蔡怡陞 副研究員

實驗室主持人

Dr.蔡怡陞

副研究員

Ph D. Imperial College, UK

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辦公室: 跨領域 B303

電話:+886-2-2787-2230

研究領域
  • 比較與群體基因體學
  • 寄生與病原機制的演化
  • 真核微生物的生態與多樣性

研究方向

  • 我們是一個藉由比較物種或個體間基因體的差異,探討物種多樣性,遺傳,演化,及寄生機制的實驗室。研究內容為分析新定序技術產生的巨量基因體資訊來做物種間的比較及族群分析。研究材料著重於醫學,林業,農業,畜牧業,及台灣生態環境上有重要地位的真菌及線蟲。主要研究方向為:

    1.亞洲相關微生物(線蟲及真菌)的基因體研究

      微生物可以存活在幾乎任何地方,也絕大部分影響它們居住的環境。比較群體或是不同病原的基因體可以讓我們了解在地球上最多且最多樣的物種群之演化過程。研究它們可以得到它們對我們環境周遭的影響,包括對植物及我們自己 。

    2. 真核病原寄生及感染動植物宿主的機制

      寄生是病原生活型態的一種機制,而基本上地球上每一種物種都會有至少一種會寄生的病原體。研究病原非常重要因為 A) 它們帶給我們及周遭(如農業)疾病及負擔,甚至死亡 B) 它們多樣的感染策略。我們分析諸多病原體的特殊演化歷史及生態(宿主內外的環境),來找出造成一個病原體的演化因素及每一個病原的特定基因及感染機制。

 

最新發表

期刊論文 ( 2016 - 2019 )

