Publications

 

Also available on google scholar 

Contributed Equally as first authors.

* Corresponding authors

  1. SE Tanaka, M Dayi, Y Maeda, IJ Tsai, R Tanaka, M Bligh, Y Takeuchi-Kaneko, K Fukuda, N Kanzaki and T Kikuchi Stage-specific transcriptome of Bursaphelenchus xylophilus reveals temporal regulation of effector genes and roles of the dauer-like stages in the lifecycle (2019) Scientific Reports 10.1038/s41598-019-42570-7 link
  2. YT Lin, YF Lin, IJ Tsai, EH Chang, SHao Jien, YJu Lin & CY Chiu Structure and Diversity of Soil Bacterial Communities in Offshore Islands (2019) Scientific Report 10.1038/s41598-019-41170-9  link

  3. LBG Luciano, IJ Tsai, I Chuma, Y Tosa, YH Chen, JY Li, MY Li, MJ Lu, H Nakayashiki and WH Li Blast fungal genomes show frequent chromosomal changes, gene gains and losses, and effector gene turnover (2019) Molecular Biology Evolution 10.1093/molbev/msz045 link

  4. SM Chaw†*, YC Liu, HY Wang, YW Wu, CI Lin, CS Wu, HM Ke, LY Chang, CY Hsu, HT Yang, E Sudianto, MH Hsu, KP Wu, NN Wang, J Leebens-Mack, and IJ Tsai†* Stout camphor tree genome fills gaps in understanding of flowering plant genome evolution (2019) Nature Plants  5 63–73 link ; 中研院:搶救國寶牛樟! 牛樟全基因體定序重寫植物族譜 ; 中央社:國寶牛樟基因體定序解碼 可望用於復育

  5. International Helminth Genomes Consortium (including IJ Tsai, TH Kuo, HM Ke and TJ Lee), A Coghlan, M Mitreva and M Berriman Comparative genomics of the major parasitic worms (2018) Nature Genetics 10.1038/s41588-018-0262-1 link
  6. N Kanzaki, IJ Tsai†, R Tanaka, VL Hunt, D Liu, K Tsuyama, Y Maeda, S Namai, R Kumagai, A Tracey, N Holroyd, SR Doyle, GC Woodruff, K Murase, H Kitazume, C Chai,  A Akagi, O Panda, HM Ke, FC Schroeder, J Wang, M Berriman, PW Sternberg, A Sugimoto and T Kikuchi Discovery, biology and genome of Caenorhabditis inopinata, a sibling of C. elegans  (2018) Nature Communications 9:3216 link
    Author commentry: Caenorhabditis inopinata: the unexpected sibling species of C. elegans
  7. HM Ke*, D Liu, Y Ogura, T Hayashi, H Urbanczyk* and IJ Tsai* Tracing genomic divergence of Vibrio bacteria in the Harveyi clade (2018) Journal of Bacteriology 10.1128/JB.00001-18 link
  8. D Liu, M Hunt and IJ Tsai* Inferring synteny between genome assemblies: a systematic evaluation BMC Bioinformatics (2018) 19:26 link
  9. HM Ke†, CP Yu YC Liu and IJ Tsai Popmarker: identifying phylogenetic markers at the population level Evolutionary Bioinformatics (2017) 13:1176934317724404 link
  10. CL Chung†*, TJ Lee, M Akiba, HH Lee, TH Kuo, D Liu, HM Ke, T Yokoi, MB Roa, MJ Lu, YY Chang, PJ Ann, JN Tsai, CY Chen, SS Tzean, Y Ota, T Hattori, N Sahashi, RF Liou, T Kikuchi* and IJ Tsai†* Comparative and population genomics landscape of Phellinus noxius: a hypervariable fungus causing root rot in trees (2017) Molecular Ecology  10.1111/mec.14359  link
