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

  1. Yuan J, Zhou J, Wang H, Sun H: SKmDB: an integrated database of next generation sequencing information in skeletal muscle. Bioinformatics 2018 Aug 25.
  2. Sun K, Wang J, Wang H, Sun H: GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies. Bioinformatics 2018 Jun 27.
  3. Zhou J, Huang Y, Ding Y, Yuan J, Wang H, Sun H: lncFunTK: A toolkit for functional annotation of long noncoding RNAs. Bioinformatics 2018 Apr 26.
  4. Sun K, Lun FMF, Jiang P, Sun H: BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data. Bioinformatics 2017 Nov 1; 33(21):3495-3496.
  5. An Y, Wang G, Diao Y, Long Y, Fu X, Weng M, Zhou L, Sun K, Cheung TH, Ip NY, Sun H, Wang H, Wu Z: A Molecular Switch Regulating Cell Fate Choice between Muscle Progenitor Cells and Brown Adipocytes. Dev Cell 2017 May 22;41(4):382-391.e5.
  6. Peng X, So KK, He L, Zhao Y, Zhou J, Li Y, Yao M, Xu B, Zhang S, Yao H, Hu P, Sun H, Wang H: MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation. Nucleic Acids Res 2017 Jun 1.
  7. Zhou J, Zhang S, Wang H, Sun H: LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. Nucleic Acid Research 2017 Apr 4.
  8. 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 MA, Nakagawa S, Prasanth KV, Wu Z, Sun H, Wang H: Malat1 regulates myogenic differentiation and muscle regeneration through modulating MyoD transcriptional activity. Cell Discov 2017 Mar 14;3:17002.
  9. Zhao Y, Sun H, and Wang H: Long noncoding RNAs in DNA methylation: new players stepping into the old game. Cell Biosci 2016 Jul 11;6:45.
  10. Sun K, Zhou L, Zhao Y, Wang H, Sun H: 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.
  11. 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 LY, Esteban MA, Wang R, Jauch R, Sun H and Wang H: Linc-YY1, a novel functional long non-coding RNA in myogenic differentiation and muscle regeneration. Nat Commun 2015, Dec 11;6:10026.
  12. Oh J, Sanders IF, Chen EZ, Li H, Tobias JW, Isett RB, Penubarthi S, Sun H, Baldwin DA, Fraser NW: Genome wide nucleosome mapping for HSV-1 shows nucleosomes are deposited at preferred positions duringlytic infection. PLoS One 10(2):e0117471.
  13. Fu X, Xiao J, Wei Y, Li S, Liu Y, Yin J, Sun K, Sun H, Wang H, Zhang Z, Zhang BT, Sheng C, Wang H, Hu P: Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. Cell Res 2015, Jun;25(6):655-73.
  14. Wang L, Zhao Y, Bao X, Zhu X, Kwok YK, Sun K, Chen X, Huang Y, Jauch R, Esteban MA, Sun H, Wang H: LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Cell Res 2015, Mar;25(3):335-50.
  15. Chan RW, Jiang P, Peng X, Tam LS, Liao GJ, Li EK, Wong PC, Sun H, Chan KCA, Chiu RWK, Lo YMD: 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.
  16. Li L, Zhang Y, Fan Y, Sun K, Su X, Du Z, Tsao SW, Loh TK, Sun H, Chan AT, Zeng YX, Chan WY, Chan FK, Tao Q: Characterization of the nasopharyngeal carcinoma methylome identifies aberrant disruption of key signaling pathways and methylated tumor suppressor genes. Epigenomics 2014 Dec 5:1-19.
  17. Sun K, Yuen YP, Wang H, Sun H: Online Diagnosis System: a webserver for analysis of Sanger sequencing-based genetic testing data. Methods 2014 69(3):230-236.
  18. Jiang P, Sun K, Lun FMF, Guo AM, Wang H, Chan KCA, Chiu RWK, Lo YMD, Sun H: Methy-Pipe: An integrated bioinformatics pipeline for whole genome bisulfite sequencing data analysis. PLoS ONE2014 Jun 19;9(6):e100360.
  19. Tusi, NBY, Jiang P, Wong YF, Leung TY, Chan KCA, Chiu RWK, Sun H, Lo YMD: Maternal Plasma RNA Sequencing for Genomewide Transcriptomic Profiling and Identification of Pregnancy-Associated Transcripts. Clin Chem 2014 Jul;60(7):954-62..
  20. 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, Feng B: Direct activation of human and mouse Oct4 genes using engineered transcription activatior-like effector protein and Cas9 transcription factor. Nucleic Acids Res 2014 Apr;42(7):4375-90.
