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Po-Jung Huang

 

一張含有 個人, 室內, 牆, 笑臉 的圖片自動產生的描述

Po-Jung Huang

Appointments：Assistant Professor

Lab：Applied bioinformatics laboratory

Education：Ph.D.

School/Nation：Tsing Hua University, Taiwan

Tel: 3729 or 3168

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

Research website:

研究室現有： 博士後研究員  人

博士班研究生    人

碩士班研究生  人

專任研究助理  1  人

大學部專題生    人

 

Research outline:

1.  The development of trans-omics analysis platform for cancer research

2. Pathogen bioinformatics

3. The development of visual analytics tools for biological data interpretation

4. Automatic analysis pipeline development and database integration

Publications:

  1. Po-Jung Huang, Ling-Ya Chiu, Chi-Ching Lee, Yuan-Ming Yeh, Kuo-Yang Huang, Cheng-Hsun Chiu and Petrus Tang. mSignatureDB: a database for deciphering mutational signatures in human cancers. Nucleic Acids Research, 2018 Jan 4; 46(D1):D964-D970 . (SCI, IF=10.16; R/C=14/290, BIOCHEMISTRY & MOLECULAR BIOLOGY). MOST 104-2321-B-182-007- MY3.    *First author.   
  2. Shao-Min Wu, Hsuan Liu*, Po-Jung Huang*, Ian Yi-Feng Chang, Chi-Ching Lee, Chia-Yu Yang, Wen-Sy Tsai, Bertrand Chin-Ming Tan (2017, Nov). circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of non-coding RNAs. GigaScience, https://doi.org/10.1093/gigascience/gix118. (SCI, IF=6.871, R/C= 6/64, MULTIDISCIPLINARY SCIENCE). MOST 104-2321-B-182-007-MY3. *First author. 

  3. Po-Jung Huang, Chi-Ching Lee, Ling-Ya Chiu, Kuo-Yang Huang, Yuan-Ming Yeh, Chia-Yu Yang, Cheng-Hsun Chiu and Petrus Tang* (2017, Oct). VAReporter: Variant reporter for cancer research of massive parallel sequencing . BMC Genomics. (Accepted). (SCI, IF=3.518; R/C=35/160, MOLECULAR BIOLOGY & GENETICS). MOST 104-2321-B-182-007-MY3. *First author. 

  4. 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, Jul). FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Sci Rep., 7(1):10430. 

  5. Chen TW, Lee CC, Liu H, Wu CS, Pickering CR, Huang PJ, Wang J, Chang IY, Yeh YM, Chen CD, Li HP, Luo JD, Tan BC, Chan TEH, Hsueh C, Chu LJ, Chen YT, Zhang B, Yang CY, Wu CC, Hsu CW, See LC, Tang P, Yu JS, Liao WC, Chiang WF, Rodriguez H, Myers JN, Chang KP*, Chang YS* (2017, Jul). APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism. Nat Commun., 8(1):465. (SCI, IF=12.124; R/C=3/64, MULTIDISCIPLINARY SCIENCES). MOST 104-2321-B-182-007- MY3. 

  6. Bradic M, Warring SD, Tooley GE, Scheid P, Secor WE, Land KM, Huang PJ, Chen TW, Lee CC, Tang P, Sullivan SA, Carlton JM* (2017, Jun). Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis. Genome Biol Evol., 9(6):1658-1672. 

  7. Sablok G*, Chen TW, Lee CC, Yang C, Gan RC, Varotto C, Porta NL, Nayak KC, Huang PJ, Wegrzyn JL, Tang P* (2017, Mar). ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.. DNA Research , 24(3):327-332. 

  8. 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. 

  9. 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. 

  10. Lin CC, Lee CC, Lin SH, Huang PJ, Li HP, Chang YS, Tang P*, Chao M* (2016, Feb). RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant.. J Microbiol Immunol Infect., doi: 10.1016/j.jmii.2015.10.013. 

  11. 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 6891-6903. 

  12. 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. 

  13. Chen WH, Huang KY, Huang PJ, Hsu JH, Fang YK, Chiu CH, Tang P* (2015, Jul). Nitric oxide maintains cell survival of Trichomonas vaginalis upon iron depletion. . Parasites & Vectors, 8:393. 

