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黃柏榕

 

一張含有 個人, 室內, 牆, 笑臉 的圖片自動產生的描述

黃柏榕 (Po-Jung Huang)

職稱：副教授

研究室名稱：應用生物資訊研究室

最高學歷：Ph.D.

學校/國家：清華大學/台灣

分機號碼：3729 or 3934

電子郵件帳號： pjhuang@mail.cgu.edu.tw

個人網頁網址：

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 1 人

專任研究助理    人

大學部專題生   2 人

 已畢業碩士生：5

專長:

 應用生物資訊、LDTS生物資訊、生物大數據自動化分析流程開發與資料庫整合

研究方向:

  1. 癌症體學大數據應用分析平台
  2. 病原微生物生物資訊學
  3. 生物大數據視覺化輔助分析工具開發
  4. 生物大數據自動化分析流程開發與資料庫整合

研究室特色:

  1. 推動前瞻性癌症基因體、蛋白體學、病原微生物生物資訊學研究
  2. 跨體學大數據資料庫整合
  3. 生物資訊、程式設計、大數據資料庫整合人才的培育
  4. 跨科系、學院的整合

最近五年所發表論文：

一、 癌症基因體突變相關研究 (共 10 篇)

精準醫學癌症基因檢測分析系列工具及應用

  1. 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. CPAP: Cancer panel analysis pipeline (2013) Human Mutation, 34 (10), pp. 1340-1346. 第一作者
  2. 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. Vanno: A visualization-aided variant annotation tool (2015) Human Mutation, 36 (2), pp. 167-174. 第一作者
  3. 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. CMPD: Cancer mutant proteome database (2015) Nucleic Acids Research, 43 (D1), pp. D849-D855. 第一作者
  4. Chen, S.-J. †, Liu, H. †, Liao, C.-T. †, Huang, P.-J., Huang, Y., Hsu, A., Tang, P., Chang, Y.-S., Chenx, H.-C., Yen, T.-C. Ultra-deep targeted sequencing of advanced oral squamous cell carcinoma identifies a mutation-based prognostic gene signature (2015) Oncotarget, 6 (20), pp. 18066-18080. 第二作者
  5. Chen, T.-W†., Lee, C.-C†., Liu, H†., Wu, C.-S†., Pickering, C.R†., Huang, P.-J., Wang, J., Chang, I.Y.- F., Yeh, Y.-M., Chen, C.-D., Li, H.-P., Luo, J.-D., Tan, B.C.-M., Chan, T.E.H., Hsueh, C., Chu, L.J., Chen, Y.-T., Zhang, B., Yang, C.-Y., Wu, C.-C., Hsu, C.-W., See, L.-C., Tang, P., Yu, J.-S., Liao, W.- C., Chiang, W.-F., Rodriguez, H., Myers, J.N., Chang, K.-P., Chang, Y.-S. APOBEC3A is an oral cancer prognostic biomarker in Taiwanese carriers of an APOBEC deletion polymorphism (2017) Nature Communications, 8 (1), 465, .第二作者 (MOST 104-2321-B-182-007-MY3)
  6. Huang, P.-J., Chiu, L.-Y., Lee, C.-C., Yeh, Y.-M., Huang, K.-Y., Chiu, C.-H., Tang, P. MSignatureDB: A database for deciphering mutational signatures in human cancers (2018) Nucleic Acids Research, 46 (D1), pp. D964-D970. 第一作者 (MOST 104-2321-B-182-007-MY3)
  7. Huang, P.-J., Lee, C.-C., Chiu, L.-Y., Huang, K.-Y., Yeh, Y.-M., Yang, C.-Y., Chiu, C.-H., Tang, P. VAReporter: Variant reporter for cancer research of massive parallel sequencing (2018) BMC Genomics, 19, 86, . 第一作者 (MOST 104-2321-B-182-007-MY3)
  8. Wu, S.-M†., Liu, H†., Huang, P.-J†., Chang, I.Y.-F., Lee, C.-C., Yang, C.-Y., Tsai, W.-S., Tan, B.C.- M. circlncRNAnet: An integrated web-based resource for mapping functional networks of long or circular forms of noncoding RNAs (2018) GigaScience, 7 (1), pp. 1-10. †共同第一作者
    (MOST 104-2321-B-182-007-MY3)
  9. Huang, P.-J., Lin, H.-H., Lee, C.-C., Chiu, L.-Y., Wu, S.-M., Yeh, Y.-M., Tang, P., Chiu, C.-H., Lyu, P.-C., Tsai, P.-C. CoMutPlotter: A web tool for visual summary of mutations in cancer cohorts (2019) BMC Medical Genomics, 12, 99, . 第一作者 (MOST 107-2314-B-182-062)
  10. Huang, P.-J, Chang JH, Lin HH, Li YX, Lee CC, Su CT, Li YL, Chang MT, Weng S, Chiu CH, Tang P. DeepVariant-On-Spark: small-scale genome analysis using cloud-based computing framework. (2020) Computational and Mathematical Methods in Medicine vol. 2020 article ID 7231205 第一作者 (MOST 108-2221-E-182-043-MY3)

