Z, Shao C, Lim DH, Liu X, Li N, Wang W, He M, Liu YL, Ward C, Wang T, Zhang G, Wang D, Yang J, Chen Y, Zhang C, Jauch R, Yang YG, Wang Y, Qin B, Anko ML, Hutchins AP, Sun H, Wang H, Fu XD, Zhang B, Esteban MA. Capturing the interactome of newly transcribed RNA. (2018) Nature Methods 2018 Mar; 15(3):213-220. doi: 10.1038/nmeth.4595. (IF2017: 25.062)
  3. Zhou J., Zhang S., Wang H.*, Sun H.* (2017). LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. Nucleic Acid Research 2017 Apr 4. (IF2017: 10.162)
  4. Stunnenberg HG; International Human Epigenome Consortium, Hirst M. (2016). The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 2016 Dec 15;167(7):1897. doi: 10.1016/j.cell.2016.12.002. (as co-author listed in International Human Epigenome Consortium). (IF2017:30.41)
  5. Zhou L, Sun K, Zhao Y, Zhang S, Wang X, Li Y, Lu L, Chen X, Chen F, Bao X, Zhu X, Wang ZL, Tang LY, Esteban MA, Wang CC, Jauch R, Sun H*, and Wang H*. Linc-YY1 promotes myogenic differentiation and muscle regeneration through an interaction with the transcription factor YY1. Nature Communications. 2015 6:10026 | DOI: 10.1038/ncomms10026. (IF2017: 12.124)
  6. Chan, R. W., Jiang, P., Peng, X., Tam, L. S., Liao, G. J., Li, E. K., Wong, P. C., Sun, H., Chan, K. C., Chiu, R. W., and Lo, Y. M. Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing. PNAS. 2014 111(49):E5302-11. (IF2017: 9.661)
  7. Liu L, Xu Y, He M, Zhang M, Cui F, Lu L, Yao M, Tian W, Benda C, Zhuang Q, Huang Z, Li W, Li X, Zhao P, Fan W, Luo Z, Li Y, Wu Y, Hutchins AP, Wang D, Tse HF, Schambach A, Frampton J, Qin B, Bao X, Yao H, Zhang B, Sun H, Pei D, Wang H, Wang J, Esteban MA. (2014). Transcriptional Pause Release is a Rate-limiting Step for Somatic Cell Reprogramming. Cell Stem Cell. Nov 6; 15(5):574-88. DOI: 10.1016/j.stem.2014.09.018. (IF2017: 23.29)
  8. Lu, L., Sun, K., Chen, X., Zhao, Y., Wang, L., Zhou, L., Sun, H.*, and Wang, H.* (2013) Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis, EMBO J 32, 2575-2588. (IF2012: 9.822) (19 /185 in Cell Biology; 19/290 in Biochemistry and Molecular Biology)
  9. Chiu, R. W. K., Akolekar, R., Zheng, Y. W. L., Leung, T. Y., Sun, H., Chan, K. C. A., Lun, F. M. F., Go, A. T. J. I., Lau, E. T., and To, W. W. K. (2011) Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study, BMJ 342. (IF2012: 17.215) (Citations: 147 ) (4/155 in Medicine, General and Internal)
  10. Lo, Y. M., Chan, K. C., Sun, H., Chen, E. Z., Jiang, P., Lun, F. M., Zheng, Y. W., Leung, T. Y., Lau, T. K., Cantor, C. R., and Chiu, R. W. (2010) Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus, Sci Transl Med 2, 61ra91. (IF2012: 10.757) (Citations: 78) (5/121 in Medicine, Research & Experimental)

