Refereed journal papers since joining the CUHK (2009 - present)

  1. 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.
  2. Chen X., He L., Zhao Y., Li Y., Zhang S., Sun K., So K., Chen F., Zhou L., Lu L., Wang L., Zhu X., Bao X., Esteban M.A., Nakagawa S., Prasanth K.V., Wu Z., Sun H., Wang H. (2017) Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity. Cell Discov 2017 Mar 14;3:17002.
  3. Zhao Y., Sun H., and Wang H. (2016) Long noncoding RNAs in DNA methylation: new players stepping into the old game. Cell Biosci. 2016 Jul 11;6:45.
  4. Sun K., Zhou L., Zhao Y., Wang H., Sun H. (2016) Genome-wide RNA-seq and ChIP-seq reveal Linc-YY1 function in regulating YY1/PRC2 activity during skeletal myogenesis. Genomics Data 2016, Mar;7:247-249.
  5. Zhou L., Sun K., Zhao Y., Zhang S., Wang X., Li Y., Lu L., Chen X., Chen F., Bao X., Zhu X., Wang L., Tang L.Y., Esteban M.A., Wang R., Jauch R., Sun H. and Wang H. (2015) Linc-YY1, a novel functional long non-coding RNA in myogenic differentiation and muscle regeneration. Nat Commun 2015, Dec 11;6:10026.
  6. Oh J., Sanders I.F., Chen E.Z., Li H., Tobias J.W., Isett R.B., Penubarthi S., Sun H., Baldwin D.A., and Fraser N.W.(2015) Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions duringlytic infection. PLoS One. 10(2):e0117471.
  7. Fu X., Xiao J., Wei Y., Li S., Liu Y., Yin J., Sun K., Sun H., Wang H., Zhang Z., Zhang B.T., Sheng C., Wang H., and Hu P.(2015) Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. Cell Res 2015, Jun;25(6):655-73.
  8. Wang L., Zhao Y., Bao X., Zhu X., Kwok Y.K., Sun K., Chen X., Huang Y., Jauch R., Esteban M.A., Sun H., and Wang H. (2015) LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Cell Res 2015, Mar;25(3):335-50.
  9. 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. (2014) Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing. Proc Natl Acad Sci U S A. 2014 Dec 9;111(49):E5302-11.
  10. Li L., Zhang Y., Fan Y., Sun K., Su X., Du Z., Tsao S.W., Loh T.K., Sun H., Chan A.T., Zeng Y.X., Chan W.Y., Chan F.K., and Tao Q. (2014) Characterization of the nasopharyngeal carcinoma methylome identifies aberrant disruption of key signaling pathways and methylated tumor suppressor genes. Epigenomics 2014, Dec 5:1-19.
  11. Sun, K., Yuen Y.P., Wang, H. and Sun H. (2014) Online Diagnosis System: a webserver for analysis of Sanger sequencing-based genetic testing data. Methods, 2014, 69(3):230-236.
  12. Jiang, P., Sun, K., Lun, F.M.F., Guo, A.M., Wang, H., Chan, K.C.A., Chiu, R.W.K., Lo, Y.M.D., and Sun, H. (2014) Methy-Pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS ONE, Jun 19;9(6):e100360.
  13. Tusi, N.B.Y., Jiang, P., Wong, Y.F., Leung, T.Y., Chan K.C.A., Chiu, R.W.K., Sun, H., and Lo Y.M.D. (2014) Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts. Clin Chem, 2014, Jul;60(7):954-62..
