Bio:
B.S. (Genetics, 1981), Purdue University
Ph.D. (Genetics, 1987), Texas A and M University
Postdoc (Molecular Genetics, 1987-1990), Tampa Bay Research Institute
Postdoc (Genomics, 1990-1993), Lawrence Livermore Natl. Lab
Assistant/Associate Professor (Human Genetics and Pediatrics, 1993-2001), Boston University School of Medicine
Associate Member (Molecular Genetics Program, 2001-2003), Benaroya Research Institute at Virginia Mason
Full Member (Molecular Genetics Program, 2004-), Benaroya Research Institute at Virginia Mason
Affiliate Full Professor (Biology, 2004-), University of Washington
Full Member (Cell and Molecular Biology Program, 2005-),
University of Washington
Full Member (Genome Sciences Training Program, 2005-),
University of Washington
Program Director, National Science Foundation (Developmental Systems and Evo-Devo, 2007-2008), Arlington, VA
Research Interests:
 My laboratory uses an interdisciplinary approach in order to better understand evolutionary and developmental aspects of the vertebrate immune system and of morphogenesis of body plans. We actively utilize comparative genomics approaches and are involved in the construction and utilization of bacterial artificial chromosome (BAC) reagents as a platform for functional biological experiments to draw inferences relevant to biological problems. In a nutshell, we seek to unify modern genomics approaches, evolutionary biology, population genetics theory and developmental biology into a coherent line of investigation. We use "deep branches" in vertebrate phylogeny (primarily very ancestral lineages of fishes and protochordates) in our research. These deep branches serve two purposes: first, they allow us to study the genomic and genetic origins of characters germane to higher vertebrates, including humans; and second, they provide very good vantage points for making comparisons with other organisms and to understand the origins of biological innovations, such as limbs and adaptive immune systems.
We are currently addressing two major lines of investigation. (1) What are the primordial mechanisms used to generate an immune response? How is the genome involved in creating and diversifying such a response? And how did the adaptive and innate arms of the immune system co-evolve and become functionally interdigitated? Finally, how can we incorporate genomic approaches to address major problems with regard to the immunological arms race? And (2) How have changes in genomic architecture and organization contributed to differences in body plans that we see amongst all metazoan species? What are the parallels between such evolutionary changes and disease manifestation?
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Selected Publications:
(from 130)
Ota, T., Rast, J. P., Litman, G. W. and Amemiya, C. T. 2003. Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox. Proc. Natl. Acad Sci. USA 100: 2501-1506.
Traver, D., Herbomel, P., Patton, E. E., Ryan Murphy, Yoder, J. A., Litman, G. W., Catic, A., Amemiya, C. T., Zon, L. I. and Trede, N. S. 2003. The zebrafish as a model organism to study development of the immune system. Advances in Immunology 81: 253-330.
Wagner, G. P., Amemiya, C. T., and Ruddle, F. H. 2003. Hox cluster duplications and the genetics of evolutionary novelties, Proc. Natl. Acad. Sci. USA 100: 14603-14606.
Powers, T. P. and Amemiya, C. T. 2004. Evidence for vertebrate Hox14 paralog group. Current Biology 14: R183-184.
Miyake, T. and Amemiya, C. T. 2004. BAC libraries and comparative genomics of aquatic chordate species. Comparative Biochemistry and Physiology (Part C): 138: 233-244.
Powers, T. P. and Amemiya, C. T. 2004. Evolutionary plasticity of vertebrate Hox genes. Current Genomics 5: 459-472.
Danke, J., Miyake, T., Powers, T., Schein, J., Shin, H., Bosdet, I., Erdmann, M., Caldwell, R. and Amemiya, C. T. 2004. Genome resource for the Indonesian coelacanth. Journal of Experimental Zoology, 301A: 228-234.
Chiu, C.-H., Dewar, K., Wagner, G. P., Takahashi, K., Ruddle, F. H., Ledje, C., Bartsch, P., Scemama, J.-L., Stellweg, E., Fried, C., Prohaska, S. J., Stadler, P. F. and Amemiya, C. T. 2004. Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution. Genome Research 14: 11-17.
Pancer, Z., Amemiya, C. T., Ehrhardt, G. R. A., Ceitlin, J., Gartland, G. L., and Cooper, M. D. 2004. Somatic diversification of variable lymphocyte receptors in the agnathan sea lamprey. Nature 430: 174-180.
Amores, A., Suzuki, T., Yan, Y.-L., Pomeroy, J., Singer, A., Amemiya, C. T., and Postlethwait, J. 2004. Developmental roles of pufferfish Hox clusters and genome evolution in ray-fin fish. Genome Research 14: 1-10.
Shashikant, C., Bolanowski, S. A., Danke, J., and Amemiya, C. T. 2004. Hoxc8 early enhancer of the Indonesian coelacanth, Latimeria menadoensis. J. Exp. Zoology (Molecular and Evolutionary Development) 302B: 557-563.
Stavnezer, J. and Amemiya, C. T. 2004. Evolution of isotype switching, Seminars in Immunology 16: 257-275.
Force, A., Shashikant, C., Stadler, P. and Amemiya, C. T. 2004. Comparative genomics, cis-regulatory elements and gene duplication. Methods in Cell Biology 77: 545-561.
Margulies, E. H., NISC Comparative Sequencing Program, Maduro, V. V. B., Thomas, P. J., Tomkins, J. P., Amemiya, C. T., Luo, M., and Green, E. D. 2005. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes, Proceedings of the National Academy of Sciences 102: 3354-3359.
Tanzer, A., Amemiya, C. T., Kim, C.-B., and Stadler, P. F. 2005. Evolution of microRNAs located within Hox gene clusters. Journal of Experimental Zoology (Molecular and Evolutionary Development) 204B: 75-85.
