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 ( 2016 - 2019 )

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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: 4.697; SCI ranking: 8%) Link

Lab members


電  話

柯惠棉   林渝非   劉育菁

柳韋安   林展伊

李佳燁     賴政國    孫培峰

陸   敏