  1. Gómez Luciano Luis B, Jason Tsai Isheng, Chuma Izumi, Tosa Yukio, Chen Yi-Hua, Li Jeng-Yi, Li Meng-Yun, Jade Lu Mei-Yeh, Nakayashiki Hitoshi, Li Wen-Hsiung, 2019, “Blast fungal genomes show frequent chromosomal changes, gene gains and losses, and effector gene turnover”, Molecular Biology and Evolution, 36(6),1148-1161. (SCI) (IF: 6.202; SCI ranking: 12.8%,9%,10.4%) Link
  2. T Afrin, K Murase, A Kounosu, VL Hunt, M Bligh, Y Maeda, A Hino, H Maruyama, IJ Tsai and T Kikuchi, 2019, “Sequential changes in the host gut microbiota during infection with the intestinal parasitic nematode Strongyloides venezuelensis”, FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY, 9. Link
  3. Tanaka Suguru E., Dayi Mehmet, Maeda Yasunobu, Tsai Isheng J., Tanaka Ryusei, Bligh Mark, Takeuchi-Kaneko Yuko, Fukuda Kenji, Kanzaki Natsumi, Kikuchi Taisei, 2019, “Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle”, Scientific Reports, 9(1). (SCI) (IF: 4.259; SCI ranking: 15.6%) Link
  4. Lin Yu-Te, Lin Yu-Fei, Tsai Isheng J., Chang Ed-Haun, Jien Shih-Hao, Lin Yen-Ju, Chiu Chih-Yu, 2019, “Structure and Diversity of Soil Bacterial Communities in Offshore Islands”, Scientific Reports, 9(1). (SCI) (IF: 4.259; SCI ranking: 15.6%) Link
  5. Chaw Shu-Miaw, Liu Yu-Ching, Wu Yu-Wei, Wang Han-Yu, Lin Chan-Yi Ivy, Wu Chung-Shien, Ke Huei-Mien, Chang Lo-Yu, Hsu Chih-Yao, Yang Hui-Ting, Sudianto Edi, Hsu Min-Hung, Wu Kun-Pin, Wang Ling-Ni, Leebens-Mack James H., Tsai Isheng J., 2019, “Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution”, Nature Plants, 5(1), 63-73. (SCI) (IF: 10.3; SCI ranking: 1.9%) Link
  6. Lee HH, Ke HM, Lin CI, Lee TJ, Chung CL, Tsai IJ, 2019, “Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus.”, Genome biology and evolution, 11(10), 2774-2788. (SCI) (IF: 3.94; SCI ranking: 28.6%,24.6%) Link
  7. Sung CM, Lin YF, Chen KF, Ke HM, Huang HY, Gong YN, Tsai WS, Lu MJ, Cheng HT, Lin CY, Kuo CJ, Tsai IJ, Hsieh SY, 2019, “Predicting clinical outcomes of cirrhosis patients with hepatic encephalopathy from the fecal microbiome.”, Cellular and molecular gastroenterology and hepatology, 8(2),301-. Link
  8. Wu ZC, Chang YY, Lai QJ, Lin HA, Tzean SS, Liou RF, Tsai IJ, Chung CL, 2019, “Soil is not a reservoir for Phellinus noxius.”, Phytopathology, 10.1094/PHYTO-08-19-0314-R. (SCI) (IF: 3.036; SCI ranking: 17.9%) Link
  9. Kanzaki Natsumi, Tsai Isheng J., Tanaka Ryusei, Hunt Vicky L., Liu Dang, Tsuyama Kenji, Maeda Yasunobu, Namai Satoshi, Kumagai Ryohei, Tracey Alan, Holroyd Nancy, Doyle Stephen R., Woodruff Gavin C., Murase Kazunori, Kitazume Hiromi, Chai Cynthia, Akagi Allison, Panda Oishika, Ke Huei-Mien, Schroeder Frank C., Wang John, Berriman Matthew, Sternberg Paul W., Sugimoto Asako, Kikuchi Taisei, 2018, “Biology and genome of a newly discovered sibling species of Caenorhabditis elegans”, Nature Communications, 9(1), 3216. (SCI) (IF: 12.124; SCI ranking: 4.7%) Link
  10. International Helminth Genomes Consortium, 2018, “Comparative genomics of the major parasitic worms”, Nature Genetics, 51(1), 163-. (SCI) (IF: 27.959; SCI ranking: 1.2%) Link
  11. Liu D, Hunt M, Tsai IJ, 2018, “Inferring synteny between genome assemblies: a systematic evaluation.”, BMC bioinformatics, 19(1), 26. (SCI) (IF: 2.448; SCI ranking: 17.5%,42.5%,48.7%) Link
  12. Ke HM, Liu D, Ogura Y, Hayashi T, Urbanczyk H, Tsai IJ, 2018, “Tracing genomic divergence of Vibrio bacteria in the Harveyi clade.”, Journal of bacteriology, 200(15), e00001-18. (SCI) (IF: 3.143; SCI ranking: 36%) Link
  13. Chung Chia-Lin, Lee Tracy J., Akiba Mitsuteru, Lee Hsin-Han, Kuo Tzu-Hao, Liu Dang, Ke Huei-Mien, Yokoi Toshiro, Roa Marylette B., Lu Mei-Yeh J., Chang Ya-Yun, Ann Pao-Jen, Tsai Jyh-Nong, Chen Chien-Yu, Tzean Shean-Shong, Ota Yuko, Hattori Tsutomu, Sahashi Norio, Liou Ruey-Fen, Kikuchi Taisei, Tsai Isheng J., 2017, “Comparative and population genomic landscape of Phellinus noxius: A hypervariable fungus causing root rot in trees”, Molecular Ecology, 26(22), 6301-6316. (SCI) (IF: 6.086; SCI ranking: 13.4%,12.5%,5.9%) Link
