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醫學研究

醫學研究

黃凱堯 Kai-Yao Huang

醫學研究科 技術主任

  • 現職

    新竹馬偕紀念醫院醫學研究科 技術主任

    新竹馬偕紀念醫院醫學研究科 資深助研究員

    馬偕醫學院醫學系 兼任助理教授

    馬偕醫學院生物醫學研究所 兼任助理教授

    教育部部定 助理教授

     

     

    聯絡方式

    電子信箱: kyh.L765@mmh.org.tw

    院內分機: 5522-765

     

  • 主要學歷

    元智大學資訊工程系(生物與醫學資訊) 博士

     

     

    主要經歷

    香港中文大學瓦謝爾計算生物研究院 研究學者

    元智大學大數據與數位匯流創新中心 博士後研究員

     

     

    其他相關

    獲獎榮譽:

    2017 國際生物資訊學會議 最佳論文獎 (金牌、銅牌)
    (16th International Conference on Bioinformatics)

     

執行項目或專長

MAJOR SERVICE

Bioinformatics, Artificial Intelligence, Big data analytics, Computational system biology, Microarray/RNA-seq (NGS) data analysis, Cancer biomarker discovery, Metagenomics/Metatranscriptomics, Mass spectrometry data analysis, Biological databases and tools development, Data mining and machine learning.

 

期刊論文

 

iDVIP: identification and characterization of viral integrase inhibitory peptides.
Huang KY, Kao HJ, Weng TH, Chen CH, Weng SL.
Brief Bioinform. 2022 Oct 10:bbac406.
(2021 IF:13.994, BIOCHEMICAL RESEARCH METHODS 3/79; MATHEMATICAL&COMPUTATIONAL BIOLOGY 1/57.)

 

 

Global characterization of macrophage polarization mechanisms and identification of M2-type polarization inhibitors.
He L, Jhong JH, Chen Q, Huang KY, Strittmatter K, Kreuzer J, DeRan M, Wu X, Lee TY, Slavov N, Haas W, Marneros AG.
Cell Rep. 2021 Nov 2;37(5):109955.
(2021 IF:9.995, CELL BIOLOGY 33/194.)

 

 

Identification of subtypes of anticancer peptides based on sequential features and physicochemical properties.
Huang KY, Tseng YJ, Kao HJ, Chen CH, Yang HH, Weng SL.
Sci Rep. 2021 Jun 30;11(1):13594.
(2021 IF:4.996, MULTIDISCIPLINARY SCIENCES 19/73.)

 

 

UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions.
Li Z, Chen S, Jhong JH, Pang Y, Huang KY, Li S, Lee TY.
Database (Oxford). 2021 Mar 8;2021:baab010.
(2021 IF:4.462, MATHEMATICAL&COMPUTATIONAL BIOLOGY 11/57.)

 

 

Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants.
Lei WT, Huang KY, Jhong JH, Chen CH, Weng SL.
Sci Rep. 2021 Feb 3;11(1):2856.
(2021 IF:4.996, MULTIDISCIPLINARY SCIENCES 19/73.)

 

 

iDPGK: characterization and identification of lysine phosphoglycerylation sites based on sequence-based features.
Huang KY, Hung FY, Kao HJ, Lau HH, Weng SL.
BMC Bioinformatics. 2020 Dec 9;21(1):568.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

SuccSite: Incorporating Amino Acid Composition and Informative k-spaced Amino Acid Pairs to Identify Protein Succinylation Sites.
Kao HJ, Nguyen VN, Huang KY, Chang WC, Lee TY.
Genomics Proteomics Bioinformatics. 2020 Apr;18(2):208-219.
(2021 IF:6.409, GENETICS&HEREDITY 24/175.)

 

 

Incorporating deep learning and multi-omics autoencoding for analysis of lung adenocarcinoma prognostication.
Lee TY, Huang KY, Chuang CH, Lee CY, Chang TH.
Comput Biol Chem. 2020 May 12;87:107277.
(2021 IF:3.737, BIOLOGY 32/94.)

