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 ( 2015 - 2020 )

  1. 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. (SCIE) Link
  2. 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. (SCIE) (IF: 3.94; SCIE ranking: 28.6%,24.6%) Link
  3. Hoh Daphne Z., Lin Yu-Fei, Liu Wei-An, Sidique Siti Nordahliawate Mohamed, Tsai Isheng Jason*, 2020, “Nest microbiota and pathogen abundance in sea turtle hatcheries”, Fungal Ecology, 47 100964. (SCIE) (IF: 3.736; SCIE ranking: 20.7%,22.5%) Link
  4. 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. (SCIE) (IF: 6.202; SCIE ranking: 12.8%,9%,10.4%) Link
  5. 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. (SCIE) (IF: 3.52; SSCI ranking: 43%) Link
  6. 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). (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  7. 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, 9,4689. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  8. 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. (SCIE) (IF: 10.3; SCIE ranking: 1.9%) Link
  9. 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. (SCIE) (IF: 3.94; SCIE ranking: 28.6%,24.6%) Link
  10. 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),301-318.e2. Link
  11. 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. (SCIE) (IF: 3.036; SCIE ranking: 17.9%) Link
  12. 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. (SCIE) (IF: 12.124; SCIE ranking: 4.7%) Link
  13. International Helminth Genomes Consortium, 2018, “Comparative genomics of the major parasitic worms”, Nature Genetics, 51(1), 163-. (SCIE) (IF: 27.959; SCIE ranking: 1.2%) Link
  14. Liu D, Hunt M, Tsai IJ*, 2018, “Inferring synteny between genome assemblies: a systematic evaluation.”, BMC bioinformatics, 19(1), 26. (SCIE) (IF: 2.448; SCIE ranking: 17.5%,42.5%,48.7%) Link
  15. 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. (SCIE) (IF: 3.143; SCIE ranking: 36%) Link
  16. 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. (SCIE) (IF: 6.086; SCIE ranking: 13.4%,12.5%,5.9%) Link
  17. 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. (SCIE) (IF: 1.5; SCIE ranking: 50.9%,79.2%) Link
  18. 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. (SCIE) (IF: 3.743; SCIE ranking: 19.6%,20.5%) Link
  19. 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. (SCIE) (IF: 2.62; SCIE ranking: 30.6%) Link
  20. 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. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  21. 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
  22. 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. (SCIE) (IF: 4.259; SCIE ranking: 15.6%) Link
  23. 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. (SCIE) (IF: 3.63; SCIE ranking: 3.8%,24.2%,28%) Link
  24. 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. (SCIE) (IF: 2.806; SCIE ranking: 23.4%) Link
  25. 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. (SCIE) (IF: 6.608; SCIE ranking: 5.9%,5.6%,10.4%) Link
  26. 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. (SCIE) (IF: 27.959; SCIE ranking: 1.2%) Link
  27. 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. (SCIE) (IF: 4.188; SCIE ranking: 7.6%) Link
  28. Koufopanou V, Lomas S, Tsai IJ, Burt A, 2015, “Estimating the Fitness Effects of New Mutations in the Wild Yeast Saccharomyces paradoxus.”, Genome biology and evolution, 7(7), 1887-1895. (SCIE) (IF: 3.94; SCIE ranking: 28.6%,24.6%) Link
  29. Akiba M, Ota Y, Tsai IJ, Hattori T, Sahashi N, Kikuchi T, 2015, “Genetic Differentiation and Spatial Structure of Phellinus noxius, the Causal Agent of Brown Root Rot of Woody Plants in Japan.”, PloS one, 10(10), e0141792. (SCIE) (IF: 2.806; SCIE ranking: 23.4%) Link
  30. Palomares-Rius JE, Tsai IJ, Karim N, Akiba M, Kato T, Maruyama H, Takeuchi Y, Kikuchi T, 2015, “Genome-wide variation in the pinewood nematode Bursaphelenchus xylophilus and its relationship with pathogenic traits.”, BMC genomics, 16(1), 845. (SCIE) (IF: 3.729; SCIE ranking: 21.9%,29.9%) Link