  14. Huei-Mien Ke, Chun-Ping Yu, Yu-Ching Liu, Isheng J Tsai, 2017, “Popmarker: Identifying Phylogenetic Markers at the Population Level”, Evolutionary Bioinformatics, 13, 1-7. (SCI) (IF: 1.5; SCI ranking: 50.9%,79.2%) Link
  15. Liang Shih-Hsiung, Hsu Duen-Wei, Lin Chia-Ying, Kao Chih-Ming, Huang Da-Ji, Chien Chih-Ching, Chen Ssu-Ching, Tsai Isheng Jason, Chen Chien-Cheng, 2017, “Enhancement of microbial 2,4,6-trinitrotoluene transformation with increased toxicity by exogenous nutrient amendment”, Ecotoxicology and Environmental Safety, 138, 39-46. (SCI) (IF: 3.743; SCI ranking: 19.6%,20.5%) Link
  16. Hunt VL, Tsai IJ, Selkirk ME, Viney M, 2017, “The genome of Strongyloides spp. gives insights into protein families with a putative role in nematode parasitism.”, Parasitology, 144(3), 343-358. (SCI) (IF: 2.62; SCI ranking: 30.6%) Link
  17. Ke Huei-Mien, Prachumwat Anuphap, Yu Chun-Ping, Yang Yi-Ting, Promsri Sutitcha, Liu Kuan-Fu, Lo Chu-Fang, Lu Mei-Yeh Jade, Lai Mei-Chin, Tsai Isheng J., Li Wen-Hsiung, 2017, “Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade”, Scientific Reports, 7, 41394. (SCI) (IF: 4.259; SCI ranking: 15.6%) Link
  18. Cotton JA, Bennuru S, Grote A, Harsha B, Tracey A, Beech R, Doyle SR, Dunn M, Hotopp JC, Holroyd N, Kikuchi T, Lambert O, Mhashilkar A, Mutowo P, Nursimulu N, Ribeiro JM, Rogers MB, Stanley E, Swapna LS, Tsai IJ, Unnasch TR, Voronin D, Parkinson J, Nutman TB, Ghedin E, Berriman M, Lustigman S, 2017, “The genome of Onchocerca volvulus, agent of river blindness.”, Nature Microbiology, 2, 16216. Link
  19. Cotton James A., Steinbiss Sascha, Yokoi Toshiro, Tsai Isheng J., Kikuchi Taisei, 2016, “An expressed, endogenous Nodavirus-like element captured by a retrotransposon in the genome of the plant parasitic nematode Bursaphelenchus xylophilus”, Scientific Reports, 6, 39749. (SCI) (IF: 4.259; SCI ranking: 15.6%) Link
  20. Vicente CS, Nascimento FX, Barbosa P, Ke HM, Tsai IJ, Hirao T, Cock PJ, Kikuchi T, Hasegawa K, Mota M, 2016, “Evidence for an Opportunistic and Endophytic Lifestyle of the Bursaphelenchus xylophilus-Associated Bacteria Serratia marcescens PWN146 Isolated from Wilting Pinus pinaster.”, Microbial ecology, 72(3), 669-681. (SCI) (IF: 3.63; SCI ranking: 3.8%,24.2%,28%) Link
  21. Wu GL, Kuo TH, Tsay TT, Tsai IJ, Chen PJ, 2016, “Glycoside Hydrolase (GH) 45 and 5 Candidate Cellulases in Aphelenchoides besseyi Isolated from Bird's-Nest Fern.”, PloS one, 11(7), e0158663. (SCI) (IF: 2.806; SCI ranking: 23.4%) Link
  22. Suttiprapa S, Rinaldi G, Tsai IJ, Mann VH, Dubrovsky L, Yan HB, Holroyd N, Huckvale T, Durrant C, Protasio AV, Pushkarsky T, Iordanskiy S, Berriman M, Bukrinsky MI, Brindley PJ, 2016, “HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni.”, PLoS pathogens, 12(10), e1005931. (SCI) (IF: 6.608; SCI ranking: 5.9%,5.6%,10.4%) Link
  23. Hunt VL, Tsai IJ, Coghlan A, Reid AJ, Holroyd N, Foth BJ, Tracey A, Cotton JA, Stanley EJ, Beasley H, Bennett HM, Brooks K, Harsha B, Kajitani R, Kulkarni A, Harbecke D, Nagayasu E, Nichol S, Ogura Y, Quail MA, Randle N, Xia D, Brattig NW, Soblik H, Ribeiro DM, Sanchez-Flores A, Hayashi T, Itoh T, Denver DR, Grant W, Stoltzfus JD, Lok JB, Murayama H, Wastling J, Streit A, Kikuchi T, Viney M, Berriman M, 2016, “The genomic basis of parasitism in the Strongyloides clade of nematodes.”, Nature genetics, 48(3), 299-307. (SCI) (IF: 27.959; SCI ranking: 1.2%) Link
  24. Tsai IJ, Tanaka R, Kanzaki N, Akiba M, Yokoi T, Espada M, Jones JT, Kikuchi T, 2016, “Transcriptional and morphological changes in the transition from mycetophagous to phytophagous phase in the plant parasitic nematode Bursaphelenchus xylophilus.”, Molecular plant pathology, 17(1), 77-83. (SCI) (IF: 4.188; SCI ranking: 7.6%) Link