 

 

Rapid classification of group B Streptococcus serotypes based on matrix-assisted laser desorption ionization-time of flight mass spectrometry and machine learning techniques.
Wang HY, Li WC, Huang KY, Chung CR, Horng JT, Hsu JF, Lu JJ, Lee TY.
BMC Bioinformatics. 2019 Dec 24;20(Suppl 19):703.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

Characterization and Identification of Lysine Succinylation Sites based on Deep Learning Method.
Huang KY, Hsu JB, Lee TY.
Sci Rep. 2019 Nov 7;9(1):16175.
(2021 IF:4.996, MULTIDISCIPLINARY SCIENCES 19/73.)

 

 

miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database.
Huang HY, Lin YC, Li J, Huang KY, Shrestha S, Hong HC, Tang Y, Chen YG, Jin CN, Yu Y, Xu JT, Li YM, Cai XX, Zhou ZY, Chen XH, Pei YY, Hu L, Su JJ, Cui SD, Wang F, Xie YY, Ding SY, Luo MF, Chou CH, Chang NW, Chen KW, Cheng YH, Wan XH, Hsu WL, Lee TY, Wei FX, Huang HD.
Nucleic Acids Res. 2020 Jan 8;48(D1):D148-D154.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

Increase Trichomonas vaginalis detection based on urine routine analysis through a machine learning approach.
Wang HY, Hung CC, Chen CH, Lee TY, Huang KY, Ning HC, Lai NC, Tsai MH, Lu LC, Tseng YJ, Lu JJ.
Sci Rep. 2019 Aug 19;9(1):11074.
(2021 IF:4.996, MULTIDISCIPLINARY SCIENCES 19/73.)

 

 

Structural and functional characterization of β2 -glycoprotein I domain 1 in anti-melanoma cell migration.
Leu SJ, Lee TY, Cheng SW, Tsai MY, Lin YS, Chiou TJ, Huang KY, Chiang AN.
Cancer Sci. 2019 Jun;110(6):1974-1986.
(2021 IF:6.518, ONCOLOGY 62/245.)

 

 

Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites.
Huang KY, Kao HJ, Hsu JB, Weng SL, Lee TY.
BMC Bioinformatics. 2019 Feb 4;19(Suppl 13):384.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

dbPTM in 2019: exploring disease association and cross-talk of post-translational modifications.
Huang KY, Lee TY, Kao HJ, Ma CT, Lee CC, Lin TH, Chang WC, Huang HD.
Nucleic Acids Res. 2019 Jan 8;47(D1):D298-D308.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

dbAMP: an integrated resource for exploring antimicrobial peptides with functional activities and physicochemical properties on transcriptome and proteome data.
Jhong JH, Chi YH, Li WC, Lin TH, Huang KY, Lee TY.
Nucleic Acids Res. 2019 Jan 8;47(D1):D285-D297.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

Machine Learning-Based Method for Obesity Risk Evaluation Using Single-Nucleotide Polymorphisms Derived from Next-Generation Sequencing.
Wang HY, Chang SC, Lin WY, Chen CH, Chiang SH, Huang KY, Chu BY, Lu JJ, Lee TY.
J Comput Biol. 2018 Dec;25(12):1347-1360.
(2021 IF:1.549, MATHEMATICAL&COMPUTATIONAL BIOLOGY 47/57.)

 

 

Genome-wide discovery of viral microRNAs based on phylogenetic analysis and structural evolution of various human papillomavirus subtypes.
Weng SL†, Huang KY†, Weng JT, Hung FY, Chang TH, Lee TY.
Brief Bioinform. 2018 Nov 27;19(6):1102-1114.
(2021 IF:13.994, BIOCHEMICAL RESEARCH METHODS 3/79; MATHEMATICAL&COMPUTATIONAL BIOLOGY 1/57.)

 

 

State-of-the-Art on Viral microRNAs in HPV Infection and Cancer Development.
Poltronieri P, Sun B, Huang KY, Chang TH, Lee TY.
Microrna. 2018;7(2):85-91.

 

 

A new scheme for strain typing of methicillin-resistant Staphylococcus aureus on the basis of matrix-assisted laser desorption ionization time-of-flight mass spectrometry by using machine learning approach.
Wang HY, Lee TY, Tseng YJ, Liu TP, Huang KY, Chang YT, Chen CH, Lu JJ.
PLoS One. 2018 Mar 13;13(3):e0194289.
(2021 IF:3.752, MULTIDISCIPLINARY SCIENCES 29/73.)