  11. HM Ke, A Prachumwat, Y Yang, S Promsri, K Liu, C Lo, MJ Lu, M Lai, IJ Tsai* and W Li* Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade (2017) Scientific Reports doi:10.1038/srep41394  link
  12. SH Lian, DW Hsu, CY Lin, CM Kao, DJ Huang, CC Chien, SC Chen, IJ Tsai and CC Chen Enhancement of microbial 2,4,6-trinitrotoluene transformation with increased toxicity by exogenous nutrient amendment (2017) Ecotoxicology and Environmental Safety 138:39-46 link
  13. JA Cotton, S Steinbiss, T Yokoia, IJ Tsai and T Kikuchi An expressed, endogenous Nodavirus- like element captured by a retrotransposon in the genome of the plant pathogenic nematode Bursaphelenchus xylophilus (2016) Scientific Reports doi:10.1038/srep39749 link
  14. JA Cotton, S Bennuru, A Grote, B Harsha, A Tracey, R Beech, SR Doyle, M Dunn, JC Dunning Hotopp, N Holroyd, T Kikuchi, O Lambert, A Mhashilkar, P Mutowo, N Nursimulu, JMC Ribeiro, MB Rogers, E Stanley, LS Swapna, IJ Tsai, TR Unnasch, D Voronin, J Parkinson, TB Nutman, E Ghedin, M Berriman, S Lustigman The genome of Onchocerca volvulus, agent of river blindness (2016) Nature Microbiology 10.1038/nmicrobiol.2016.216 link
  15. S Suttiprapa†, G Rinaldi†, IJ Tsai†, SN Iordanskiy, VH Mann, L Dubrovsky, H Yan, N Holroyd, T Huckvale, AV Protasio, T Pushkarsky, M Berriman, MI Bukrinsky and PJ Brindley HIV-1 integrates widely throughout the genome of the human blood fluke Schistosoma mansoni (2016) PLoS Pathogens 12(10): e1005931 link
  16. VL Hunt, IJ Tsai and M Viney The genome of Strongyloides spp. gives insights into protein families which have a putative role in nematode parasitism (2016) Parasitology pp. 1–16. link
  17. CSL Vicente, FX Nascimento, P Barbosa, HM Ke, IJ Tsai, PJA Cock, T Kikuchi, K Hasegawa and M Mota The complete genome sequence and characterization of the Bursaphelenchus xylophilus-associated bacteria Serratia marcescens PWN146 isolated from wilting Pinus pinaster (2016) Microbial Ecology doi:10.1007/s00248-016-0820-y link
  18. GL Wu†, TH Kuo†, TT Tsay, IJ Tsai and P Chen, Glycoside hydrolase family 45 and 5 cellulases present in Aphelenchoides besseyi originating from bird’s-nest fern (2016) PLoS One 11(7): e0158663 link
  19. VL Hunt†, IJ Tsai†, A Coghlan†, AJ Reid†, N Holroyd, BJ Foth, A Tracey, JA Cotton, EJ Stanley, H Beasley, H Bennett, K Brooks, B Harsha, R Kajitani, A Kulkarni, D Harbecke, E Nagayasu, S Nichol, Y Ogura, MA Quail,  N  Randle,  DM Ribeiro, A Sanchez-Flores, T Hayashi,  T Itoh, DR Denver,  W  Grant, JD Stoltzfus, JB  Lok, H  Murayama,  J Wastling, A Streit, T Kikuchi, M Viney and M Berriman The Genomic Basis of Parasitism in the Strongyloides Clade 1 of Nematodes (2016) Nature Genetics 10.1038/ng.3495 link
    Media:
    中時:台日英學者破解線蟲基因 研發疫苗有望