  14. Hu J., Lei Y., Wong W., Liu S., Lee K., He X., You W., Zhou R., Guo J., Chen X., Peng X., Sun, H., Huang H., Zhao H., and Feng B.(2014) Direct activation of human and mouse Oct4 genes using engineered transcription activatior-like effector protein and Cas9 transcription factor. Nucleic Acids Res, 1-16, doi:10.1093/nar/gku109.(IF2012: 8.278; 27/290 in Biochemistry & Molecular Biology)
  15. Sun, K., Zhao, Y., Wang, H., and Sun, H. (2014) Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs) - Application in Human Skeletal Muscle Cells. PLoS One, 9(1):e84500.(IF2012: 3.73; 7/56 in Multidisciplinary Sciences)
  16. Yang, Y., Zhou, L., Lu, L., Wang, L., Li, X., Jiang, P., Chan, L.K., Zhang, T., Yu, J., Kwong, J., Cheung, T.H., Chung, T., Mak, K., Sun, H.*, and Wang, H.*.(2013) A novel miR-193a-5p-YY1-APC regulatory axis in human endometrioid endometrial adenocarcinoma. Oncogene 32, 3432-3442, *co-corresponsing author, (IF2012: 7.357; 19/196 Oncology, 15/161 Genetics & Heredity)
  17. Chan, K.C., Jiang, P., Chan, C.W., Sun, K., Wong, J., Hui, E.P., Chan, S.L., Chan, W.C., Hui, D.S., Ng, S.S., Chan, H.L., Wong, C.S., Ma, B.B., Chan, A.T., Lai, P.B., Sun, H., Chiu, R.W.K., and Lo, Y.M.(2013) Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci U S A 110, 18761-18768.(IF2012: 9.737; 4/56 Multidisciplinary Sciences)
  18. Lun, F.M., Chiu, R.W., Sun, K., Leung, T.Y., Jiang, P., Chan, K.C., Sun, H., and Lo, Y.M.(2013) Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clin Chem 59, 1583-1594.(IF2012: 7.149; 1/32 in Medical Laboratory Technology)
  19. Sun, K., Chen, X., Jiang, P., Song, X., Wang, H., and Sun, H. (2013) iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics 14 Suppl 2, S7.(IF2012: 4.397; 21/160 in Biotechnology and Applied Microbiology)
  20. Guo, A.M., Sun, K., Su, X., Wang, H., and Sun, H. (2013) YY1TargetDB: an integral information resource for Yin Yang 1 target loci. Database (Oxford) 2013, bat007.(IF2012: 4.2; 4/47 in Mathematical & Computation Biology)
  21. 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.*co-corresponding author, (IF2012: 9.822; 19 /185 in Cell Biology, 19/290 in Biochemistry and Molecular Biology)
  22. Song, X., Wang, M., Chen, Y.P., Wang, H., Han, P., and Sun, H. (2013) Prediction of pre-miRNA with multiple stem-loops using pruning algorithm. Comput Biol Med 43, 409-416.(IF2012: 1.162)
  23. Qu, J.Z., Leung, T.Y., Jiang, P., Liao, G.J., Cheng, Y.K., Sun, H., Chiu, R.W., Chan, K.C., and Lo, Y.M.(2013) Noninvasive prenatal determination of twin zygosity by maternal plasma DNA analysis. Clin Chem 59, 427-435.(IF2012: 7.149; 1/32 in Medical Laboratory Technology)
  24. Chan, K.C., Jiang, P., Zheng, Y.W., Liao, G.J., Sun, H., Wong, J., Siu, S.S., Chan, W.C., Chan, S.L., Chan, A.T., Lai, P.B., Chiu, R.W., and Lo, Y.M.(2013) Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem 59, 211-224.(IF2012: 7.149; 1/32 in Medical Laboratory Technology)
  25. Zhou, L., Wang, L., Lu, L., Jiang, P., Sun, H. *, and Wang, H.* (2012) A novel target of microRNA-29, Ring1 and YY1-binding protein (Rybp), negatively regulates skeletal myogenesis. J Biol Chem 287, 25255-25265.*Co-corresponding author, (IF2012: 4.651; 62/290 in Biochemistry and Molecular Biology)
  26. Zhou, L., Wang, L., Lu, L., Jiang, P., Sun, H. *, and Wang, H.* (2012) Inhibition of miR-29 by TGF-beta-Smad3 signaling through dual mechanisms promotes transdifferentiation of mouse myoblasts into myofibroblasts. PLoS One 7, e33766.*co-corresponding author, (IF2012: 3.73; 7/56 in Multidisciplinary Sciences).
