Person
Amemiya, Chris
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Biography and Research Interest
I have been interested in the origins of novelty and innovation in organisms (primarily vertebrates) and how changes in the genome can facilitate molecular and organismal adaptation in the long term, and the onset of disease in the short term. My laboratory uses whatever tools are necessary to address fundamental biological questions. This includes large-insert cloning, comparative genomics, computational biology, molecular genetics, imaging, biochemistry, and developmental biology. We often employ "deep branches" in vertebrate phylogeny as they allow us to study the origin of characters germane to higher vertebrates, and they provide very good vantage points for making comparisons with other organisms for deducing the genetic basis of biological innovations, such as limbs, lungs, and adaptive immune systems. A common thread in my laboratory's research is the use of comparative genomics methods for deducing genomic features that may be important for emergence of novelty. I have been involved in genomics from my early career as a postdoctoral fellow with the Human Genome Project, and I developed early PAC and BAC libraries of the zebrafish (which were critical for physical mapping and positional cloning of many developmental genes. We have used zebrafish experimentally for many years in order to verify our molecular analyses and to validate our inferences. My lab continues to work in areas germane to evolution and development of cellular structures and morphologies. I am a new faculty member at UC Merced (started in Fall 2017) and was brought on as a senior member. My new roles include research mentorship of junior faculty and contributing to the growth of a new research university. I am also the newest Chair of the Quantitative & Systems Biology program at UC Merced.
Complete List of Published Work in MyBibliography:
http://www.ncbi.nlm.nih.gov/sites/myncbi/chris%20t..amemiya.2/bibliograpahy/40448317/public/?sort=date&direction=descending
Complete List of Published Work in MyBibliography:
http://www.ncbi.nlm.nih.gov/sites/myncbi/chris%20t..amemiya.2/bibliograpahy/40448317/public/?sort=date&direction=descending
Non-Zebrafish Publications
Recent non-ZF Pubs:
Olsen, A.S., Combs, J., Garcia, E., Elliott, J., Amemiya, C., de Jong, P. and Threadgill, G. 1993. Automated production of high density cosmid and YAC colony filters with a robotic workstation. Biotechniques 14: 116-123.
Litman, G.W., Rast, J.P., Shamblott, M.J., Haire, R.N., Hulst, M., Roess, W., Litman, R.T., Hinds-Frey, K.R. and Amemiya, C.T. 1993. Phylogenetic diversification of immunoglobulin genes and the antibody repertoire. Molecular Biology and Evolution 10: 60-72.
Mahadevan, M.S., Amemiya, C., Jansen, G., Sabourin, L., Baird, S., Neville, C.E., Lamerdin, J., Batzer, M., de Jong, P. and Korneluk, R. 1993. Structure and genomic sequence of the myotonic dystrophy (DM kinase) gene. Human Molecular Genetics 2: 299-304.
Bellefroid, E., Marine, J-C., Ried, T., Riviere, M., Coulie, P.J., Lecocq, P.J., Amemiya, C.T., de Jong, P.J., Szpirer, J., Poncelet, D.A., Szpirer, C., Ward, D.C. and Martial, J.A. 1993. Lymphoid restricted expression of multiple differentially spliced krab-finger genes clustered on human chromosome 19p12-p13.1. EMBO Journal 12: 1363-1374.
Amemiya, C.T., Ohta, Y., Litman, R.T. Haire, R.N., Rast, J.P. and Litman, G.W. 1993. Implications of the immunoglobulin VH gene organization in the coelacanth, Latimeria chalumnae. Proceedings of the National Academy of Sciences 90: 6661-6665.
Litman, G.W., Amemiya, C.T., Hinds, K.R., Litman, R.S., Kokubu, F., Suzuki, D., Shamblott, M.J., Harding, F.A. and Haire, R.N. 1993. Evolutionary origins of immunoglobulin genes. In: Cooper, E.L., ed. Developmental Immunology, pp 108-128, Oxford University Press, New York.
Ioannou, P., Amemiya, C.T., Garnes, J., Kroisel, P.M., Shizuya, H., Chen, C., Batzer, M.A., and de Jong, P.J. 1994. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genetics 6:84-89. (Co-first author).
