人員 研究人員 蔡怡陞 副研究員

蔡怡陞 副研究員

實驗室主持人

Dr.蔡怡陞

副研究員

Ph D. Imperial College, UK

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辦公室: 跨領域 B303

電話:+886-2-2787-2230
研究領域
  • 比較與群體基因體學
  • 寄生與病原機制的演化
  • 真核微生物的生態與多樣性

研究方向

  • 我們是一個藉由比較物種或個體間基因體的差異，探討物種多樣性，遺傳，演化，及寄生機制的實驗室。研究內容為分析新定序技術產生的巨量基因體資訊來做物種間的比較及族群分析。研究材料著重於醫學，林業，農業，畜牧業，及台灣生態環境上有重要地位的真菌及線蟲。主要研究方向為：

    1.亞洲相關微生物（線蟲及真菌）的基因體研究

      微生物可以存活在幾乎任何地方，也絕大部分影響它們居住的環境。比較群體或是不同病原的基因體可以讓我們了解在地球上最多且最多樣的物種群之演化過程。研究它們可以得到它們對我們環境周遭的影響，包括對植物及我們自己 。

    2. 真核病原寄生及感染動植物宿主的機制

      寄生是病原生活型態的一種機制，而基本上地球上每一種物種都會有至少一種會寄生的病原體。研究病原非常重要因為 A) 它們帶給我們及周遭（如農業）疾病及負擔，甚至死亡 B) 它們多樣的感染策略。我們分析諸多病原體的特殊演化歷史及生態（宿主內外的環境），來找出造成一個病原體的演化因素及每一個病原的特定基因及感染機制。

 

最新發表

期刊論文 ( 2016 - 2021 )

  1. YF Lin, CM Sung, HM Ke, WA Liu, HY Huang, MJ Lu, IJ Tsai* and SY Hsieh*, 2021, “Assessing the rectal mucosal microbiota improves mild ulcerative colitis detection sensitivity and evaluation”, gut microbes, 13, 1-13. (SCIE) (IF: 7.74; SCIE ranking: 12.5%,9.6%)
  2. YH Cheng, CFJ Liu, YH Yu, YT Jhou, M Fujishima, IJ Tsai, JY Leu, 2020, “Genome plasticity in Paramecium bursaria revealed by population genomics”, BMC BIOLOGY, 18, 180. (SCIE, Scopus) (IF: 6.765; SCIE ranking: 46.2%,84.8%) Link
  3. 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 OF THE UNITED STATES OF AMERICA, 117(12), 6762-6770. (SCIE) (IF: 9.412; SCIE ranking: 11.3%) Link
  4. Chang Ed-Haun, Tsai Isheng Jason, Jien Shih-Hao, Tian Guanglong, Chiu Chih-Yu, 2020, “Biogeographic Changes in Forest Soil Microbial Communities of Offshore Islands—A Case Study of Remote Islands in Taiwan”, Forests, 12(1) 4. (SCIE) (IF: 2.221; SCIE ranking: 46.2%,84.8%) Link
  5. 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: 3.462; SCIE ranking: 35.3%,34.8%) Link
  6. EP Chu, CH Lin, CHH Cho, IF Cheng, TC Kuo, RY Chen, CN Liao, JC Cheng, IJ Tsai, PC Wang, SJ Chang and CN Shen, 2020, “Establishment of three human induced pluripotent stem cell lines from a type 1 diabetic family harboring sequence variants associated with autoimmunity”, STEM CELL RESEARCH, 10.1016/j.scr.2020.102029. (SCIE) (IF: 4.495; SCIE ranking: 34.9%,37.9%,17.9%)
  7. Ke Huei-Mien, Lee Hsin-Han, Lin Chan-Yi Ivy, Liu Yu-Ching, Lu Min R., Hsieh Jo-Wei Allison, Chang Chiung-Chih, Wu Pei-Hsuan, Lu Meiyeh Jade, Li Jeng-Yi, Shang Gaus, Lu Rita Jui-Hsien, Nagy László G., Chen Pao-Yang, Kao Hsiao-Wei, Tsai Isheng Jason*, 2020, “Mycena genomes resolve the evolution of fungal bioluminescence”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 202010761. (SCIE) (IF: 9.412; SCIE ranking: 11.3%) Link
  8. M Dayi, S Sun, Y Maeda, R Tanaka, A Yoshida, IJ Tsai, T Kikuchi, 2020, “Nearly Complete Genome Assembly of the Pinewood Nematode Bursaphelenchus xylophilus Strain Ka4C1”, Microbiology Resource Announcements, 10.1128/MRA.01002-20.
  9. 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: 2.656; SCIE ranking: 33.7%,51.7%) Link
  10. 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: 11.062; SCIE ranking: 6.1%,7.8%,3.9%) Link
  11. 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: 4.123; SCIE ranking: 35.8%,27.9%) Link
  12. 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: 3.998; SCIE ranking: 23.9%) Link
  13. 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: 3.998; SCIE ranking: 23.9%) Link
  14. 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: 13.256; SCIE ranking: 1.3%) Link
  15. 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: 3.462; SCIE ranking: 35.3%,34.8%) Link
  16. 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. (SCIE) (IF: 7.076; SCIE ranking: 17%) Link
  17. 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: 3.234; SCIE ranking: 18.8%) Link
  18. 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: 12.121; SCIE ranking: 8.5%) Link
  19. International Helminth Genomes Consortium, 2018, “Comparative genomics of the major parasitic worms”, Nature Genetics, 51(1), 163-. (SCIE) (IF: 27.605; SCIE ranking: 1.1%) Link
  20. Liu D, Hunt M, Tsai IJ*, 2018, “Inferring synteny between genome assemblies: a systematic evaluation.”, BMC bioinformatics, 19(1), 26. (SCIE) (IF: 3.242; SCIE ranking: 15.3%,37.2%,31.2%) Link
  21. 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: 3.006; SCIE ranking: 48.5%) Link
  22. 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: 5.163; SCIE ranking: 16.8%,11.2%,13.7%) Link
  23. 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: 1.018; SCIE ranking: 92.2%,84.7%) Link
  24. 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: 4.872; SCIE ranking: 12%,16.6%) Link
  25. 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: 2.783; SCIE ranking: 26.3%) Link
  26. 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: 3.998; SCIE ranking: 23.9%) Link
  27. 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. (SCIE) (IF: 15.54; SCIE ranking: 2.9%) Link
  28. 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: 3.998; SCIE ranking: 23.9%) Link
  29. 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: 3.356; SCIE ranking: 25.4%,39%,9.3%) Link
  30. 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: 2.74; SCIE ranking: 38%) Link
  31. 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: 6.218; SCIE ranking: 8.1%,14%,10.5%) Link
  32. 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: 27.605; SCIE ranking: 1.1%) Link
  33. 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: 4.326; SCIE ranking: 9%) Link