  21. Sun K, Zhao Y, Wang H, Sun H: Sebnif: An Integrated Bioinformatics Pipeline for the Identification of Novel Large Intergenic Noncoding RNAs (lincRNAs) - Application in Human Skeletal Muscle Cells. PLoS One 2014 Jan 6, 9(1):e84500.
  22. Yang Y, Zhou L, Lu L, Wang L, Li X, Jiang P, Chan LK, Zhang T, Yu J, Kwong J, Cheung TH, Chung T, Mak K, Sun H, Wang H: A novel miR-193a-5p-YY1-APC regulatory axis in human endometrioid endometrial adenocarcinoma. Oncogene 32, 3432-3442.
  23. Chan KCA, Jiang P, Chan CW, Sun K, Wong J, Hui EP, Chan SL, Chan WC, Hui DS, Ng SS, Chan HL, Wong CS, Ma BB, Chan AT, Lai PB, Sun H, Chiu RWK, Lo YMD: Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing. Proc Natl Acad Sci U S A 2013 Nov 19;110(47):18761-8.
  24. Lun FMF, Chiu RWK, Sun K, Leung TY, Jiang P, Chan KCA, Sun H, Lo YMD: Noninvasive prenatal methylomic analysis by genomewide bisulfite sequencing of maternal plasma DNA. Clin Chem 2013 Nov;59(11):1583-94.
  25. Sun K Chen, X, Jiang, P, Song, X, Wang, H, and Sun H: iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data. BMC Genomics 2013; 14 Suppl 2, S7.
  26. Guo AM, Sun K, Su X, Wang H, Sun H: YY1TargetDB: an integral information resource for Yin Yang 1 target loci. Database (Oxford) 2013, bat007.
  27. Lu L, Sun K, Chen X, Zhao Y, Wang L, Zhou L, Sun H, Wang H: Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis. EMBO J 2013; 32, 2575-2588.
  28. Song X, Wang M, Chen YP, Wang H, Han P, and Sun H: Prediction of pre-miRNA with multiple stem-loops using pruning algorithm. Comput Biol Med 2013; 43, 409-416.
  29. Qu JZZ, Leung TY, Jiang P, Liao GJ, Cheng YK, Sun H, Chiu RWK, Chan KCA, Lo YMD: Noninvasive prenatal determination of twin zygosity by maternal plasma DNA analysis. Clin Chem 2013; 59, 427-435.
  30. Chan KCA, Jiang P, Zheng YW, Liao GJ, Sun H, Wong J, Siu SS, Chan WC, Chan SL, Chan AT, Lai PB, Chiu RWK, Lo YMD: Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem 2013; 59, 211-224.
  31. Zhou L, Wang L, Lu L, Jiang P, Sun H, Wang H: A novel target of microRNA-29, Ring1 and YY1-binding protein (Rybp), negatively regulates skeletal myogenesis. J Biol Chem 2012 Jul 20;287(30):25255-65.
  32. Zhou L, Wang L, Lu L, Jiang P, Sun H, Wang H: Inhibition of miR-29 by TGF-beta-Smad3 signaling through dual mechanisms promotes transdifferentiation of mouse myoblasts into myofibroblasts. PLoS One 2012; 7, e33766.
  33. Zheng YWL, Chan KCA, Sun H, Jiang P, Su X, Chen EZ, Lun FMF, Hung ECW, Lee V, Wong J, Lai PB, Li CK, Chiu RWK, Lo YMD: Nonhematopoietically derived DNA is shorter than hematopoietically derived DNA in plasma: a transplantation model. Clin Chem 2012 Mar;58(3):549-58.
  34. Wang L, Zhou L, Jiang P, Lu L, Chen X, Lan H, Guttridge DC, Sun H, Wang H: Loss of miR-29 in myoblasts contributes to dystrophic muscle pathogenesis. Molecular Therapy 2012 Jun;20(6):1222-33
  35. Tsui NBY, Jiang P, Chow KCK, Su X, Leung TY, Sun H, Chan KCA, Chiu RWK, Lo YMD: High Resolution Size Analysis of Fetal DNA in the Urine of Pregnant Women by Paired-End Massively Parallel Sequencing. PLoS one 2012; 7, e48319.
  36. Lu L, Zhou L, Chen EZ, Sun K, Jiang P, Wang L, Su X, Sun H, Wang H: A Novel YY1-miR-1 regulatory circuit in skeletal myogenesis revealed by genome-wide prediction of YY1-miRNA network. PLoS One 2012; 7, e27596.
