Biodiversity Research Center, Academia Sinica

Dr. Isheng Jason Tsai Associate Research Fellow

Lab PI

Dr. Isheng Jason Tsai

Associate Research Fellow

Ph D. Imperial College, UK

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Office: Interdisciplinary Research Building for Science and Technology B303


Research Fields
  • Comparative and population genomics
  • Evolution of parasitism and pathogenicity
  • Eukaryotic microbe (fungi and helminths) ecology and biodiversity

Research Directions

The principal objective of our research lies in the fundamental mechanisms and evolution or pathogenicity and parasitism. We are mainly interested in fungi and nematodes that are of medical, agricultural, forestry, and Taiwan biodiversity importance.

  • 1.Comparative population genomics of microbes in nature
    Microbes can survive in almost any environment and play a major role in shaping their surroundings. Comparing genomes between and within populations of microbes allows us to understand the process of evolution of one of the most diverse and dominant life forms on earth. Additionally, insights regarding their impact on their environment or hosts such as human health can also be achieved.
  • 2.Evolution of parasitic pathogens
    Parasitism is a common way of life and coexists with almost every species including humans. Pathogens are interesting for two reasons: (A) for the disease burdens that they incur on humans, and the plants and animals of economic importance that we depend on, and (B) their diverse strategies of infection. We have been trying to identify the unique evolutionary signatures that have made a parasite what it is and have studied pathogens across many ecological niches (helminthes and fungi) as well as different hosts (mammals and plants).

Latest published paper

期刊論文 ( 2017 - 2020 )

  1. Lu MR, Lai CK, Liao BY, Tsai IJ, 2020, “Comparative transcriptomics across nematode life cycles reveal gene expression conservation and correlated evolution in adjacent developmental stages.”, Genome biology and evolution, 10.1093/gbe/evaa110. (SCI) (IF: 3.94; SCI ranking: 28.6%,24.6%) Link
  2. Yang Ching-Ting, Vidal-Diez de Ulzurrun Guillermo, Gonçalves A. Pedro, Lin Hung-Che, Chang Ching-Wen, Huang Tsung-Yu, Chen Sheng-An, Lai Cheng-Kuo, Tsai Isheng J., Schroeder Frank C., Stajich Jason E., Hsueh Yen-Ping, 2020, “Natural diversity in the predatory behavior facilitates the establishment of a robust model strain for nematode-trapping fungi”, Proceedings of the National Academy of Sciences, 117(12) 6762-6770. (SCI) Link
  3. 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
  4. 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. (SCI) (IF: 3.52; SSCI ranking: 43%) Link
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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