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鄧致剛

鄧致剛 (Petrus Tang)

Appointment : Professor

LabMolecular Regulation & Bioinformatics Laboratory (MRBLab)

Education : Ph.D.

University/NationCambridge Univ./UK

Tel: 5136

E-mail : petang@mail.cgu.edu.tw

Research website : http://petang.cgu.edu.tw

Research interests:

My work involves using bioinformatics approaches to integrate data generated from multi-omics (including genomics, proteomics, transcriptomics, metablomics, etc.) techniques to study parasite-host interaction and to develop visualization methods that makes computational biology accessible to research scientists with no programming experience.

Recent Research Project: The role of microproteins on the regulation of iron stress response in Trichomonas vaginalis

Microprotein (MP) is defined as a protein composed of less than 100 amino acids. Accumulated experimental data showed that microproteins play important regulatory roles in various biological processes, including tumor progression, stress response, and signaling transduction. However, microprotein has been under-studied because classical genome annotation methods do not consider open reading frames (ORF) less than 100 amino acids as putative genes. Recent developments in new-generation sequencing techniques allowed us to identify novel MPs and obtain a more comprehensive view of these novel MP's expression profiles. Up to date, MP research had not been explored in any protozoan. Our research will use Trichomonas vaginals as a model system to identify and characterize the putative functional roles of MP under iron stress. T. vaginalis is the causing agent of the most common sexually transmitted infection (STI) of nonviral origin in humans trichomoniasis. Iron is an essential element for the survival of T. vaginalis, which sustains hydrogenosomal quality, energy metabolism, and redox homeostasis.

Our preliminary study based on an integrated genome-wide ORF screening, transcriptomic and exosome proteomic data analysis showed that MP did express in the T. vaginalis transcriptome and proteome. These exciting results prompted us to initiate studies on unexplored field. We aimed to investigate the functional roles of iron-dependent microproteins in T. vaginalis and to establish an experimental and analytical platform for studying microproteins.

Publications:

1.     Cheng WH, Huang KY, Ong SC, Ku FM, Huang PJ, Lee CC, Yeh YM, Lin R, Chiu CH. Tang P. (2020, Sep). Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency. Parasites & Vectors, 13(1): 477-491. (SCI, 3/23, TROPICAL MEDICINE). MOST 107-2320-B-182-021-MY3. 本人為通訊作者.

2.     Lin HC, Chu LJ, Huang PJ, Cheng WH, Zheng YH, Huang CY, Hong SW, Chen LC, Lin HA, Wang JY, Chen RM, Lin WN, Tang P, Huang KY. (2020, Jun). Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance. Parasites & Vectors, 13(1):274. (SCI, 3/23, TROPICAL MEDICINE).

3.     Huang KY, Ong SC, Wu CC, Lin HC, Fang YK, Cheng WH, Huang PJ, Chiu CH, Tang P. (2019, Aug). Metabolic reprogramming of hydrogenosomal amino acids in Trichomonas vaginalis under glucose restriction. J Microbiol Immunol Infect., 52(4):630-637. (SCI, 33/93, INFECTIOUS DISEASES). MOST 105-

2320-B-016-019-MY2. 本人為通訊作者.

4.     Lee CC, Chen WH, Huang PJ, Yeh YM, Chen SY, Chiu CH, Tang P. (2019, Jul). Pathogenic Protist Transmembranome database (PPTdb): A web-based platform for searching for and analysis of protist transmembrane proteins. BMC Bioinformatics 20(S13):382. (SCI, 9/59, MATHEMATICAL & COMPUTATIONAL BIOLOGY). MOST 107-2320-B-182-021-MY3. 本人為通訊作者.

5.     Huang KY, Chen RM, Lin HC, Lin HA, Lin WN, HuangPJ, Chiu CH, Tang P (2019, Apr). Potential role of autophagy in proteolysis in Trichomonas vaginalis. J Microbiol Immunol Infect., 52(2), 336-344. (SCI, 33/93, INFECTIOUS DISEASES). MOST 105-2320-B-016-019. 本人為通訊作者.

6.     Huang PJ, Lee CC, Chiu LY, Huang KY, Yeh YM, Yang CY, Chiu CH, Tang P. (2018, May). VAReporter: Variant reporter for cancer research of massive parallel sequencing. BMC Genomics 19(S2):86, 19(S2):86. (SCI, 43/156, BIOTECHNOLOGY & APPLIED MICROBIOLOGY). 本人為通訊作者.