  27. Zheng, Y.W.L., Chan, K.C.A., Sun, H., Jiang, P., Su, X., Chen, E.Z., Lun, F.M.F., Hung, E.C.W., Lee, V., and Wong, J.(2012) Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model. Clin Chem.2011.169318 v169311.(IF2012: 7.149; 1/32 in Medical Laboratory Technology)
  28. Wang, L., Zhou, L., Jiang, P., Lu, L., Chen, X., Lan, H., Guttridge, D.C., Sun, H.*, and Wang, H.*.(2012) Loss of miR-29 in myoblasts contributes to dystrophic muscle pathogenesis. Molecular Therapy 20, 1222-1233.*Co-corresponding author (IF2012: 7.041; 9/159 in Biotechnology and Applied Microbiology, 16/161 in Genetics and Heredity; 10/121 in Medicine, Research and Experimental)
  29. Tsui, N.B.Y., Jiang, P., Chow, K.C.K., Su, X., Leung, T.Y., Sun, H., Chan, K.C.A., Chiu, R.W.K., and Lo, Y.M.D.(2012) High Resolution Size Analysis of Fetal DNA in the Urine of Pregnant Women by Paired-End Massively Parallel Sequencing. PLoS one 7, e48319.(IF2012: 3.73; 7/56 in Multidisciplinary Sciences)
  30. Lu, L., Zhou, L., Chen, E.Z., Sun, K., Jiang, P., Wang, L., Su, X., Sun, H. *, and Wang, H.* (2012) A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS One 7, e27596.*Co-corresponding author, (IF2012: 3.73; 7/56 in Multidisciplinary Sciences).
  31. Liao, G.J., Chan, K.C., Jiang, P., Sun, H., Leung, T.Y., Chiu, R.W., and Lo, Y.M.(2012) Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA. PLoS One 7, e38154.(IF2012: 3.73; 7/56 in Multidisciplinary Sciences)
  32. Jiang, P., Chan, K.C., Liao, G.J., Zheng, Y.W., Leung, T.Y., Chiu, R.W., Lo, Y.M., and Sun, H. (2012) FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. Bioinformatics 28, 2883-2890.(IF2012: 5.323; 2/47 in Mathematical & Computation Biology, 7/75 in Biochemical Research Methods, 15/159 in Biotechnology & Applied Microbiology)
  33. Diao, Y., Guo, X., Li, Y., Sun, K., Lu, L., Jiang, L., Fu, X., Zhu, H., Sun, H., and Wang, H.(2012) Pax3/7BP Is a Pax7-and Pax3-Binding Protein that Regulates the Proliferation of Muscle Precursor Cells by an Epigenetic Mechanism. Cell Stem Cell 11, 231-241.(IF2012: 25.315; 3/185 in Cell Biology)
  34. van Abel, D., Holzel, D.R., Jain, S., Lun, F.M.F., Zheng, Y.W.L., Chen, E.Z., Sun, H., Chiu, R.W.K., Lo, Y.M.D., and van Dijk, M.(2011) SFRS7-Mediated Splicing of Tau Exon 10 Is Directly Regulated by STOX1A in Glial Cells. PLoS one 6, e21994.(IF2012: 3.73; 7/56 in Multidisciplinary Sciences)
  35. Lun, F.M., Jin, Y.Y., Sun, H., Leung, T.Y., Lau, T.K., Chiu, R.W., and Lo, Y.M.(2011) Noninvasive prenatal diagnosis of a case of Down syndrome due to robertsonian translocation by massively parallel sequencing of maternal plasma DNA. Clin Chem 57, 917-919.(IF2012: 7.149; 1/32 in Medical Laboratory Technology)
  36. 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)
  37. Chen, E.Z., Chiu, R.W., Sun, H., Akolekar, R., Chan, K.C., Leung, T.Y., Jiang, P., Zheng, Y.W., Lun, F.M., Chan, L.Y., Jin, Y., Go, A.T., Lau, E.T., To, W.W., Leung, W.C., Tang, R.Y., Au-Yeung, S.K., Lam, H., Kung, Y.Y., Zhang, X., van Vugt, J.M., Minekawa, R., Tang, M.H., Wang, J., Oudejans, C.B., Lau, T.K., Nicolaides, K.H., and Lo, Y.M.(2011) Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 6, e21791.(IF2012: 3.73; Citations:65; 7/56 in Multidisciplinary Sciences)
  38. Sun, H., Wu, J., Wickramasinghe, P., Pal, S., Gupta, R., Bhattacharyya, A., Agosto-Perez, F.J., Showe, L.C., Huang, T.H.M., and Davuluri, R.V.(2010) Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res 39, 190.(IF2012: 8.278; 27/290 in Biochemistry & Molecular Biology)