二、生物資訊應用於致病源基因體與模式生物相關研究 (共 32 篇)

Small RNA/microRNA 相關應用

  1. Lin, W.-C., Huang, K.-Y., Chen, S.-C., Huang, T.-Y., Chen, S.-J., Huang, P.-J., Tang, P. Malate dehydrogenase is negatively regulated by miR-1 in Trichomonas vaginalis (2009) Parasitology Research, 105 (6), pp. 1683-1689.
  2. Lin, W.-C., Li, S.-C., Lin, W.-C., Shin, J.-W., Hu, S.-N., Yu, X.-M., Huang, T.-Y., Chen, S.-C., Chen, H.-C., Chen, S.-J., Huang, P.-J., Ruei-Chi Gan, R., Chiu, C.-H., Tang, P. Identification of microRNA in the protist Trichomonas vaginalis (2009) Genomics, 93 (5), pp. 487-493.
  3. Huang, P.-J., Liu, Y.-C., Lee, C.-C., Lin, W.-C., Gan, R.R.-C., Lyu, P.-C., Tang, P. DSAP: Deep- sequencing small RNA analysis pipeline (2010) Nucleic Acids Research, 38 (SUPPL. 2), gkq392, pp. W385-W391.
  4. Huang, P.-J., Lin, W.-C., Chen, S.-C., Lin, Y.-H., Sun, C.-H., Lyu, P.-C., Tang, P. Identification of putative miRNAs from the deep-branching unicellular flagellates (2012) Genomics, 99 (2), pp. 101- 107.
  5. Hackenberg, M., Huang, P.-J., Huang, C.-Y., Shi, B.-J., Gustafson, P., Langridge, P. A Comprehensive expression profile of micrornas and other classes of non-coding small RNAs in barley under phosphorous-deficient and-sufficient conditions (2013) DNA Research, 20 (2), pp. 109-125.

轉錄體相關應用

  1. Chen, T.W., Gan, R.C., Wu, T.H., Huang, P.-J., Lee, C.Y., Chen, Y.Y., Chen, C.C., Tang, P. FastAnnotator--an efficient transcript annotation web tool. (2012) BMC genomics, 13 Suppl 7, .
  2. Horváthová, L., Šafaříková, L., Basler, M., Hrdý, I., Campo, N.B., Shin, J.-W., Huang, K.-Y., Huang, P.-J., Lin, R., Tang, P., Tachezy, J. Transcriptomic identification of iron-regulated and iron- independent gene copies within the heavily duplicated trichomonas vaginalis genome (2012) Genome Biology and Evolution, 4 (10), pp. 1017-1029.
  3. Fang, Y.-K., Huang, K.-Y., Huang, P.-J., Lin, R., Chao, M., Tang, P. Gene-expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis (2015) Journal of Microbiology, Immunology and Infection, 48 (6), pp. 662-675.
  4. Gan, R.-C., Chen, T.-W., Wu, T.H., Huang, P.-J., Lee, C.-C., Yeh, Y.-M., Chiu, C.-H., Huang, H.-D., Tang, P. PARRoT- a homology-based strategy to quantify and compare RNA-sequencing from non-model organisms (2016) BMC Bioinformatics, 17, 513, .
  5. Chen, T.-W., Gan, R.-C., Fang, Y.-K., Chien, K.-Y., Liao, W.-C., Chen, C.-C., Wu, T.H., Chang, I.Y.- F., Yang, C., Huang, P.-J., Yeh, Y.-M., Chiu, C.-H., Huang, T.-W., Tang, P. FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation (2017) Scientific Reports, 7 (1), 10430,.