    BBC:英日台專家聯手破解致命寄生蟲基因密碼
  20. M Akiba, Y Ota, IJ Tsai, T Hattori, N Sahashi and T Kikuchi Genetic differentiation and spatial structure of Phellinus noxius, the causal agent of brown root rot of woody plants in Japan (2015) PLOS one  10(10): e0141792 link
  21. JE Palomares-Rius, IJ Tsai, N Karim, M Akiba, T Kato, H Maruyama, Y Takeuchi and T Kikuchi Genome-wide variation in the pinewood nematode Bursaphelenchus xylophilus and its relationship with pathogenic traits (2015) BMC genomics 16:845
  22. V Koufopanou, S Lomas, IJ Tsai and A Burt Estimating the fitness effects of new mutations in the wild yeast Saccharomyces paradoxus (2015) Genome biology and evolution 7 (7), 1887-1895
  23. IJ Tsai, Ryusei Tanaka, Natsumi Kanzaki, Mitsuteru Akiba, Toshiro Yokoi, Margarida Espada, John T. Jones and Taisei Kikuchi Transcriptional and morphological changes in the transition from mycetophagous to phytophagous phase in the plant parasitic nematode Bursaphelenchus xylophilus (2015) Molecular Plant Pathology link
  24. Hayley M Bennett, Hoi Ping Mok, Effrossyni Gkrania-Klotsas, Isheng J Tsai, Eleanor J Stanley, Nagui M Antoun, Avril Coghlan, Bhavana Harsha, Alessandra Traini, Diogo M Ribeiro, Sascha Steinbass, Sebastian B Lucas, Kieren S.J Allinson, Stephen J Price, Thomas S Santarius, Andrew J Carmichael, Peter L Chiodini, Nancy Holroyd, Andrew F Dean and Matthew Berriman The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion (2014) Genome Biology  open access pdf
    Media:
    Guardian: Man’s headaches due to tapeworm living in his brain for four years
    Business Insider: This Tapeworm Was Living In A Man’s Brain For 4 Years
  25. Ryusei Tanaka, Akina Hino, Isheng J Tsai, Juan E Palomares-Rius, Ayako Yoshida, Yoshitoshi Ogura, Tetsuya Hayashi, Haruhiko Maruyama and Taisei Kikuchi (2014) Assessment of Helminth Biodiversity in Wild Rats Using 18S rDNA Based Metagenomics PLOS one link open access pdf 
  26. Bernardo J Foth*, Isheng J Tsai*, Adam J Reid*, Allison J Bancroft*, Sarah Nichol, Alan Tracey, Nancy Holroyd, James A Cotton, Eleanor J Stanley, Magdalena Zarowiecki, Jimmy Z Liu, Thomas Huckvale, Philip J Cooper, Richard K Grencis & Matthew Berriman Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction (2014) Nature Genetics link open access pdf
    Media:
    BBC news Asia : 台灣與英國科學家聯手破解鞭蟲鑽孔基因
  27. Juan E Palomares-Rius, Yuuri Hirooka, Isheng J Tsai, Hayato Masuya, Akina Hino, Natsumi Kanzaki, John T Jones and Taisei Kikuchi Distribution and evolution of Glycoside Hydrolase Family 45 cellulases in Nematodes and Fungi (2014) BMC Evolutionary Biology pdf
  28. Isheng J. Tsai, Eiji Tanaka, Hayato Masuya, Ryusei Tanaka, Yuuri Hirooka, Rikiya Endoh, Norio Sahashi and Taisei Kikuchi (2014) Comparative genomics of Taphrina fungi causing varying degrees of tumourous deformity in plants Genome Biology and Evolution  pdf
  29. Cotton, J.A*., Lilley, C.J.* , Laura M. Jones, Taisei Kikuchi, A.J. Reid, Peter Thorpe, Isheng J Tsai, Helen Beasley, Vivia Blok, P.J.A. Cock, S. Eves-van den Akker, N. Holryod, M. Hunt, S. Mantellin, H. Naghra, A. Pain, J.E. Palomares-Rius, M. Zarowiecki, M. Berriman, J.T. Jones and P.E. Urwin. (2014) The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode. Genome Biology  pdf
  30. Isheng J Tsai*, M Zarowiecki*, N Holroyd*, A Garciarrubio*, A Sanchez-Flores, KL Brooks, A Tracey, R J Bobes, G Fragoso, E Sciutto, M Aslett, H Beasley, X Cai, F Camicia, R Clark, M C, N De Silva, T A Day, P Deplazes, K Estrada, C Fernández, PWH Holland, J Hou, S Hu, T Huckvale, SS Hung, L Kamenetzky, JA Keane, F Kiss, U Koziol, O Lambert, K Liu, X Luo, Y Luo, N Macchiaroli, S Nichol, J Paps, Jn Parkinson, N Pouchkina-Stantcheva, N Riddiford, M Rosenzvit, G Salinas, JD Wasmuth, M Zamanian, Y Zheng, The Taenia soliumGenome Consortium, J Cai, X Soberón, PD Olson, JP Laclette, K Brehm and M Berriman. (2013) The genomes of four tapeworm species reveal adaptations to parasitism. Nature 10.1038/nature12031  link open access pdf
    Media:
    pansci: 基因體解析顯露絛蟲治療新策略
    BBC news Asia : 抗癌藥可以用來抗擊絛蟲感染
    Reuters: Tapeworm genome points way to better drug treatments
    BBC news: ‘Weakness mining’ for tapeworm drugs”