  39. Nicoloso, M.S.*, Sun, H.*, Spizzo, R., Kim, H., Wickramasinghe, P., Shimizu, M., Wojcik, S.E., Ferdin, J., Kunej, T., Xiao, L., Manoukian, S., Secreto, G., Ravagnani, F., Wang, X., Radice, P., Croce, C.M., Davuluri, R.V., and Calin, G.A.(2010) Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer Res 70, 2789-2798.*co-first author, (IF2012: 8.650, Citations: 82; 11/196 in Oncology Journals)
  40. 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)
  41. Chiu, R.W., Sun, H., Akolekar, R., Clouser, C., Lee, C., McKernan, K., Zhou, D., Nicolaides, K.H., and Lo, Y.M.(2010) Maternal plasma DNA analysis with massively parallel sequencing by ligation for noninvasive prenatal diagnosis of trisomy 21. Clin Chem 56, 459.(IF2012: 7.149; Citations: 53; 1/32 in Medical Laboratory Technology)
  42. Wang, H., Sun, H., and Guttridge, D.C.(2009) microRNAs: novel components in a muscle gene regulatory network. Cell Cycle 8, 1833-1837.(IF2012: 5.321; 44/185 in Cell Biology)
  43. Smith, S.T., Wickramasinghe, P., Olson, A., Loukinov, D., Lin, L., Deng, J., Xiong, Y., Rux, J., Sachidanandam, R., and Sun, H. (2009) Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Developmental biology 328, 518-528.(IF2012: 3.868; 8/41 in Development Biology)

Research Grants (2009 - present)

Awarded Grants in the Capacity of Principal Investigator (4 in total)

Competitive Grants
  1. Role: Principal Investigator
    Title: Genome-wide identification and characterization of functional long noncoding RNAs in skeletal muscle stem cells using integrated high-throughput sequencing and regulatory network analysis (CUHK473713)
    Funding Agency: Hong Kong SAR University Grants Committee, Research Grants Council, General Research Fund (GRF)
    Duration: 01/01/2014-31/12/2016
    Funding Amount: HK$ 1,125,842.00
  2. Role: Principal Investigator
    Title: Genome-wide identification of transcription factor-microRNA regulatory circuitries in skeletal muscle differentiation using chromatin immunopreciptation coupled with massively parallel sequencing (ChIP-Seq) (CUHK473211)
    Funding Agency: Hong Kong SAR University Grants Committee, Research Grants Council, General Research Fund (GRF)
    Duration: 01/01/2012-31/12/2013
    Funding Amount: HK$ 1,373,000.00
Non-Competitive Grants
  1. Role: Principal Investigator
    Title: High-speed Networking and Storage System for Next Generation Sequencing (NGS) data analysis
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Academic Equipment Grant
    Duration: 2009/2010
    Funding Amount: HK$ 1,254,680.00
  2. Role: Principal Investigator
    Title: Systematic identification of YY1 mediated regulatory networks by chromatin immunoprecipitation (ChIP) couple to massively parallel DNA sequencing (ChIP-seq) (MD09302)
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Research Committee Fund (Direct grant)
    Duration: 30/06/2010-29/06/2011
    Funding Amount: HK$ 73,000.00

Awarded Grants in the Capacity of Co-Principal Investigator/Co-Investigator (14 in total)

Competitive Grants
  1. Role: Co-Principal Investigator
    Title: Massively Parallel Sequencing of Plasma Nucleic Acids for the Molecular Diagnostics of Cancers (T12-404/11)
    Funding Agency: Hong Kong SAR University Grants Committee, Theme-based Research Scheme (TRS) 1st round
    Duration: 01/12/2011-30/11/2016
    Funding Amount: HK$ 27,825,000.00
  2. Role: Co-Investigator
    Title: Centre for Research into Circulating Fetal Nucleic Acids (AoE/M-04/06)
    Funding Agency: Hong Kong SAR University Grants Committee, Areas of Excellence Schema (AoE) 4th round
    Duration: 01/1/2008-31/12/2015
    Funding Amount: HK$ 65,280,000.00
  3. Role: Co-Investigator