Prof LIU Xin

Director, BGI Group, North China Area, Beijing China

Research Interests

  1. Population genetics
  2. Application of second-generation sequencing
  3. Bioinformatics

Selected Publications

  1. Varshney, R. K., M. Roorkiwal, S. Sun, P. Bajaj, A. Chitikineni, M. Thudi, N. P. Singh, X. Du, H. D. Upadhyaya, A. W. Khan, Y. Wang, V. Garg, G. Fan, W. A. Cowling, J. Crossa, L. Gentzbittel, K. P. Voss-Fels, V. K. Valluri, P. Sinha, V. K. Singh, C. Ben, A. Rathore, R. Punna, M. K. Singh, B. Tar'an, C. Bharadwaj, M. Yasin, M. S. Pithia, S. Singh, K. R. Soren, H. Kudapa, D. Jarquin, P. Cubry, L. T. Hickey, G. P. Dixit, A. C. Thuillet, A. Hamwieh, S. Kumar, A. A. Deokar, S. K. Chaturvedi, A. Francis, R. Howard, D. Chattopadhyay, D. Edwards, E. Lyons, Y. Vigouroux, B. J. Hayes, E. von Wettberg, S. K. Datta, H. Yang, H. T. Nguyen, J. Wang, K. H. M. Siddique, T. Mohapatra, J. L. Bennetzen, X. Xu and X. Liu# (2021). "A chickpea genetic variation map based on the sequencing of 3,366 genomes." Nature 599(7886): 622-627.
  2. Zhao, H., S. Sun, Y. Ding, Y. Wang, X. Yue, X. Du, Q. Wei, G. Fan, H. Sun, Y. Lou, H. Yang, J. Wang, X. Xu, L. Li, K. Yang, H. Xu, J. Wang, C. Zhu, S. Wang, X. Shan, Y. Hou, Y. Wang, B. Fei, X. Liu#, Z. Jiang and Z. Gao (2021). "Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits." Nat Commun 12(1): 5466.
  3. Xu, M., L. Guo, X. Du, L. Li, B. A. Peters, L. Deng, O. Wang, F. Chen, J. Wang, Z. Jiang, J. Han, M. Ni, H. Yang, X. Xu, X. Liu#, J. Huang and G. Fan (2021). "Accurate Haplotype-Resolved Assembly Reveals The Origin Of Structural Variants For Human Trios." Bioinformatics.
  4. Wei, T., R. van Treuren, X. Liu, Z. Zhang, J. Chen, Y. Liu, S. Dong, P. Sun, T. Yang, T. Lan, X. Wang, Z. Xiong, Y. Liu, J. Wei, H. Lu, S. Han, J. C. Chen, X. Ni, J. Wang, H. Yang, X. Xu, H. Kuang, T. van Hintum, X. Liu# and H. Liu (2021). "Whole-genome resequencing of 445 Lactuca accessions reveals the domestication history of cultivated lettuce." Nat Genet.
  5. Wang, Y., S. Liao, Y. Gai, G. Liu, T. Jin, H. Liu, L. Gram, M. L. Strube, G. Fan, S. K. Sahu, S. Liu, S. Gan, Z. Xie, L. Kong, P. Zhang, X. Liu# and D. Z. Wang (2021). "Metagenomic Analysis Reveals Microbial Community Structure and Metabolic Potential for Nitrogen Acquisition in the Oligotrophic Surface Water of the Indian Ocean." Front Microbiol 12: 518865.
  6. Guo, L., M. Xu, W. Wang, S. Gu, X. Zhao, F. Chen, O. Wang, X. Xu, I. Seim, G. Fan, L. Deng and X. Liu# (2021). "SLR-superscaffolder: a de novo scaffolding tool for synthetic long reads using a top-to-bottom scheme." BMC Bioinformatics 22(1): 158.
  7. Zhang, P., Y. Zhao, C. Li, M. Lin, L. Dong, R. Zhang, M. Liu, K. Li, H. Zhang, X. Liu, Y. Zhang, Y. Yuan, H. Liu, I. Seim, S. Sun, X. Du, Y. Chang, F. Li, S. Liu, S. M. Lee, K. Wang, D. Wang, X. Wang, M. R. McGowen, T. A. Jefferson, M. T. Olsen, J. Stiller, G. Zhang, X. Xu, H. Yang, G. Fan, X. Liu# and S. Li (2020). "An Indo-Pacific Humpback Dolphin Genome Reveals Insights into Chromosome Evolution and the Demography of a Vulnerable Species." iScience 23(10): 101640.
  8. Wang, S., L. Li, H. Li, S. K. Sahu, H. Wang, Y. Xu, W. Xian, B. Song, H. Liang, S. Cheng, Y. Chang, Y. Song, Z. Cebi, S. Wittek, T. Reder, M. Peterson, H. Yang, J. Wang, B. Melkonian, Y. Van de Peer, X. Xu, G. K. Wong, M. Melkonian, H. Liu and X. Liu# (2020). "Genomes of early-diverging streptophyte algae shed light on plant terrestrialization." Nat Plants 6(2): 95-106.
  9. Sun, S., Y. Wang, W. Zeng, X. Du, L. Li, X. Hong, X. Huang, H. Zhang, M. Zhang, G. Fan, X. Liu# and S. Liu (2020). "The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation." Sci Rep 10(1): 8164.
  10. Liu, J., C. Shi, C. C. Shi, W. Li, Q. J. Zhang, Y. Zhang, K. Li, H. F. Lu, C. Shi, S. T. Zhu, Z. Y. Xiao, H. Nan, Y. Yue, X. G. Zhu, Y. Wu, X. N. Hong, G. Y. Fan, Y. Tong, D. Zhang, C. L. Mao, Y. L. Liu, S. J. Hao, W. Q. Liu, M. Q. Lv, H. B. Zhang, Y. Liu, G. R. Hu-Tang, J. P. Wang, J. H. Wang, Y. H. Sun, S. B. Ni, W. B. Chen, X. C. Zhang, Y. N. Jiao, E. E. Eichler, G. H. Li, X. Liu# and L. Z. Gao (2020). "The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis." Mol Plant 13(2): 336-350.
  11. * co-first author

