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HUANG, Hsien-Da



Education Background

PhD (Computer Science and Information Engineering, National Central University, Taiwan)

Research Field
Bioinformatics, Genomics, Metagenomics & Microbiome, Intelligent Biomedical Technologies (Drug Development, Genetic Test, & Precision Medicine), AI & Machine Learning, Biological Database Design & Development
Personal Website



Prof. Hsien-Da Huang is a professor at the School of Life and Health Sciences & Arieh Warshel Institute of Computational Biology, The Chinese University of Hong Kong, Shenzhen. He received PhD at Department of Computer Science and Information Engineering, National Central University, Taiwan, in 2003. He was a chair professor and vice dean at the College of Biological Science and Technology, National Chiao Tung University, Taiwan. During 2009-2016, he was the Chairman at Department of Biological Science and Technology, NCTU. He was the President of Taiwan Society of Bioinformatics and Systems Biology (2014-2017).

Prof. Huang’s group majorly focuses on biological multi-disciplinary research topics, including Bioinformatics, Genomics, Metagenomics & Microbiome, Intelligent Biomedical Technologies (Drug Development, Genetic Test, & Precision Medicine), AI & Machine Learning, and Biological Database Design & Development. During last ten years, He published more than 130 peer-reviewed publications, mostly in prestigious journals, including Science, Molecular Cell, Circulation, The Journal of Clinical Investigation, PLoS Biology, Hepatology, Cancer Research, and Nucleic Acids Research. If using several popular measures to assess the impacts of Prof. Huang’s research, he receives 13 highly-cited papers, more than 40 papers with 10.0 or higher impact factor, H-index as 41, more than 6000 citations in Web of Science and more than 9800 citations in Google Scholar.

Prof. Huang’s group developed a microRNA database, miRTarBase, which is an internationally recognized repository for collecting experimental miRNA-Target interaction (MTI). The users are majorly from the United States, China, Japan, Germany, and the UK. The database is continuously maintained and now broadly utilized and referred in life science and medical research field.

Prof. Huang received Outstanding Research Award (2010 and 2015) and Ta-You Wu Memorial Award (2009) of Ministry of Science and Technology, Taiwan.

Academic Publications:

1.      miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. (2018) Nucleic Acids Res., Vol. 46, D1, pp. D296-D302. (SCI, highly-cited paper)

2.      Plants send small RNAs in extracellular vesicles to fungal pathogen to silence virulence genes. (2018) Science, Vol. 360, No. 6393, pp. 1126-1129.

3.      MicroRNA-224 down-regulates Glycine N-methyltransferase gene expression in Hepatocellular Carcinoma. (2018) Scientific Report, Vol.8, No.1, pp.12284.

4.      Large-Scale Functional Analysis of CRP-Mediated Feed-Forward Loops. (2018) Int. J. Mol. Sci., Vol. 19, No.8, pp. E2335.

5.      Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis. (2018) BMC Genomics, Vol.19 (Suppl. 2), pp.171.

6.      MicroRNA-92a Mediates Endothelial Dysfunction in CKD. (2017) J. Am Soc. Nephrology, Vol. 28, No. 11, pp. 3251-3261.

7.      α-ketoglutarate orchestrates macrophage activation through metabolic and epigenetic reprogramming. (2017) Nature Immunology, Vol. 18, No. 9, pp. 985-994.

8.      Bidirectional cross-kingdom RNAi and fungal uptake of external RNAs confer plant protection. (2016) Nature Plants, Vol. 2, pp. 16151. (SCI, highly-cited paper)

9.      Krüppel-Like Factor 4 Regulation of Cholesterol-25-Hydroxylase and Liver X Receptor Mitigates Atherosclerosis Susceptibility. (2017) Circulation, Vol. 136, No. 14, pp. 1315-1330.

10.   dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. (2016) Nucleic Acids Research, Vol. 44, D1, pp. D435-46.