    Title: Functional Characterization of PCDH10 in Endometrioid Endometrial Adenocarcinoma (01120446)
    Funding Agency: Hong Kong SAR, Food and Health Bureau, Health and Medical Research Fund (HMRF)
    Duration: 01/01/2014-31/12/2015
    Funding Amount: HK$ 882,866.00
  4. Role: Co-Investigator
    Title: The role of STAT3 in muscle stem cells and muscle regeneration (663512)
    Funding Agency: Hong Kong SAR University Grants Committee, Research Grants Council, General Research Fund (GRF)
    Duration: 01/10/2012-30/09/2013
    Funding Amount: HK$ 1,036,000.00
  5. Role: Co-Investigator
    Title: The role of Transcripts of Ultra-conserved Regions (T-UCRs) in Skeletal Myogenesis (476310)
    Funding Agency: Hong Kong SAR University Grants Committee, Research Grants Council, General Research Fund (GRF)
    Duration: 01/01/2011-31/12/2013
    Funding Amount: HK$ 1,200,000.00
  6. Role: Co-Investigator
    Title: The role of miR-29 in Duchenne muscular dystrophy (CU09763)
    Funding Agency: Hong Kong SAR University Grants Committee, Research Grants Council, General Research Fund (GRF)
    Duration: 01/01/2010-31/12/2011
    Funding Amount: HK$ 890,852.00
  7. Role: Co-Investigator
    Title: Development of Non-Invasive Prenatal Diagnosis for Trisomy 18 and 13 Using Massively Parallel Genomic Sequencing (MD09460)
    Funding Agency: Hong Kong SAR Innovation and Technology Commission, Innovation and Technology Fund (ITF)
    Duration: 01/11/2009-31/10/2011
    Funding Amount: HK$ 4,028,248.00
  8. Role: Co-Investigator
    Title: Development of Non-Invasive Prenatal Diagnosis for Trisomy 18 and 13 Using Massively Parallel Genomic Sequencing (MD09460)
    Funding Agency: Sequenom Inc., USA and ITF.
    Duration: 01/11/2009-31/10/2011
    Funding Amount: HK$ 156,000.00
  9. Role: Co-Investigator
    Title: Development of Non-Invasive Prenatal Diagnosis for Trisomy 18 and 13 Using Massively Parallel Genomic Sequencing (MD09460)
    Funding Agency: Applied Biosystems Inc., and ITF
    Duration: 01/11/2009-31/10/2011
    Funding Amount: HK$ 310,000.00
Non-Competitive Grants
  1. Role: Co-Investigator
    Title: Capture the Transcriptome Dynamics from Epiblast Stem Cells to Primordial Germ Cells by RNA-seq (BL10628)
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Research Committee Fund (Direct grant)
    Duration: 30/06/2011-29/06/2012
    Funding Amount: HK$ 80,000.00
  2. Role: Co-Investigator
    Title: TGFbeta-Smad-miR29 Axis in Muscle Fibrogenesis (MD10379)
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Research Committee Fund (Direct grant)
    Duration: 30/06/2011-29/06/2012
    Funding Amount: HK$ 22,500.00
  3. Role: Co-Investigator
    Title: Transcriptome Sequencing to Detect Gene Dosage Imbalance in Fetal Brains of Down's Syndrome: A Pilot Study (MD10448)
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Research Committee Fund (Direct grant)
    Duration: 01/04/2011-31/05/2012
    Funding Amount: HK$ 45,000.00
  4. Role: Co-Investigator
    Title: The regulation of miR-1/133 by YY1 in skeletal myogenesis (BL09982)
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Research Committee Fund (Direct grant)
    Duration: 01/01/2010-31/12/2011
    Funding Amount: HK$ 73,000.00
  5. Role: Co-Investigator
    Title: The involvement of Transcripts of Ultra-conserved Regions (T-UCRs) in skeletal myogenesis (BL08423)
    Funding Agency: Hong Kong SAR, Chinese University of Hong Kong Research Committee Fund (Direct grant)
    Duration: 10/06/2010-09/06/2011
    Funding Amount: HK$ 44,000.00
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