    # corresponding author

Prof. CAO Qin Cara

Research Assistant Professor, School of Biomedical Sciences

509A, Lo Kwee-Seong Integrated Biomedical Sciences Building, Area 39, CUHK


Prof. CAO Qin completed her B.Eng. in Computer Science and Technology from Wuhan University, and her Ph.D. in Computer Science and Engineering (CSE) from The Chinese University of Hong Kong (CUHK). She then continued her postdoctoral research at School of Biomedical Sciences (SBS) and CSE in CUHK for three years and became a Research Assistant Professor in 2020. Her research areas are Bioinformatics and Computational Biology. Prof. Cao has received awards including Young Scholars Thesis Award from CUHK, Young Scientist Award 2nd Runner-up from Hong Kong Institution of Science and Top-10 paper in 2016-17 at RECOMB/ISCB Regulatory Systems Genomics. She has published papers in international journals including Nature Genetics, Nature Machine Intelligence, Nature Communications, Cell Reports, Briefings in Bioinformatics and BMC Genomics.

Teaching & Research Interests

  1. Reconstruction of gene regulatory networks.
  2. Analysis of multi-omics data and 3D genome structures.
  3. Development of bioinformatics algorithms, pipelines and tools.

Selected Publications

  1. Jiang, Q.#, Ang, J. Y.#, Lee, A. Y., Cao, Q., Li, K. Y., Yip, K. Y., & Leung, D. C. (2020). G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping. Cell Reports, 33(4), 108315.
  2. Cao, Q.#, Zhang, Z.#, Fu, A.X., Wu, Q., Lee, T.L., Lo, E., Cheng, A.S.L., Cheng, C., Leung, D., & Yip, K.Y. (2020). A unified framework for integrative study of heterogeneous gene regulatory mechanisms. Nature Machine Intelligence, 2(8), 447-456.
  3. Ho, E.Y.K.#, Cao, Q.#, Gu, M., Chan, R.W.L, Wu, Q., Gerstein, M., & Yip, K.Y. (2020). Shaping the nebulous enhancer in the era of high-throughput assays and genome editing. Briefings in Bioinformatics, 21(3), 836-850.
  4. Zhang, J. #, Lee, D. #, Dhiman, V. #, Jiang, P. #, Xu, J., McGillivray, P., Yang, H., Liu, J., Meyerson, W., Clarke, D., Gu, M., Li, S., Lou, S., Xu, J., Lochovsky, L., Ung, M., Ma, L., Yu, S., Cao, Q., Harmanci, A., Yan, K.K., Sethi, A., Gursoy, G., Schoenberg, M.R., Rozowsky, J., Warrell, J., Emani, P., Yang, Y.T., Galeev, T., Kong, X., Liu, S., Li, X., Krishnan, J., Feng, Y., Rivera-Mulia, J.C., Adrian, J., Broach, J.R., Bolt, M., Moran, J., Fitzgerald, D., Dileep, V., Liu, T., Mei, S., Sasaki, T., Trevilla-Garcia, C., Wang, S., Wang, Y., Zang, C., Wang, D., Klein, R.J., Snyder, M., Gilbert, D.M., Yip, K., Cheng, C., Yue, F.*, Liu, X.S.*, White, K.P.*, & Gerstein, M.* (2020). An integrative ENCODE resource for cancer genomics. Nature Communications, 11(1), 1-11.
  5. Qian, Y., Liao, J., Suen, A.H.C., Lee, A.W.T., Chung, H.S., Tang, N.L.S., Chow, K.L., Cao, Q., Yip, K.L., Leung, T.Y., Chan, W.Y., Chan, D.Y.L., Li, T.C., & Lee, T.L. (2019). Comparative analysis of single-cell parallel sequencing approaches in oocyte application. The International Journal of Biochemistry and Cell Biology, 107, 1-5.
  6. Cao, Q., Anyansi, C., Hu, X., Xu, L., Xiong, L., Tang, W., Mok, M.T.S., Cheng, C., Fan, X., Gerstein, M., Cheng, A.S.L., & Yip, K.Y. (2017). Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines. Nature Genetics, 49, 1428-1436.
  7. Cao, Q., & Yip, K.Y. (2016). A survey on computational methods for enhancer and enhancer target predictions. Computational biology and bioinformatics: Gene regulation, 3-27.
  8. Ho, E.D., Cao, Q., Lee, S.D., & Yip, K.Y. (2014). VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants. BMC Genomics, 15(1), 886.
  9. #Co-first author

