Jr_Kai_Yu
  • 專長領域:演化發育學、海洋生物學、基因體學
  • 學經歷:
    • 1990-1994臺灣大學動物學系學士
    • 1994-1996臺灣大學海洋研究所碩士
    • 2000-2005加州大學聖地牙哥海洋研究所博士
    • 2005-2007加州理工學院生物系博士後研究學者
    • 2007~中央研究院細胞與個體生物學研究所助研究員
    • 2007~臺灣大學海洋研究所合聘助理教授
  • 研究成果與著作:
      Journal Papers:
    • Zieger, E., Garbarino, G., Robert, N. S. M., Yu, J. K., Croce, J. C., Candiani, S., and Schubert, M. (2018) Retinoic acid signaling and neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus. Cellular and Molecular Life Sciences, 75(13), 2407-2429.
    • Hu, H. Y., Uesaka, M., Guo, S., Shimai, K., Lu, T. M., Li, F., Fujimoto, S., Ishikawa, M., Liu, S. P., Sasagawa, Y., Zhang, G. J., Kuratani, S., Yu, J. K., Kusakabe, T. G., Khaitovich, P., and Irie, N. (2017) Constrained vertebrate evolution by pleiotropic genes. Nature Ecology & Evolution, 1(11), 1722-1730.
    • Yong, L. W., Bertrand, S., Yu, J. K., Escriva, H., and Holland, N. D. (2017) Conservation of BMP2/4 expression patterns within the Glade Branchiostoma (amphioxus): Resolving interspecific discrepancies. Gene Expression Patterns, 25-26, 71-75.
    • Su, Y. H. and Yu, J. K. (2017) EvoDevo: Changes in developmental controls underlying the evolution of animal body plans. Developmental Biology, 427(2), 177-178. SI.
    • Kozmikova, I.* and Yu, J. K.* (2017) Dorsal-ventral patterning in amphioxus: current understanding, unresolved issues, and future directions. International Journal of Developmental Biology, 61(10-12), 601-610.
    • Yong, L. W., and Yu, J.-K.* (2016) Tracing the evolutionary origin of vertebrate skeletal tissues: insights from cephalochordate amphioxus. Current Opinion in Genetics & Development, 39, 55-62.
    • Yue, J. X., Kozmikova, I., Ono, H., Nossa, C. W., Kozmik, Z., Putnam, N. H., Yu, J. K., and Holland, L. Z. (2016) Conserved Noncoding Elements in the Most Distant Genera of Cephalochordates: The Goldilocks Principle. Genome Biology and Evolution, 8(8) 2387-2405.
    • Chang, Y.C., Pai, C.Y., Chen, Y.C., Ting, H.C., Martinez, P., Telford, M.J ., Yu, J.K., and Su, Y.H. (2016) Regulatory circuit rewiring and functional divergence of the duplicate admp genes in dorsoventral axial patterning, Developmental Biology, 410(1) 108-118.
    • Lin, C.Y., Tung, C.H., Yu, J.K.*, and Su, Y.H. (2016) Reproductive periodicity, spawning induction, and larval metamorphosis of the hemichordate acorn worm Ptychoderaflava, Journal of Experimental Zoology Part B-Molecular and Developmental Evolution, 326(1) 47-60.
    • Yue, J.X., Li, K.L., and Yu, J.K.* (2015) Discovery of germline-related genes in Cephalochordate amphioxus: A genome wide survey using genome annotation and transcriptome data, Marine Genomics, 24(2) SI, 147-157.
    • Soukup, V., Yong, L.W., Lu, T.M., Huang, S.W., Kozmik, Z., and Yu, J.K.* (2015) The Nodal signaling pathway controls left-right asymmetric development in amphioxus. EvoDevo, 6, 5.
    • Stumpp, M., Hu, M.Y, Tseng, Y.C., Guh, Y.J., Chen Y.C., Yu, J.K., Su, Y.H., and Hwang, P.P. (2015) Evolution of extreme stomach pH in bilateria inferred from gastric alkalization mechanisms in basal deuterostomes. Scientific Reports, 5, 10421.
    • Jandzik, D., Garnett, A.T., Square, T.A., Cattell, M.V., Yu, J.K., and Medeiros, D.M. (2015) Evolution of the new vertebrate head by co-option of an ancient chordate skeletal tissue. Nature, 518, 534-537.
    • Satoh, N., Tagawa, K., Lowe, C., Yu, J.K., Kawashima, T., Takahashi, H., Ogasawara, M., Kirschner, M., Hisata, K., Su, Y.H., and Gerhart, J. (2014) On a possible evolutionary link of the stomochord of hemichordates to pharyngeal organs of chordates. Genesis, 52(12), 925-934.