7.     Huang PJ, Chiu LY, Lee CC, Yeh YM, Huang KY, Chiu CH, Tang P (2018, Jan). mSignatureDB: a database for deciphering mutational signatures in human cancers. Nucleic Acids Research, 46(D1), D964-D970. (SCI, IF 11.5201, 15/297,

BIOCHEMISTRY & MOLECULAR BIOLOGY). 本人為通訊作者.

8.     Chen TW, Gan RC, Fang YK, Chien KY, Liao WC, Chen CC, Wu TH, Chang IY, Yang C, Huang PJ, Yeh YM, Chiu CH, Huang TW, Tang P (2017, Sep). FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Scientific Reports, 7(1):10430. (SCI, IF 4.259, 10/64, MULTIDISCIPLINARY SCIENCES). 本人為通訊作者.

9.     Cheng WH, Huang KY, Huang PJ, Lee CC, Yeh YH, Ku FM, Lin R, Cheng ML, Chiu CH Tang P (2017, Sep). γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. Parasites & Vectors, 10(1):443. (SCI, IF 3.163, 2/20, TROPICAL MEDICINE). MOST 104-2320-B-182-025-MY3. 本人為通訊作者.

10.   Sablok G, Chen TW, Lee CC, Varotto C, Gan RC, Nayak KC, Huang PJ, Tang P (2017, Jun). ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.. DNA Research, 24(3):327- 332. (SCI, IF 5.415, 23/171, GENETICS & HEREDITY). 本人為通訊作者.

11.   Gan RC, Chen TW, Wu TH, Huang PJ, Lee CC, Yeh YM, Chiu CH, Huang HD, Tang P. (2016, Dec). PARRoT- A homology-based strategy to quantify and compare RNA-Sequencing from non-model organisms. BMC Bioinformatics, 17(S19):513. (SCI, IF 2.435, 10/56, MATHEMATICAL & COMPUTATIONAL BIOLOGY). 本人為通訊作者.

12.   Fang YK, Chien KY, Huang KY, Cheng WH, Ku FM, Lin R, Chen TW, Huang PJ, Chiu CH, Tang P (2016, Nov). Responding to a zoonotic emergency with multi-omics research: Pentatrichomonas hominis hydrogenosomal protein characterization with use of RNA sequencing and proteomics. OMICS: A Journal of Integrative Biology, 20(11): 662-669. (SCI, IF 2.896, 27/254, PHARMACOLOGY & PHARMACY). 本人為通訊作者.

13.   Huang KY, Ku FM, Cheng WH, Lee CC, Huang PJ, Chu LCJ, Cheng CC, Fang YK, Wu HH, Tang P (2015, Nov). Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis. Antimicrob. Agents Chemother, 59(11):6891-903. (SCI, IF 4.476, 27/254, PHARMACOLOGY & PHARMACY). MOST 101-2320-B- 182-025-MY3. 本人為通訊作者.

14.   Chen TW, Gan RC, Chang YF, Liao WC, Wu TH, Lee CC, Huang PJ, Lee CY, Chen YYM, Chiu CH, Tang P (2015, Aug). Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing. BMC Genomics, 16:648. (SCI, IF 3.986, 26/162, BIOTECHNOLOGY & APPLIED MICROBIOLOGY). 本人為通訊作者.

15.   Chen WH, Huang KY, Huang PJ, Hsu JH, Fang YK, Chiu CH, Tang P (2015,

Aug). Nitric oxide maintains cell survival of Trichomonas vaginalis upon iron depletion. Parasites & Vectors, 8, 393. (SCI, IF 3.163, 2/20, TROPICAL MEDICINE). MOST 104-2320-B-182-025-MY3. 本人為通訊作者.

16.   Huang PJ, Lee CC, Yeh YM, Huang KY, Gan RC, Chen TW, Lee CY, Yang ST, Liao CS, Liu H, Tang P. (2015, Feb). Vanno: A Visualization-aided Variant Annotation Tool. Human Mutation, 36(2):167-74. (SCI, IF 5.144, 26/167;

GENETICS & HEREDITY). 本人為通訊作者.

17.   Huang PJ, Lee CC, Tan BCM, Yeh YM, Chu JLC, Chen TW, Chang KP, Gan RC, Liu H, Tang P (2015, Jan). CMPD: cancer mutant proteome database. Nucleic Acids Research, 43:D849-55. (SCI, IF 11.561, 10/292, BIOCHEMISTRY & MOLECULAR BIOLOGY). MOST 103-2632-B-182-001. 本人為通訊作者.

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