    *Co-corresponding author

Dr WONG Kwong Fai Tony

Chief Technology Officer, Arbele Limited


Dr. Wong received his PhD degree in Biomedical Sciences from the University of Hong Kong and had his postdoctoral training in National University of Singapore. He has over twelve years' experience of drug development in multinational pharmaceutical companies and biotech start-up, with two drug candidates being tested in clinical trials in Mainland China and Asia-Pacific region. Over the years, Dr. Wong has published more than 30 peer-reviewed articles in top-tier journals including Nature Genetics and New England Journal of Medicine. He is also an author of 4 book chapters and an inventor of 3 patents.

Patents and Book Chapters

  1. Patent: Luk JM, Wong KF, Poon RT, Fan ST. Methods and compositions for treatment of endotoxin- mediated pro-inflammatory response. US 7,960,338 B2, issued June 14, 2011
  2. Patent: Luk JM, Wong KF, Poon RT, Fan ST. Integrin peptide, anti-cd18 βA antibody for treatment of endotoxin-mediated pro-inflammatory response and the use. CN 102239179, issued January 1, 2014
  3. Patent: Luk JM, Wong KF, Chow CQ. Composition of multispecific antibodies targeting CDH17-expressing tumors and method of making and using thereof. WO 2023/060277 A1, published April 13, 2023
  4. Book Chapter: Wong KF, Jiang X, Luk JM (2013). MicroRNA as cancer biomarkers and targets in New Advances on Disease Biomarkers and Molecular Targets in Biomedicine (pp.39-56). New York, NY: Humana Press.
  5. Book Chapter: Wong KF, Luk JM (2012). Discovery of lamin B1 and vimentin as circulating biomarkers for early hepatocellular carcinoma in Liver Proteomics Methods and Protocols (pp. 295-310). New York, NY: Humana Press.
  6. Book Chapter: Luk JM, Liu AM, Wong KF, Poon RT (2012). Genetic biomarkers for the diagnosis and prognosis of hepatocellular carcinoma in From Inflammation to Cancer: Advances in Diagnosis and Therapy for Gastrointestinal and Hepatological Diseases (pp. 331-48). London: World Scientific.
  7. Book Chapter: Luk JM, Wong KF (2010). Antibody therapies for liver malignancy and transplantation in Targeted Delivery of Small and Macromolecular Drugs (pp.13-30). New York, NY: CRC Press.