    • Yue, J.X., Yu, J.K., Putnam, N.H., and Holland, L.Z. (2014) The transcriptome of an amphioxus, Asymmetronlucayanum, from the Bahamas: A window into chordate evolution. Genome Biology and Evolution, 6, 2681-2696.
    • Chen, S.H., Li, K.L., Lu, I.H., Wang, Y.B., Tung, C.H., Ting, H.C., Lin, C.Y., Lin, C.Y.*, Su, Y.H.*, and Yu, J.K.* (2014) Sequencing and analysis of the transcriptome of the acorn worm Ptychodera flava, an indirect developing hemichordate. Marine Genomics, 15, 35-43.
    • Tung, C.H. # , Cheng Y.R. # , Lin, C.Y., Ho, J.S., Kuo, C.H., Yu, J.K.*, and Su, Y.H.* (2014) A new copepod with transformed body plan and unique phylogenetic position parasitic in the acorn worm Ptychodera flava. Biological Bulletin, (#contributed equally) 226, 69-80.
    • Ikuta, T.#, Chen, Y.C.#, Annunziata, R., Ting, H.C., Tung, C.H., Koyanagi, R., Tagawa, K., Humphreys, T., Fujiyama, A., Saiga, H., Satoh, N., Yu, J.K., Arnone, M.I., and Su, Y.H.* (2013) Identification of an intact ParaHox cluster with temporal colinearity but residual spatial colinearity in the hemichordate Ptychodera flava. BMC Evolutionary Biology, 13, 129 (#contributed equally). Introduced by a commentary article in BMC Biology.
    • Wu, H.R., Chen, Y.T., Su, Y.H., Luo, Y.J., Holland, L.Z., and Yu, J.K. (2011) Asymmetric localization of germline markers Vasa and Nanos during early development in the amphioxus Branchiostoma floridae. Developmental Biology, 353, 147-159.
    • Yu, J.K., Meulemans, D., McKeown, S.J., and Bronner-Fraser, M. (2008) Insights from the amphioxus genome on the origin of vertebrate neural crest. Genome Research, 18, 1127-1132.
    • Putnam, N.H., Butts, T., Ferrier, D.E.K., Furlong, R.F., Hellsten, U., Kawashima, T., Robinson-Rechavi, M., Shoguchi, E., Terry, A., Yu, J.K., Benito-Gutiérrez, È., Dubchak, I., Garcia-Fernàndez, J., Grigoriev, I.V., Horton, A.C., Jong, P.J.d., Jurka, J., Kapitonov, V., Kohara, Y., Kuroki, Y., Lindquist, E., Lucas, S., Osoegawa, K., Pennacchio, L.A., Salamov, A.A., Satou, Y., Sauka-Spengler, T., Schmutz, J., Shin-I, T., Toyoda, A., Gibson-Brown, J.J., Bronner-Fraser, M., Fujiyama, A., Holland, L.Z., Holland, P.W.H., Satoh, N., and Rokhsar, D.S. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature, 453, 1064-1071.
    • Holland, L.Z., Albalat, R., Azumi, K., Benito-Gutiérrez, È., Blow, M.J., Bronner-Fraser, M., Brunet, F., Butts, T., Candiani, S., Dishaw, L.J., Ferrier, D.E.K., Garcia-Fernàndez, J., Gibson-Brown, J.J., Gissi, C., Godzik, A., Hallböök, F., Hirose, D., Hosomichi, K., Ikuta, T., Inoko, H., Kasahara, M., Kasamatsu, J., Kawashima, T., Kimura, A., Kobayashi, M., Kozmik, Z., Kubokawa, K., Laudet, V., Litman, G.W., McHardy, A.C., Meulemans, D., Nonaka, M., Olinski, R.P., Pancer, Z., Pennacchio, L.A., Pestarino, M., Rast, J.P., Rigoutsos, I., Robinson-Rechavi, M., Roch, G., Saiga, H., Sasakura, Y., Satake, M., Satou, Y., Schubert, M., Sherwood, N., Shiina, T., Takatori, N., Tello, J., Vopalensky, P., Wada, S., Xu, A., Ye, Y., Yoshida, K., Yoshizaki, F., Yu, J.K., Zhang, Q., Zmasek, C.M., Putnam, N.H., Rokhsar, D.S., Satoh, N., and Holland, P.W.H. (2008) The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Research, 18, 1100-1111.
    • Yu, J.K., Mazet, F., Chen, Y.T., Huang, S.W., Jung, K.C. and Shimeld, S.M. (2008) The Fox genes of Branchiostoma floridae. Development Genes and Evolution, 218(11), 629-638.