  37. Liao GJ, Chan KCA, Jiang P, Sun H, Leung TY, Chiu RWK, Lo YMD: Noninvasive prenatal diagnosis of fetal trisomy 21 by allelic ratio analysis using targeted massively parallel sequencing of maternal plasma DNA. PLoS One 2012; 7, e38154.
  38. Jiang P, Chan KCA, Liao GJ, Zheng YW, Leung TY, Chiu RWK, Lo YMD, Sun H: FetalQuant: deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma. Bioinformatics 2012; 28, 2883-2890.
  39. Diao Y, Guo X, Li Y, Sun K, Lu L, Jiang L, Fu X, Zhu H, Sun H, Wang H: Pax3/7BP Is a Pax7-and Pax3-Binding Protein that Regulates the Proliferation of Muscle Precursor Cells by an Epigenetic Mechanism. Cell Stem Cell 2012; 11, 231-241.
  40. van Abel D, Holzel DR, Jain S, Lun FMF, Zheng YWL, Chen EZ, Sun H, Chiu RWK, Lo YMD, van Dijk M: SFRS7-Mediated Splicing of Tau Exon 10 Is Directly Regulated by STOX1A in Glial Cells. PLoS one 2011; 6, e21994.
  41. Lun FMF, Jin YY, Sun H, Leung TY, Lau TK, Chiu RWK, Lo, YMD: Noninvasive prenatal diagnosis of a case of Down syndrome due to robertsonian translocation by massively parallel sequencing of maternal plasma DNA. Clin Chem 2011; 57, 917-919.
  42. Chiu RWK, Akolekar R, Zheng YWL, Leung TY, Sun H, Chan KCA, Lun FMF, Go ATJI, Lau ET, To WWK, Leung WC, Tang RY, Au-Yeung SK, Lam H, Kung YY, Zhang X, van Vugt JM, Minekawa R, Tang MH, Wang J, Oudejans CB, Lau TK, Nicolaides KH, Lo YMD: Non-invasive prenatal assessment of trisomy 21 by multiplexed maternal plasma DNA sequencing: large scale validity study. BMJ 2011 Jan 11;342:c7401.
  43. Chen EZ, Chiu RWK, Sun H, Akolekar R, Chan KCA, Leung TY, Jiang P, Zheng YW, Lun FMF, Chan LY, Jin Y, Go AT, Lau ET, To WW, Leung WC, Tang RY, Au-Yeung SK, Lam H, Kung YY, Zhang X, van Vugt JM, Minekawa R, Tang MH, Wang J, Oudejans CB, Lau TK, Nicolaides KH, Lo YMD: Noninvasive prenatal diagnosis of fetal trisomy 18 and trisomy 13 by maternal plasma DNA sequencing. PLoS One 2011; 6, e21791.
  44. Sun H, Wu J, Wickramasinghe P, Pal S, Gupta R, Bhattacharyya A, Agosto-Perez FJ, Showe LC, Huang THM, Davuluri RV: Genome-wide mapping of RNA Pol-II promoter usage in mouse tissues by ChIP-seq. Nucleic Acids Res 2011 Jan;39(1):190-201.
  45. Nicoloso MS, Sun H, Spizzo R, Kim H, Wickramasinghe P, Shimizu M, Wojcik SE, Ferdin J, Kunej T, Xiao L, Manoukian S, Secreto G, Ravagnani F, Wang X, Radice P, Croce CM, Davuluri RV, Calin GA: Single-nucleotide polymorphisms inside microRNA target sites influence tumor susceptibility. Cancer Res 2010 Apr 1;70(7):2789-98.
  46. Lo YMD, Chan KCA, Sun H, Chen EZ, Jiang P, Lun FMF, Zheng YW, Leung TY, Lau TK, Cantor CR, Chiu RWK: Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus. Sci Transl Med 2010; 2, 61ra91.
  47. Chiu RWK, Sun H, Akolekar R, Clouser C, Lee C, McKernan K, Zhou D, Nicolaides KH, Lo YMD: Maternal plasma DNA analysis with massively parallel sequencing by ligation for noninvasive prenatal diagnosis of trisomy 21. Clin Chem 2010 Mar;56(3):459-63.
  48. Wang, H Sun H, Guttridge DC: microRNAs: novel components in a muscle gene regulatory network. Cell Cycle 2009 Jun 15;8(12):1833-7.
  49. Smith ST, Wickramasinghe P, Olson A, Loukinov D, Lin L, Deng J, Xiong Y, Rux J, Sachidanandam R, Sun H: Genome wide ChIP-chip analyses reveal important roles for CTCF in Drosophila genome organization. Developmental biology 2009 Apr 15;328(2):518-28.

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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