 

 

MDD-carb: a combinatorial model for the identification of protein carbonylation sites with substrate motifs.
Kao HJ, Weng SL, Huang KY, Kaunang FJ, Hsu JB, Huang CH, Lee TY.
BMC Syst Biol. 2017 Dec 21;11(Suppl 7):137.
(2018 IF:2.048, MATHEMATICAL&COMPUTATIONAL BIOLOGY 22/59.)

 

 

Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions.
Su MG, Weng JT, Hsu JB, Huang KY, Chi YH, Lee TY.
BMC Syst Biol. 2017 Dec 21;11(Suppl 7):132.
(2018 IF:2.048, MATHEMATICAL&COMPUTATIONAL BIOLOGY 22/59.)

 

 

Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas.
Huang KY, Chang TH, Jhong JH, Chi YH, Li WC, Chan CL, Robert Lai K, Lee TY.
BMC Syst Biol. 2017 Dec 21;11(Suppl 7):131.
(2018 IF:2.048, MATHEMATICAL&COMPUTATIONAL BIOLOGY 22/59.)

 

 

Poly-γ-glutamic Acid Synthesis, Gene Regulation, Phylogenetic Relationships, and Role in Fermentation.
Hsueh YH, Huang KY, Kunene SC, Lee TY.
Int J Mol Sci. 2017 Dec 7;18(12):2644.
(2021 IF:6.208, CHEMISTRY, MULTIDISCIPLINARY 76/224.)

 

 

Investigation and identification of protein carbonylation sites based on position-specific amino acid composition and physicochemical features.
Weng SL, Huang KY, Kaunang FJ, Huang CH, Kao HJ, Chang TH, Wang HY, Lu JJ, Lee TY.
BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):66.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation.
Nguyen VN, Huang KY, Weng JT, Lai KR, Lee TY.
Database (Oxford). 2016 Apr 25;2016:baw054.
(2021 IF:4.462, MATHEMATICAL&COMPUTATIONAL BIOLOGY 11/57.)

 

 

A New Scheme to Characterize and Identify Protein Ubiquitination Sites.
Nguyen VN, Huang KY, Huang CH, Lai KR, Lee TY.
IEEE/ACM Trans Comput Biol Bioinform. 2017 Mar-Apr;14(2):393-403.
(2021 IF:3.702, STATISTICS&PROBABILITY 15/125.)

 

 

Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis.
Lee SW, Wu LS, Huang GM, Huang KY, Lee TY, Weng JT.
BMC Bioinformatics. 2016 Jan 11;17 Suppl 1(Suppl 1):3.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases.
Huang KY, Weng JT, Lee TY, Weng SL.
BMC Syst Biol. 2016 Jan 11;10 Suppl 1(Suppl 1):3.
(2018 IF:2.048, MATHEMATICAL&COMPUTATIONAL BIOLOGY 22/59.)

 

 

A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs.
Kao HJ, Huang CH, Bretaña NA, Lu CT, Huang KY, Weng SL, Lee TY.
BMC Bioinformatics. 2015;16 Suppl 18(Suppl 18):S10.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins.
Huang KY, Su MG, Kao HJ, Hsieh YC, Jhong JH, Cheng KH, Huang HD, Lee TY.
Nucleic Acids Res. 2016 Jan 4;44(D1):D435-46.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

GSHSite: exploiting an iteratively statistical method to identify s-glutathionylation sites with substrate specificity.
Chen YJ, Lu CT, Huang KY, Wu HY, Chen YJ, Lee TY.
PLoS One. 2015 Apr 7;10(4):e0118752.
(2021 IF:3.752, MULTIDISCIPLINARY SCIENCES 29/73.)

