Faculty list

Dr. Isheng Jason Tsai

Assistant Research Fellow
Ph D. Imperial College, UK,
Research Fields
Evolution of parasitism and pathogenicity. Eukaryotic microbe (fungi and helminths) ecology and biodiversity.
Major Research Achievements (2013-2017)
  • The principal objective of my research lies in the analysis of DNA sequence variation in large-scale genome sequencing studies, to identify how microorganisms adapt to their unique environment and in some cases, gain pathogenicity. Over these years, I have been leading or involved the de novo and comparative genome projects of various medicinally, veterinary, and agriculturally important pathogens, including the parasitic worms (helminths) and yeast re-sequencing genome projects by taking the advantage of next-generation sequencing (NGS).
Research Interests
  • Evolution and genetics of reproduction life cycles in microbes
  • Evolution of parasitism and pathogenicity in microbial pathogens
  • Chromosome evolution in nematodes and fungi
    Ongoing projects
    • Comparative and population genomics of various eukaryotic pathogens important in Taiwan, Japan and Asia
    • Metagenomics and genetic studies relating to complex human diseases
      Publications (2009-2017)
      1. 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, ., .-.. (SCI) (IF: 5.947; SCI ranking: 12.1%,7.3%,10.9%)
      2. 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: 1.404; SCI ranking: 53.6%,82.6%)
      3. 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: 3.13; SCI ranking: 24.4%,25.6%)
      4. 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: 3.031; SCI ranking: 27.8%)
      5. 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.
      6. 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: 5.228; SCI ranking: 11.1%)
      7. 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: 5.228; SCI ranking: 11.1%)
      8. 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: 3.232; SCI ranking: 3.8%,35%,24.7%)
      9. 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: 3.057; SCI ranking: 17.5%)
      10. 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: 7.003; SCI ranking: 9.8%,8.3%,6.1%)
      11. 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: 31.616; SCI ranking: 1.2%)
      12. 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, 77-83. (SCI) (IF: 4.335; SCI ranking: 7.7%)
      13. 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. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
      14. 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. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      15. 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. (SCI) (IF: 3.867; SCI ranking: 25.9%,19.9%)
      16. Tanaka R, Hino A, Tsai IJ, Palomares-Rius JE, Yoshida A, Ogura Y, Hayashi T, Maruyama H, Kikuchi T, 2014, “Assessment of helminth biodiversity in wild rats using 18S rDNA based metagenomics.”, PloS one, 9(10), e110769. (SCI) (IF: 3.057; SCI ranking: 17.5%)
      17. Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T, 2014, “Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants.”, Genome biology and evolution, 6(4), 861-872. (SCI) (IF: 4.098; SCI ranking: 19.9%,21.7%)
      18. Palomares-Rius JE, Hirooka Y, Tsai IJ, Masuya H, Hino A, Kanzaki N, Jones JT, Kikuchi T, 2014, “Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi.”, BMC evolutionary biology, 14, 69. (SCI) (IF: 3.406; SCI ranking: 32.6%,31.3%)
      19. Bennett HM, Mok HP, Gkrania-Klotsas E, Tsai IJ, Stanley EJ, Antoun NM, Coghlan A, Harsha B, Traini A, Ribeiro DM, Steinbiss S, Lucas SB, Allinson KS, Price SJ, Santarius TS, Carmichael AJ, Chiodini PL, Holroyd N, Dean AF, Berriman M, 2014, “The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion.”, Genome biology, 15(11), 510. (SCI) (IF: 11.313; SCI ranking: 3.1%,4.2%)
      20. Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman M, 2014, “Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.”, Nature genetics, 46(7), 693-700. (SCI) (IF: 31.616; SCI ranking: 1.2%)