Force, A., Cresko, W., Pickett, B., Amemiya, C. and Lynch, M. 2005. The origin of gene subfunctions and modular gene regulation. Genetics 170: 433-446.
Metscher, B. D., Takahashi, K., Crow, K., Amemiya, C., Nonaka, D., and Wagner, G. P. 2005. Expression of Hoxa-11 and Hoxa-13 in the pectoral fin of a basal ray finned fish, Polyodon spathula: implications for the origin of tetrapod limbs. Evolution and Development, 7: 186-195.
Wagner, G. P., Takahashi, K., Roth, J., Lynch, V., Prohaska, S., Fried, C., Stadler, P., and Amemiya, C. 2005. Molecular evolution of duplicated ray finned fish HoxA clusters. Journal of Molecular Evolution 60: 665-676.
Pancer, Z., Saha, N.R., Kasamatsu, J., Suzuki, T., Amemiya, C.T., Kasahara, M., and Cooper, M.D. 2005. Variable lymphocyte receptors in hagfish. Proceedings of the National Academy of Sciences USA 102: 9224-9229.
Ferrier, D. E. K., Dewar, K., Cook, A., Chang, J. L., Hill-Force, A. and Amemiya, C. 2005. The chordate ParaHox cluster. Current Biology 15: R820-822.
Amemiya, C. T., Miyake, T., and Rast, J. P. 2005. Quick Guide: Echinoderms. Current Biology 15: R944-946.
Mazet, F., Amemiya, C. T. and Shimeld, S. M. 2006. An ancient gene cluster for mesoderm patterning. Current Biology 16: R314-R316.
Amemiya, C. T. and Wagner, G. P. 2006. Animal Evolution: When Did the "Hox system" Arise? (Dispatch). Current Biology 16: R546-548.
Amemiya, C. T. and Gomez-Chiarri, M. 2006. Comparative genomics in vertebrate evolution and development. Journal of Experimental Zoology (Comparative Experimental Biology, part A) 305: 672-682.
Wang, Z., Miyake, T., Edwards, S. V. and Amemiya, C. T. 2006. Tuatara (Sphenodon) Genomics: BAC library construction, sequence survey and application to the DMRT gene family. Journal of Heredity 96: 541-548.
Kurokawa, D., Sakurai, Y., Inoue, A., Nakayama, R., Takasaki, N., Suda, Y., Miyake, T., Amemiya, C. T., and Aizawa, S. 2006. Evolutionary constraint on Otx2-neuroectoderm enhancers; deep conservation from skate to mouse and a unique divergence in teleosts. Proceedings of the National Academy of Sciences USA 103: 19350-19355.
Trede, N. S., Medenbach. J., Damianov, A., Hung, L. H., Weber, G. J., Paw, B. H., Zhou, Y., Hersey, C., Zapata, A., Keefe, M., Barut, B. A., Stuart, A. B., Katz, T., Amemiya, C. T., Zon, L. I., and Bindereif, A. 2007. Network of coregulated spliceosome components revealed by zebrafish mutant in recycling factor p110. Proc. Natl. Acad. Sci. USA 104: 6608-6613.
Amemiya, C.T., Saha, N.R., and Zapata, A. 2007. Evolution and development of immunological structures in the lamprey.
Curr Opin Immunol. 19: 535-541.
Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT,... et at. 2007. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. 2007. Nature 447: 167-177.
Yu, Wei-Ping, Rajasegaran, V., Yew, K., Loh, W.-L., Amemiya, C. T., Brenner, S., and Venkatesh, B. 2008. Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: a comparative analysis of the protocadherin cluster, Proceedings of the National Academy of Sciences USA 105: 3819-3824.
Amemiya, C. T., Prohaska, S. J., Hill-Force, A., Ferrier, D. E. K., Anaya, J. P., Garcia-Fernandez, J., Dewar, K., and Stadler, P. F. 2008. The amphioxus Hox cluster: Characterization, comparative genomics, and evolution. Journal of Experimental Zoology (Molecular and Evolutionary Development) 310: 465-477.
Gwee, P. C., Amemiya, C. T., Brenner, S., Venkatesh, B. 2008. Sequence and organization of coelacanth neurohypophysial hormone genes: evolutionary history of the vertebrate neurohypophysial hormone gene locus. BMC Evolutionary Biology 8: 93-104.
Nikolaus S. Trede, N. S., Ota, T., Kawasaki, H., Paw, B. H., Katz, T., Demarest, B., Hutchinson, S., Zhou, Y., Hersey, C., Zapata, A., Amemiya, C. T., and Zon, L. I. 2008. Zebrafish mutants with disrupted early T cell and thymus development identified in early pressure screen. Developmental Dynamics 237: 2575-2584.
Dishaw, L. J., Mueller, G., Gwatney, N., Cannon, J. P., Haire, R. N., Litman, R. T., Amemiya, C. T., Ota, T., Rowen, L., Glusman, G., and Litman, G. W. 2008. Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus. BMC Genetics 9: 78.
Crow, K., Amemiya, C. T., Roth, J., and Wagner, G. P. 2009. Hypermutability of Hoxa13a and functional divergence from its paralog are associated with the origin of a novel developmental feature in zebrafish and related taxa (Cypriniformes). Evolution 63: 1574-1592.
Danilova, N. and Amemiya, C. T. 2009. Going adaptive: the saga of antibodies. Ann. NY Acad Sci. 1168: 130-155.
Smith, J. J., Antonacci, F., Eichler, E. E., and Amemiya, C. T. 2009. Programmed loss of millions of base pairs from a vertebrate genome. Proceedings of the National Academy of Sciences USA 106: 11212-11217.
Teaching Interests:
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