    • Yu, J.K., Wang, M.C., Shin-i, T., Kohara, Y., Holland, L.Z., Satoh, N. and Satou, Y. (2008) A cDNA resource for the cephalochordate amphioxus Branchiostoma floridae. Development Genes and Evolution, 218(11), 723-727.
    • Yu, J.K., Satou, Y., Holland, N.D., Shin, I.T., Kohara, Y., Satoh, N., Bronner-Fraser, M., and Holland, L.Z. (2007) Axial patterning in cephalochordates and the evolution of the organizer. Nature, 445, 613-617.
    • Schubert, M., Yu, J.K., Holland, N.D., Escriva, H., Laudet, V., and Holland, L.Z. (2005) Retinoic acid signaling acts via Hox1 to establish the posterior limit of the pharynx in the chordate amphioxus. Development, 132, 61-73.
    • Yu, J.K., Holland, N.D., and Holland, L.Z. (2004) Tissue-specific expression of FoxD reporter constructs in amphioxus embryos. Developmental Biology, 274, 452-461.
    • Holland, L.Z. and Yu, J.K. (2004) Cephalochordate (amphioxus) embryos: procurement, culture, and basic methods. Methods in Cell Biology, 74, 195-215.
    • Yu, J.K., Holland, N.D., and Holland, L.Z. (2003) AmphiFoxQ2, a novel winged helix/forkhead gene, exclusively marks the anterior end of the amphioxus embryo. Development Genes and Evolution, 213, 102-105.
    • Mazet, F., Yu, J.K., Liberles, D.A., Holland, L.Z., and Shimeld, S.M. (2003) Phylogenetic relationships of the Fox (Forkhead) gene family in the Bilateria. Gene, 316, 79-89.
    • Yu, J.K., Holland, L.Z., and Holland, N.D. (2002). An amphioxus nodal gene (AmphiNodal) with early symmetrical expression in the organizer and mesoderm and later asymmetrical expression associated with left-right axis formation. Evolution & Development, 4, 418-425.
    • Yu, J.K., Holland, L.Z., Jamrich, M., Blitz, I.L., and Hollan, N.D. (2002) AmphiFoxE4, an amphioxus winged helix/forkhead gene encoding a protein closely related to vertebrate thyroid transcription factor-2: expression during pharyngeal development. Evolution & Development, 4, 9-15.
    • Yu, J.K., Holland, N.D., and Holland, L.Z. (2002) An amphioxus winged helix/forkhead gene, AmphiFoxD: insights into vertebrate neural crest evolution. Developmental Dynamics, 225, 289-297.
    • Holland, N.D., and Yu, J.K. (2002) Epidermal receptor development and sensory pathways in vitally stained amphioxus (Branchiostoma floridae). Acta Zoologica, 83, 309-319.
    • Chen, C.A., Chen, C.P., Fan, T.Y., Yu, J.K., and Hsieh, H.L. (2002) Nucleotide sequences of ribosomal internal transcribed spacers and their utility in distinguishing closely related Perinereis polychaets (Annelida; Polychaeta; Nereididae). Marine Biotechnology, 4, 17-29.
    • Yu, J.K., Liao, T.H., Chen, C.A., Liao, T.H., Fang, L.S., and Tsai, W.S. (2000) Do color patterns of Pocillopora damicornis reflect Zooxanthellae diversity? Coral Reefs, 19, 98-99.
    • Dai, C.F., Fan, T.Y., and Yu, J.K. (2000) Reproductive isolation and genetic differentiation of a scleractinian coral Mycedium elephantotus. Marine Ecology Progress Series, 201, 179-187.
    • Chen, C.A., Wallace, G.C., Yu, J.K., and Wei, N.V. (2000) Strategies for amplification by polymerase chain reaction of the complete sequence of the gene encoding nuclear large subunit ribosomal RNA in corals. Marine Biotechnology, 2, 558-570.
    • Chen, C.A., and Yu, J.K. (2000). Universal primers for amplification of mitochondrial small subunit ribosomal RNA-encoding gene in scleractinian corals. Marine Biotechnology, 2, 146-153.
    • Yu, J.K., Wang, H.Y., Lee, S.C., and Dai, C.F. (1999) Genetic structure of a scleractinian coral, Mycedium elephantotus, in Taiwan. Marine Biology, 133, 21-28.
    • Book Chapter
    • Yu, J.K.S. and Holland, L.Z. (2010) Cephalochordates (Amphioxus, or Lancelets): A Model for Understanding the Evolution of Chordate Characters, pp. 335-363. In: “Emerging Model Organisms, A Laboratory Manual, Volume 2”. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.