蛋白質體相關應用

  1. Huang, K.-Y., Chien, K.-Y., Lin, Y.-C., Hsu, W.-M., Fong, I.-K., Huang, P.-J., Yueh, Y.-M., Gan, R.R.-C., Tang, P. A proteome reference map of Trichomonas vaginalis (2009) Parasitology Research, 104 (4), pp. 927-933.
  2. Huang, K.-Y., Ong, S.-C., Wu, C.-C., Hsu, C.-W., Lin, H.-C., Fang, Y.-K., Cheng, W.-H., Huang, P.- J., Chiu, C.-H., Tang, P. Metabolic reprogramming of hydrogenosomal amino acids in Trichomonas vaginalis under glucose restriction (2019) Journal of Microbiology, Immunology and Infection, 52 (4), pp. 630-637.
  1. Lee, C.-C., Huang, P.-J., Yeh, Y.-M., Chen, S.-Y., Chiu, C.-H., Cheng, W.-H., Tang, P.Pathogenic Protist Transmembranome database (PPTdb): A web-based platform for searching and analysis of protist transmembrane proteins (2019) BMC Bioinformatics, 20, 382, .
  2. Huang, K.-Y., Chen, R.-M., Lin, H.-C., Cheng, W.-H., Lin, H.-A., Lin, W.-N., Huang, P.-J., Chiu, C.- H., Tang, P. Potential role of autophagy in proteolysis in Trichomonas vaginalis (2019) Journal of Microbiology, Immunology and Infection, 52 (2), pp. 336-344.
  3. Lin HC, Chu LJ, Huang, P.-J, Cheng WH, Zheng YH, Huang CY, Hong SW, Chen LC, Lin HA, Wang JY, Chen RM, Lin WN, Tang P, Huang KY. Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance. Parasites &Vectors (2020);13(1):274.
  4. Cheng, W.-H., Huang, K.-Y., Ong, S.-C., Ku, F.-M., Huang, P.-J., Lee, C.-C., Yeh, Y.-M., Lin, R., Chiu, C.-H., Tang, P. Protein cysteine S-nitrosylation provides reducing power by enhancing lactate dehydrogenase activity in Trichomonas vaginalis under iron deficiency (2020) Parasites & vectors, 13 (1), p. 477.