11.   miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. (2016) Nucleic Acids Research, Vol. 44, D1, pp. D239-47. (SCI, highly-cited paper)

12.   PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants. (2016) Nucleic Acids Research, Vol. 44, D1, pp. D1154-60.

13.   CircNet: a database of circular RNAs derived from transcriptome sequencing data. (2016) Nucleic Acids Research, Vol. 44, D1, pp. D209-15. (SCI, highly-cited paper)

14.   MethHC: a database of DNA methylation and gene expression in human cancer. (2015) Nucleic Acids Research, Vol. 43 (Database issue), pp. D856-61.

15.   Oxidative stress activates endothelial innate immunity via sterol regulatory element binding protein 2 (SREBP2) transactivation of microRNA-92a. (2015) Circulation, Vol. 131, No. 9, pp. 805-14.

16.   The effects of actin cytoskeleton perturbation on keratin intermediate filament formation in mesenchymal stem/stromal cells. (2014) Biomaterials, Vol. 35, No. 13, pp. 3934-44.

17.   miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. (2014) Nucleic Acids Research, Vol. 42, pp. D78-85. (SCI, highly-cited paper)

18.   COL11A1 Promotes Tumor Progression, and Predicts Poor Clinical Outcome in Ovarian Cancer. (2013) Oncogene, Vol. 33, No. 26, pp. 3432-40.

19.   Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma. (2013) Nucleic Acids Research, Vol. 41, No. 6, pp. 3734-47.

20.   Sterol Regulatory Element Binding Protein 2 Activation of NLRP3 Inflammasome in Endothelium Mediates Hemodynamic-Induced Atherosclerosis Susceptibility. (2013) Circulation, Vol. 128, No. 6, pp. 632-42.

21.   Hypoxia-responsive miRNAs target argonaute 1 to promote angiogenesis. (2013) Journal of Clinical Investigation, Vol. 123, No. 3, pp. 1057-67.

22.   Fungal small RNAs as novel effectors to suppress plant immunity by hijacking the host RNAi machinery. Science, Vol. 342, No. 6154, pp. 118-123. (SCI, highly-cited paper)

23.   MicroRNA-122 plays a critical role in liver homeostasis and hepatocarcinogenesis. (2012) Journal of Clinical Investigation, Vol. 122, No. 8, pp. 2884-97. (SCI, highly-cited paper)

24.   Let-7b is a novel regulator of hepatitis C virus replication. (2012) Cellular and Molecular Life Sciences, Vol. 69, No. 15, pp. 2621-33.

25.   Clusters of nucleotide substitutions and insertion/deletion mutations are associated with repeat sequences. (2011) PLoS Biology, Vol. 9, No. 6, e1000622.

26.   RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. (2011) Nucleic Acids Research, Vol.39, pp. D777-87.

27.   miRTarBase: a database curates experimentally validated microRNA-target interactions. (2011) Nucleic Acids Research, Vol.39, pp. D163-9. (SCI, highly-cited paper)

28.   miR-103/107 promote metastasis of colorectal cancer by targeting the metastasis suppressors DAPK and KLF4. (2012) Cancer Research, Vol. 72, No. 14, pp. 3631-41. (SCI, highly-cited paper)

29.   Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. (2011) Nucleic Acids Research, Vol. 39, No. 21, pp.9345-9356.

30.   Arabidopsis Argonaute 2 Regulates Innate Immunity via miRNA393*-Mediated Silencing of a Golgi-Localized SNARE Gene, MEMB12. (2011) Molecular Cell, Vo. 42, No. 3, pp. 356-366.

31.   Flow-regulation of Krüppel-like Factor 2 Is Mediated by MicroRNA-92a (2011) Circulation, Vol. 124, No. 5, pp. 633-41.

32.   MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma. (2009) Hepatology, Vol. 49, No. 5, pp. 1571-82. (SCI, highly-cited paper)