  31. Claudia L. L. Valentim, Donato Cioli, Frédéric D. Chevalier, Xiaohang Cao, Alexander B. Taylor, Stephen P. Holloway, Livia Pica-Mattoccia, Alessandra Guidi, Annalisa Basso, Isheng J. Tsai, Matthew Berriman, Claudia Carvalho-Queiroz, Marcio Almeida, Hector Aguilar, Doug E. Frantz, P. John Hart, Philip T. LoVerde, Timothy J. C. Anderson. (2013) Genetic and Molecular Basis of Drug Resistance and Species-Specific Drug Action in Schistosome Parasites. Science
  32. Isheng J. Tsai*, Martin Hunt*, Nancy Holroyd, Thomas Huckvale, Matthew Berriman and Taisei Kikuchi (2013) Summarising specific profiles in Illumina sequencing from whole genome amplified (WGA) DNA. DNA Research 10.1093/dnares/dst054
  33. Roz Laing, Taisei Kikuchi , Axel Martinelli, Isheng J. Tsai, Robin N. Beech, Elizabeth Redman, Nancy Holroyd, David J. Bartley, Helen Beasley, Collette Britton, David Curran, Eileen Devaney, Aude Gilabert, Martin Hunt, Frank Jackson, Stephanie Johnston, Ivan Kryukov, Keyu Li, Alison A. Morrison, Adam J. Reid, Neil Sargison, GarySaunders, James D. Wasmuth, Adrian Wolstenholme, Matthew Berriman, John S. Gillearde, James A. Cotton (2013) The genome and transcriptome of Haemonchus contortus: a key model parasite for drug and vaccine discovery. Genome Biology
  34. Gabriel Rinaldi*, Sabine E. Eckert*, Isheng J. Tsai*, Sutas Suttiprapa, Kristine J. Kines, José F. Tort, Victoria H. Mann, Daniel J. Turner, Matthew Berriman, Paul J. Brindley (2012) Germline transgenesis in human blood fluke Schistosoma mansoni PLoS Pathogens 8(7)e1002820.
  35. LTY Cho, SE Wamaitha, Isheng J Tsai, RI Sherwood, J Artus, RA Pedersen, AK Hadjantonakis and KK Niakan (2012) Conversion from mouse embryonic to extraembryonic stem cells reveals roles for FGF signalling and primitive endoderm transcription factors Development 2012 139:2866-2877
  36. Martin T Swain, Isheng J Tsai, Sammy A Assefa, Chris Newbold, Matthew Berriman and Thomas D Otto (2012) Post-assembly genome- improvement from contigs to annotated genomes Nature Protocols
  37. Isheng J. Tsai  (2012) Genome watch: The first green revolution Nature Review Microbiology
  38. Anna V. Protasio*, Isheng J. Tsai*, Anne Babbage, Sarah Nichol, Martin Hunt, Nishadi De Silva, Tim J.C. Anderson, Richard C. Clark, Claire Davidson, Gary P. Dillon, Nancy E. Holroyd, Philip T. LoVerde, Christine Lloyd, Jacquelline McQuillan, Guilherme Oliveira,Thomas D. Otto, Sophia J. Parker-Manuel, Michael A. Quail, R. Alan Wilson, Adhemar Zerlotini, David W. Dunne, Matthew Berriman. (2012) A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni. PLoS Neglected Tropical Diseases PLoS Negl Trop Dis 6(1): e1455
  39. Taisei Kikuchi, James A. Cotton, Jonathan J. Dalzell, Koichi Hasegawa, Natsumi Kanzaki, Paul McVeigh, Takuma Takanashi, Isheng J. Tsai, Samuel A. Assefa, Peter J.A. Cock, Thomas Dan Otto, Martin Hunt, Adam J. Reid, Alejandro Sanchez-Flores, Kazuko Tsuchihara, Toshiro Yokoi, Mattias C Larsson, Johji Miwa, Aaron G Maule, Norio Sahashi, John T. Jones and Matthew Berriman. (2011) Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PLoS Pathogens 7(9):e1002219.
  40. Isheng J. Tsai  (2011) Genome watch: Honey, I shrunk the mimiviral genome Nature Review Microbiology
  41. Isheng J. Tsai, Austin Burt , Vassiliki Koufopanou (2010) Conservation of recombination hotspots in yeast. Proc Natl Acad Sci USA Apr 107(17):7847-7852
  42. Isheng J. Tsai, Thomas D Otto and Matthew Berriman. (2010) Method Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps Genome Biology
  43. Gianni Liti, David M. Carter, Alan M. Moses, Jonas Warringer, Leopold Parts, Stephen A. James, Robert P. Davey, Ian N. Roberts, Austin Burt, Vassiliki Koufopanou, Isheng J. Tsai, Casey M. Bergman, Douda Bensasson, Michael J. T. O’Kelly, Alexander van Oudenaarden, David B. H. Barton, Elizabeth Bailes, Alex N. Nguyen, Matthew Jones, Michael A. Quail, Ian Goodhead, Sarah Sims, Frances Smith, Anders Blomberg, Richard Durbin & Edward J. Louis (2009) Population genomics of domestic and wild yeasts Nature 458 (7236), 337-341
  44. Isheng J Tsai, Douda Bensasson, Austin Burt and Vassiliki Koufopanou Population genomics of the wild yeast Saccharomyces paradoxus: (2008) Quantifying the life cycle Proc Natl Acad Sci USA
  45.