跨體學相關應用

  1. Huang, K.-Y., Shin, J.-W., Huang, P.-J., Ku, F.-M., Lin, W.-C., Lin, R., Hsu, W.-M., Tang, P. Functional profiling of the Tritrichomonas foetus transcriptome and proteome (2013) Molecular and Biochemical Parasitology, 187 (1), pp. 60-71.
  2. Fang, Y.-K., Chien, K.-Y., Huang, K.-Y., Cheng, W.-H., Ku, F.-M., Lin, R., Chen, T.-W., Huang, P.- J., Chiu, C.-H., Tang, P. Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics (2016) OMICS A Journal of Integrative Biology, 20 (11), pp. 662-669.
  3. Huang, K-Y., Huang, P.-J., Ku, F.-M., Lin, R., Alderete, J.F., Tanga, P. Comparative transcriptomic and proteomic analyses of Trichomonas vaginalis following adherence to fibronectin (2012) Infection and Immunity, 80 (11), pp. 3900-3911. 
微生物、病毒基因體相關應用
  1. Chiu, S.-F. †; Huang, P.-J. †; Cheng, W.-H.; Huang, C.-Y.; Chu, L.J.; Lee, C.-C.; Lin, H.-C.; Chen, L.-C.; Lin, W.-N.; Tsao, C.-H.; Tang, P.; Yeh, Y.-M.; Huang, K.-Y. Vaginal Microbiota of the Sexually Transmitted Infections Caused by Chlamydia trachomatis and Trichomonas vaginalis in Women with Vaginitis in Taiwan. Microorganisms 2021, 9, 1864. 共同第一作者 (MOST 108-2221-E-182-043-MY3)
  2. Yang, C.-Y., Yeh, Y.-M., Yu, H.-Y., Chin, C.-Y., Hsu, C.-W., Liu, H., Huang, P.-J., Hu, S.-N., Liao, C.-T., Chang, K.-P., Chang, Y.-L. Oral microbiota community dynamics associated with oral squamous cell carcinoma staging (2018) Frontiers in Microbiology, 9 (MAY), 862, .
  3. Lin, C.-C., Lee, C.-C., Lin, S.-H., Huang, P.-J., Li, H.-P., Chang, Y.-S., Tang, P., Chao, M. RNA recombination in Hepatitis delta virus: Identification of a novel naturally occurring recombinant (2017) Journal of Microbiology, Immunology and Infection, 50 (6), pp. 771-780.
  4. Bradic, M., Warring, S.D., Tooley, G.E., Scheid, P., Secor, W.E., Land, K.M., Huang, P.-J., Chen, T.- W., Lee, C.-C., Tang, P., Sullivan, S.A., Carlton, J.M. Genetic indicators of drug resistance in the highly repetitive genome of. trichomonas vaginalis (2017) Genome Biology and Evolution, 9 (6), pp. 1658-1672.
  5. Cheng, W.-H., Huang, K.-Y., Huang, P.-J., Lee, C.-C., Yeh, Y.-M., Ku, F.-M., Lin, R., Cheng, M.-L., Chiu, C.-H., Tang, P. γ-Carboxymuconolactone decarboxylase: A novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis (2017) Parasites and Vectors, 10 (1), 443, .
  6. Huang, K.-Y., Ku, F.-M., Cheng, W.-H., Lee, C.-C., Huang, P.-J., Chu, L.J., Cheng, C.-C., Fang, Y.- K., Wu, H.-H., Tang, P. Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis (2015) Antimicrobial Agents and Chemotherapy, 59 (11), pp. 6891-6903.
  7. Chen, T.-W., Gan, R.-C., Chang, Y.-F., Liao, W.-C., Wu, T.H., Lee, C.-C., Huang, P.-J., Lee, C.-Y., Chen, Y.-Y.M., Chiu, C.-H., Tang, P. Is the whole greater than the sum of its parts? De novo assembly strategies for bacterial genomes based on paired-end sequencing (2015) BMC Genomics, 16 (1), 648,
  8.  Cheng, W.-H., Huang, K.-Y., Huang, P.-J., Hsu, J.-H., Fang, Y.-K., Chiu, C.-H., Tang, P. Nitric oxide maintains cell survival of Trichomonas vaginalis upon iron depletion (2015) Parasites and Vectors, 8 (1), 393, . 

蛋白質結構、計算生物學相關
  1. Lo, W.-C., Huang, P.-J., Chang, C.-H., Lyu, P.-C. Protein structural similarity search by Ramachandran codes (2007) BMC Bioinformatics, 8, 307.
  2. 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). ChIPseek, a web-based analysis tool for ChIP data. BMC Genomics, 15 (1), 539.
  3. Sablok, G., Chen, T.-W., Lee, C.-C., Yang, C., Gan, R.-C., Wegrzyn, J.L., La Porta, N., Nayak, K.C., Huang, P.-J., Varotto, C., Tang, P. ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications (2017) DNA Research, 24 (3), pp. 327-332.

模式生物相關應用

1. Lu, C.-Y., Huang, P.-J., Hsu, C.-Y. The cholesterol-hydroxyecdysone-vitellogenin pathway is involved in the longevity of trophocytes and oenocytes of queen honey bees (Apis mellifera) (2018) Apidologie, 49 (6), pp. 721-733.

 

 

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