      21. Valentim CL, Cioli D, Chevalier FD, Cao X, Taylor AB, Holloway SP, Pica-Mattoccia L, Guidi A, Basso A, Tsai IJ, Berriman M, Carvalho-Queiroz C, Almeida M, Aguilar H, Frantz DE, Hart PJ, LoVerde PT, Anderson TJ, 2013, “Genetic and molecular basis of drug resistance and species-specific drug action in schistosome parasites.”, Science, 342(6164), 1385-1389. (SCI) (IF: 34.661; SCI ranking: 3.2%)
      22. Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN, Redman E, Holroyd N, Bartley DJ, Beasley H, Britton C, Curran D, Devaney E, Gilabert A, Hunt M, Jackson F, Johnston SL, Kryukov I, Li K, Morrison AA, Reid AJ, Sargison N, Saunders GI, Wasmuth JD, Wolstenholme A, Berriman M, Gilleard JS, Cotton JA, 2013, “The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.”, Genome biology, 14(8), R88. (SCI) (IF: 11.313; SCI ranking: 3.1%,4.2%)
      23. Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A, Brooks KL, Tracey A, Bobes RJ, Fragoso G, Sciutto E, Aslett M, Beasley H, Bennett HM, Cai J, Camicia F, Clark R, Cucher M, De Silva N, Day TA, Deplazes P, Estrada K, Fernandez C, Holland PW, Hou J, Hu S, Huckvale T, Hung SS, Kamenetzky L, Keane JA, Kiss F, Koziol U, Lambert O, Liu K, Luo X, Luo Y, Macchiaroli N, Nichol S, Paps J, Parkinson J, Pouchkina-Stantcheva N, Riddiford N, Rosenzvit M, Salinas G, Wasmuth JD, Zamanian M, Zheng Y, Cai X, Soberon X, Olson PD, Laclette JP, Brehm K, Berriman M, 2013, “The genomes of four tapeworm species reveal adaptations to parasitism.”, Nature, 496(7443), 57-63. (SCI) (IF: 38.138; SCI ranking: 1.6%)
      24. Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M, Aslett MA, De Silva N, Velarde GS, Anderson TJ, Clark RC, Davidson C, Dillon GP, Holroyd NE, LoVerde PT, Lloyd C, McQuillan J, Oliveira G, Otto TD, Parker-Manuel SJ, Quail MA, Wilson RA, Zerlotini A, Dunne DW, Berriman M, 2012, “A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.”, PLoS neglected tropical diseases, 6(1), e1455. (SCI) (IF: 3.948; SCI ranking: 5.3%,16.7%)
      25. Cho LT, Wamaitha SE, Tsai IJ, Artus J, Sherwood RI, Pedersen RA, Hadjantonakis AK, Niakan KK, 2012, “Conversion from mouse embryonic to extra-embryonic endoderm stem cells reveals distinct differentiation capacities of pluripotent stem cell states.”, Development, 139(16), 2866-2877. (SCI) (IF: 6.059; SCI ranking: 9.8%)
      26. Rinaldi G, Eckert SE, Tsai IJ, Suttiprapa S, Kines KJ, Tort JF, Mann VH, Turner DJ, Berriman M, Brindley PJ, 2012, “Germline transgenesis and insertional mutagenesis in Schistosoma mansoni mediated by murine leukemia virus.”, PLoS pathogens, 8(7), e1002820. (SCI) (IF: 7.003; SCI ranking: 9.8%,8.3%,6.1%)
      27. Tsai IJ, 2012, “The first green revolution.”, Nature Reviews Microbiology, 10(5), 314. (SCI) (IF: 24.727; SCI ranking: 0.8%)
      28. Tsai IJ, 2011, “Genome watch: Honey, I shrunk the mimiviral genome.”, Nature Reviews Microbiology, 9(8), 563. (SCI) (IF: 24.727; SCI ranking: 0.8%)
      29. Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N, McVeigh P, Takanashi T, Tsai IJ, Assefa SA, Cock PJ, Otto TD, Hunt M, Reid AJ, Sanchez-Flores A, Tsuchihara K, Yokoi T, Larsson MC, Miwa J, Maule AG, Sahashi N, Jones JT, Berriman M, 2011, “Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.”, PLoS pathogens, 7(9), e1002219. (SCI) (IF: 7.003; SCI ranking: 9.8%,8.3%,6.1%)
      30. Tsai IJ, Burt A, Koufopanou V, 2010, “Conservation of recombination hotspots in yeast.”, Proceedings of the National Academy of Sciences of the United States of America, 107(17), 7847-7852. (SCI) (IF: 9.423; SCI ranking: 6.3%)
      31. Tsai IJ, Otto TD, Berriman M, 2010, “Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.”, Genome biology, 11(4), R41. (SCI) (IF: 11.313; SCI ranking: 3.1%,4.2%)
      32. Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R, Louis EJ, 2009, “Population genomics of domestic and wild yeasts.”, Nature, 458(7236), 337-341. (SCI) (IF: 38.138; SCI ranking: 1.6%)