  14. Chen SJ, Liu H, Liao CT, Huang PJ, Huang Y, Hsu A, Tang P, Chang YS, Chen HC, Yen Tc (2015, Apr). Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature. Oncotarget , 6(20):18066-18080.
  15. Huang, P.-J., Lee, C.-C., Tan, B.C.-M., Yeh, Y.-M., Huang, K.-Y., Gan, R.-C., Chen, T.-W., Lee, C.-Y., Yang, S.-T., Liao, C.-S., Liu, H., Tang, P. (2015, Feb). 
Vanno: A visualization-aided variant annotation tool . Human Mutation, 36 (2), pp. 167-174. (SCI, IF=5.34; R/C=25/165, GENETICS & HEREDITY). *First author.
  16. Huang, P.-J., Lee, C.-C., Tan, B.C.-M., Yeh, Y.-M., Chu, L.J., Chen, T.W., Chang, K.-P., Lee, C.-Y., Gan, R.-C., Liu, H., Tang, P. (2015, Jan). CMPD: Cancer mutant proteome database. Nucleic Acids Research, 43 (D1), pp. D849-D855. (SCI, IF=10.16; R/C=14/290, BIOCHEMISTRY & MOLECULAR BIOLOGY). *First author. 

  17. Fang YK, Huang KY, Huang PJ, Lin R, Chao M, Tang P (2014, Oct). Gene expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis. Journal of Microbiology, Immunology and Infection, S1684-1182(14)00175-3. (SCI, IF=2.077; R/C=72/119, MICROBIOLOGY). 

  18. Chen, T.-W., Li, H.-P., Lee, C.-C., Gan, R.-C., Huang, P.-J., Wu, T.H., Lee, C.-Y., Chang, Y.-F., Tang, P. (2014, Jun). ChIPseek, a web-based analysis tool for ChIP data. BMC Genomics, 15 (1), 539. (SCI, IF=4.041; R/C=29/165, BIOTECHNOLOGY & APPLIED MICROBIOLOGY). 

  19. Huang, P.-J., Yeh, Y.-M., Gan, R.-C., Lee, C.-C., Chen, T.-W., Lee, C.-Y., Liu, H., Chen, S.-J., Tang, P. (2013, Oct). CPAP: Cancer panel analysis pipeline. Human Mutation, 34 (10), pp. 1340-1346. (SCI, IF=5.34; R/C=25/165, GENETICS & HEREDITY). *First author.

  20. Hackenberg, M., Huang, P.-J., Huang, C.-Y., Shi, B.-J., Gustafson, P., Langridge, P. (2013, Apr). A Comprehensive expression profile of micrornas and other classes of non-coding small RNAs in barley under phosphorous-deficient and- sufficient conditions. DNA Research, 20 (2), pp. 109-125. (SCI, IF=4.975; R/C=27/165, GENETICS & HEREDITY). 

  21. Huang, K.-Y., Shin, J.-W., Huang, P.-J., Ku, F.-M., Lin, W.-C., Lin, R., Hsu, W.- M., Tang, P. (2013, Jan). Functional profiling of the Tritrichomonas foetus transcriptome and proteome. Molecular and Biochemical Parasitology, 187 (1), pp. 60-71. (SCI, IF=2.243; R/C=15/37, PARASITOLOGY). 

  22. Huang KY, Huang PJ, Ku FM, Lin R, Alderete JF, Tang P. (2012, Nov). Comparative transcriptomic and proteomic analyses of Trichomonas vaginalis following adherence to fibronectin. . Infection and Immunity, 80 (11), pp. 3900- 3911. (SCI, IF=4.156; R/C=14/72, INFECTIOUS DISEASES). 

  23. Chen, T.W., Gan, R.C., Wu, T.H., Huang, P.J., Lee, C.Y., Chen, Y.Y., Chen, C.C., Tang, P. (2012, Jun). FastAnnotator--an efficient transcript annotation web tool.. BMC Genomics, 13 Suppl 7, S9. (SCI, IF=4.041; R/C=29/165, BIOTECHNOLOGY & APPLIED MICROBIOLOGY). 

  24. Horváthová L, Šafaríková L, Basler M, Hrdy I, Campo NB, Shin JW, Huang KY, 
Huang PJ, Lin R, Tang P, Tachezy J. (2012, Apr). Transcriptomic identification of iron-regulated and iron-independent gene copies within the heavily duplicated trichomonas vaginalis genome. Genome Biology and Evolution, 4 (10), pp. 1017- 1029. (SCI, IF=4.532; R/C=34/165, GENETICS & HEREDITY).
  25. Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC, Tang P. (2012, Feb). Identification of putative miRNAs from the deep-branching unicellular flagellates. Genomics, 99 (2), pp. 101-107. (SCI, IF=2.793; R/C=51/165, BIOTECHNOLOGY & APPLIED MICROBIOLOGY). *First author. 

  26. Huang PJ, Liu YC, Lee CC, Lin WC, Gan RR, Lyu PC, Tang P. (2010, Jul). DSAP: deep-sequencing small RNA analysis pipeline. . Nucleic Acids Research, 38 (SUPPL. 2), gkq392, pp. W385-W391. (SCI, IF=9.112; R/C=22/291, BIOCHEMISTRY & MOLECULAR BIOLOGY). *First author.
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