Selected Publications

  1. Zheng BH, Shen Sheng, Wong KF*, et al., Clinical correlation of cadherin-17 marker with advanced tumor stages and poor prognosis of cholangiocarcinoma. J Surg Oncol. 2021; 123(5):1253-62. (*Equal first author)
  2. Wong KF, Liu AM, Hong W, Xu Z, Luk JM. Integrin α2β1 inhibits MST1 kinase phosphorylation and activates Yes-associated protein oncogenic signaling in hepatocellular carcinoma. Oncotarget. 2016; 7(47): 77683-95.
  3. Wang Y, Shek FH, Wong KF*, Liu LX, Zhang XQ, Yuan Y, Khin E, Hu MY, Wang JH, Poon RT, Hong W, Lee NP, Luk JM. Anti-cadherin-17 antibody modulates Beta-catenin signaling and tumorigenicity of hepatocellular carcinoma PLoS One. 2013; 8(9): e72386. (*Equal first author)
  4. Yong KJ, Gao C, Lim JS, Yan B, Yang H, Dimitrov T, Kawasaki A, Ong CW, Wong KF, et al., Oncofetal protein SALL4 defines an aggressive hepatocellular carcinoma subtype. N Engl J Med 2013; 368(24): 2266-76.
  5. Wong KF, Xu Z, Chen J, Lee NP, Luk JM. Circulating markers for prognosis of hepatocellular carcinoma. Expert Opin Med Diagn. 2013; 7(4): 319-29.
  6. Sung WK, Zheng H, Li S, Chen R, Liu X, Li Y, Lee NP, Lee WH, Ariyaratne PN, Tennakoon C, Mulawadi FH, Wong KF, et al., Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma. Nat Genet 2012; 44(7): 765-9.
  7. Liu AM, Wong KF*, Jiang X, Qiao Y, Luk JM. Regulators of mammalian Hippo pathway in cancer. Biochim Biophys Acta. 2012; 1826(2): 357-64. (*Equal first author)
  8. Zhu R, Wong KF*, Lee NP, Lee KF, Luk JM. HNF1α and CDX2 transcriptional factors bind to cadherin-17 (CDH17) gene promoter and modulate its expression in hepatocellular carcinoma. J Cell Biochem. 2010; 111(3):618-26. (*Equal first author)
  9. Wong KF, Wo J, Ho D, Poon RT, Casasnovas JM, Luk JM. Prophylactic uses of integrin CD18- betaA peptide in a murine polymicrobial peritonitis model. World J Gastroenterol. 2010 Jun 7;16(21):2648-56.
  10. Wong KF, Luk JM, Cheng RH, Klickstein LB, Fan ST. Characterization of two novel LPS- binding sites in leukocyte integrin betaA domain. FASEB J. 2007; 21(12):3231-9.

Dr HUANG Yongjie Jessie

Lecturer, School of Biomedical Sciences

BSc, PhD
Room G03, G/F., Lo Kwee-Seong Integrated Biomedical
Sci. Bldg, Area 39, CUHK


Dr. Huang Yongjie Jessie received her PhD degree at the Institute of Bioinformatics at the University of Georgia, USA and her Master's Degree in Electrical Engineering at the University of South Carolina, USA. She has joined the MSc program in Genomics and Bioinformatics as a lecturer since 2017.

Research Interests

  1. Computational methods for understanding structure, composition and evolution of prokaryotic genomes
  2. Roles of environmental factors in the evolution of bacteria & archaea
  3. Software program development for comparative genome analysis

Selected Publications

  1. X. Wang*, Y. Zhang*, M. Ren*, T. Xia, X. Chu, C. Liu, X. Lin, Y. Huang, Z. Chen, A. Yan, and H. Luo. 2020. Cryptic speciation of a pelagic Roseobacter population varying at a few thousand nucleotide sites. The ISME Journal (In Press) (*equal contribution)
  2. C-X. Xue*, H. Zhang*, H-Y. Lin*, Y. Sun, D. Luo, Y. Huang, X-H. Zhang*, and H. Luo. 2020. Ancestral niche separation and evolutionary rate differentiation between sister marine Flavobacteria lineages. Environmental Microbiology 22 (8): 3234-3247
  3. M. Ren*, X. Feng*, Y. Huang, H. Wang, Z. Hu, S. Clingenpeel, B.K. Swan, M.M. Fonseca, D. Posada, R. Stepanauskas, J.T. Hollibaugh, P.G. Foster, T. Woyke, H. Luo*. 2019. Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution. The ISME Journal 13 (9):2150-2161 (*equal contribution)
  4. H. Zhang, S. Yoshizawa, Y. Sun, Y. Huang, X. Chu, J.M. Gonzalez, J. Pinhassi, H. Luo*. 2019. Repeated evolutionary transitions of flavobacteria from marine to non-marine habitats. Environmental Microbiology 21 (2):648-666
  5. F.L. Hellweger, Y. Huang, H. Luo. (2018) Carbon Limitation Drives GC Content Evolution of a Marine Bacterium in an Individual-Based Genome-Scale Model. The ISME Journal. 12 (5):1180-1187.
  6. H. Luo*, Y. Huang*, R. Stepanauskas, J. Tang. (2017) Accumulation of Non-Conservative Amino Acid Replacement during Genome Streamlining of Marine Bacterial Lineages. Nature Microbiology. 2, Article Number: 17091. (* co-first author)
  7. X. Li, Y. Huang, W. B. Whitman. (2015) The relationship of the whole genome sequence identity to DNA hybridization varies between genera of prokaryotes. Antonie van Leeuwenhoek. 107:241-249.
  8. Y. Huang, J. Mrazek. (2014) Assessing diversity of DNA structure-related sequence features in prokaryotic genomes. DNA Research. 21, 285-297.