 

 

ViralmiR: a support-vector-machine-based method for predicting viral microRNA precursors.
Huang KY, Lee TY, Teng YC, Chang TH.
BMC Bioinformatics. 2015;16 Suppl 1(Suppl 1):S9.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients.
Huang GM, Huang KY, Lee TY, Weng J.
BMC Bioinformatics. 2015;16 Suppl 1(Suppl 1):S5.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities.
Nguyen VN, Huang KY, Huang CH, Chang TH, Bretaña N, Lai K, Weng J, Lee TY.
BMC Bioinformatics. 2015;16 Suppl 1(Suppl 1):S1.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation.
Chen YJ, Lu CT, Su MG, Huang KY, Ching WC, Yang HH, Liao YC, Chen YJ, Lee TY.
Nucleic Acids Res. 2015 Jan;43(Database issue):D503-11.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection.
Wu LS, Lee SW, Huang KY, Lee TY, Hsu PW, Weng JT.
Biomed Res Int. 2014;2014:895179.
(2021 IF:3.246, BIOTECHNOLOGY&APPLIED MICROBIOLOGY 90/158.)

 

 

RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals.
Huang KY, Wu HY, Chen YJ, Lu CT, Su MG, Hsieh YC, Tsai CM, Lin KI, Huang HD, Lee TY, Chen YJ.
Database (Oxford). 2014 Apr 25;2014(0):bau034.
(2021 IF:4.462, MATHEMATICAL&COMPUTATIONAL BIOLOGY 33/67.)

 

 

ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins.
Huang KY, Lu CT, Bretaña N, Lee TY, Chang TH.
BMC Bioinformatics. 2013;14 Suppl 16(Suppl 16):S10.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

Incorporating significant amino acid pairs and protein domains to predict RNA splicing-related proteins with functional roles.
Hsu JB, Huang KY, Weng TY, Huang CH, Lee TY.
J Comput Aided Mol Des. 2014 Jan;28(1):49-60.
(2021 IF:4.179, BIOPHYSICS 21/72.)

 

 

topPTM: a new module of dbPTM for identifying functional post-translational modifications in transmembrane proteins.
Su MG, Huang KY, Lu CT, Kao HJ, Chang YH, Lee TY.
Nucleic Acids Res. 2014 Jan;42(Database issue):D537-45.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Lu CT†, Huang KY†, Su MG†, Lee TY, Bretaña NA, Chang WC, Chen YJ, Chen YJ, Huang HD.
Nucleic Acids Res. 2013 Jan;41(Database issue):D295-305.
(2021 IF:19.160, BIOCHEMISTRY&MOLECULAR BIOLOGY 5/321.)

 

 

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.
Bretaña NA, Lu CT, Chiang CY, Su MG, Huang KY, Lee TY, Weng SL.
PLoS One. 2012;7(7):e40694.
(2021 IF:3.752, MULTIDISCIPLINARY SCIENCES 29/73.)

 

 

Investigation and identification of protein γ-glutamyl carboxylation sites.
Lee TY, Lu CT, Chen SA, Bretaña NA, Cheng TH, Su MG, Huang KY.
BMC Bioinformatics. 2011;12 Suppl 13(Suppl 13):S10.
(2021 IF:3.328, MATHEMATICAL&COMPUTATIONAL BIOLOGY 20/57.)

 

 

 

研討會論文

 

Kai-Yao Huang, Hui-Ju Kao, Justin Bo-Kai Hsu, Shun-Long Weng and Tzong-Yi Lee (2018, Sept) Characterization and identification of lysine glutarylation based on intrinsic interdependence between positions in the substrate sites. The 17th International Conference on Bioinformatics (InCoB 2018).

 

 

Kai-Yao Huang+, Tzu-Hao Chang+, Jhih-Hua Jhong, Yu-Hsiang Chi, Wen-Chi Li, Chien-Lung Chan, K. Robert Lai and Tzong-Yi Lee* (2017, Sept) Identification of natural antimicrobial peptides from bacteria through metagenomic and metatranscriptomic analysis of high-throughput transcriptome data of Taiwanese oolong teas. The 16th International Conference on Bioinformatics (InCoB 2017). Best Paper Awards (Gold Awards)

 

 

Min-Gang Su+, Julia Tzu-Ya Weng+, Justin Bo-Kai Hsu, Kai-Yao Huang, Yu-Hsiang Chi and Tzong-Yi Lee* (2017, Sept) Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. The 16th International Conference on Bioinformatics (InCoB 2017). Best Paper Awards (Bronze Awards)

 

 

Kai-Yao Huang*, Julia Tzu-Ya Weng, Tzong-Yi Lee, Shun-Long Weng (2016, Jan) A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016).

 

 

Shih-Wei Lee, Lawrence Shih-Hsin Wu, Guan-Mau Huang, Kai-Yao Huang, Tzong-Yi Lee, Julia Tzu-Ya Weng (2016, Jan) Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. The Fourteenth Asia Pacific Bioinformatics Conference (APBC 2016).

 

 

Hui-Ju Kao, Chien-Hsun Huang, Neil Arvin Bretana, Cheng-Tsung Lu, Kai-Yao Huang, Shun-Long Weng, and Tzong-Yi Lee (2015, Sep) A two-layered machine learning method to identify protein O-GlcNAcylation sites with O-GlcNAc transferase substrate motifs. 14th International Conference on Bioinformatics (GIW/InCoB 2015).

 

 

Kai-Yao Huang, Tzong-Yi Lee, Pin-Hao Ho, Tzu-Hao Chang (2015, Jun) Computational Identification of Novel Epstein-Barr Virus MicroRNA using RNA-seq data in Nasopharyngeal Carcinoma. The 2015 International Forum – Agriculture, Biology, and Life Science (IFABL 2015).

 

 

Guan-Mau Huang, Tzong-Yi Lee, Kai-Yao Huang, Shih-Hsin Wu, Tzu-Ya Weng (2015, Jan) An interpretable rule-based diagnostic classification of diabetic nephropathy among type 2 diabetes patients. The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015).

 

 

Kai-Yao Huang*, Tzong-Yi Lee, Yu-Chuan Teng, Tzu-Hao Chang (2015, Jan) ViralmiR: identification of viral microRNA precursor based on sequence and structure information. The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015).

 

 

Van-Nui Nguyen, Kai-Yao Huang, Chien-Hsun Huang, Tzu-Hao Chang, Neil Arvin Bretana, K. Robert Lai, Julia Tzu-Ya Weng, Tzong-Yi Lee (2015, Jan) Characterization and Identification of Ubiquitin Conjugation Sites with E3 Ligase Recognition Specificities. The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015).

 

 

Kai-Yao Huang*, Ming-Gang Su, Hui-Ju Kao, Ya-Han Chang, Tzong-Yi Lee (2014, May) PhosNet: A Web Tool to Reconstruct the Protein Kinase–substrate Phosphorylattion Network Integrating Protein-protein Interaction and Biological Pathway Data. The 3rd International Congress on Natural Sciences and Engineering (ICNSE 2014).

 

 

Julia Tzu-Ya Weng, Kai-Yao Huang, Shih-Wei Lee, Lawrence Shih-Hsin Wu, Yi-Cheng Chen, Tzong-Yi Lee (2014, Apr) Systematic Pipeline for the analysis of microRNA-gene interactions in active and latent TB infection. IEEE International Symposium on Bioelectronics and Bioinformatics (IEEE ISBB 2014).

 

 

Kai-Yao Huang, Cheng-Tsung Lu, Neil Arvin Bretana, Tzong-Yi Lee, Tzu-Hao Chang (2013, Oct) ViralPhos: incorporating a recursively statistical method to predict phosphorylation sites on virus proteins. 12th International Conference on Bioinformatics (InCoB 2013).

 

 

Cheng-Tsung Lu, Kai-Yao Huang, Neil Arvin Bretana, Wen-Chi Chang, Tzong-Yi Lee (2013, Jun) Exploiting two-layered support vector machine to predict phosphorylation sites on virus proteins. 2nd International Conference on Bioinformatics and Biomedical Science (ICBBS2013).

 

 

Min-Gang Su, Kai-Yao Huang, Chi-Hua Tung, Tzong-Yi Lee (2013, Jun) A new scheme to predict phosphorylation sites on protein structures. 2nd International Conference on Bioinformatics and Biomedical Science (ICBBS2013).

 

 

Kai-Yao Huang*, Tzong-Yi Lee (2012, Dec) SplicePred: a Novel Resource for Identifying RNA Splicing-related Proteins. The 6th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB2012).