Anderson, M., Amemiya, C., Luer, C., Litman, R., Rast, J., Niimura, Y. and Litman, G. 1994. Complete genomic sequence and patterns of transcription of a member of an unusual family of closely related, chromosomally dispersed immunoglobulin gene loci in Raja. International Immunology 6:1661-1670.
Litman, G.W., Rast, J.P., Hulst, M.A., Litman, R.T., Shamblott, M. J., Haire, R.N., Hinds-Frey, K.R., Buell, R.D., Margittai, M. Ohta, Y., Zilch, A.C., Good, R.A. and Amemiya, C.T. 1995. Evolutionary origins of immunoglobulin gene diversity. Progress in Immunology 8: 107-114.
Ohta, Y., Haire, R.N., Amemiya, C.T., Litman, R.T., Träger, T., Riess, O. and Litman, G.W. 1996. Human Txk: Genomic organization, structure, and contiguous physical linkage with the Tec gene. Oncogene 12: 937-942.
Ota, T. and Amemiya, C.T. 1996. An efficient, non-radioactive method for detection of restriction fragments from large P1 artificial chromosome clones. Genetic Analysis, Biomolecular Engineering 12: 173-178.
Ota, T., Rast, J.P., Margittai, M., Litman, G.W. and Amemiya, C.T. 1996. Studies on the early evolution of immunoglobulin genes. Current Topics on Molecular Evolution 1: 151-158.
Amemiya, C.T., Ota, T., Rast, J., Zon, L., and Litman, G.W. 1996. Organization and evolution of immunoglobulin genes, and identification of genes involved in regulation and ontogeny of the immune system. Current Topics on Molecular Evolution 1: 159-168.
Hoffman, S.M.G., Hromas, R., Amemiya, C. and Mohrenweiser, H.W. 1996. The localization of MZF-1 at the telomere of human chromosome 19q makes it vulnerable to degeneration in aging cells. Leukemia Research 20:81-283.
Amemiya, C.T., Ota, T. and Litman, G.W. 1996. Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. In: Birren, B. and Lai, E., eds. Nonmammalian Genomic Analysis: A Practical Guide, pp 223-256, Academic Press, NY.
Litman, G.W., Anderson, M.K., Rast, J.P. and Amemiya, C.T. 1997. Organization and mechanism of rearrangement of immunoglobulin genes in lower vertebrates. In: Herzenberg, L.A., Weir, D.M., Herzenberg, L.A. and Blackwell, C., eds. Weir's Handbook of Experimental Immunology, Chapter 18, Blackwell Science Limited, NY.
Strong, S.J., Ohta, Y., Litman, G.L. and Amemiya, C.T. 1997. Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Research: 25: 3959-3961.
Rast, J.P., Amemiya, C.T., Litman, R.T., Strong, S., and Litman, G.W. 1998. Distinct forms of immunoglobulin heavy chain organization in the ratfish, Hydrolagus colliei. Immunogenetics 47: 234-245.
Anderson, M.K., Strong, S.J., Litman, R.T., Luer, C.A., Amemiya, C.T., Rast, J.P. and Litman, G.W. 1999. A long form of the IgX in the skate exhibits a striking resemblance to the novel IgW and IgNARC genes in the shark. Immunogenetics 49: 56-67.
Bhargava, J., Shashikant, C.S., Carr, J.L., Bentley, K.L., Amemiya, C.T., and Ruddle, F.H. pPAC-ResQ: a yeast-bacterial shuttle vector for capturing inserts from P1 and PAC clones by recombinogenic targeted cloning. Genomics 56: 337-339.
Ruddle, F.H., Amemiya, C.T., Carr, J.L., Ledje, C., Shashikant, C.S., and Wagner, G. P. 1999. Evolution of chordate Hox gene clusters. New York Academy of Sciences 870: 238-248.
Strong, S. P., Mueller, M. G., Litman, R. T., Hawke, N. A., Haire, R. P., Miracle, A. L., Rast, J. P., Amemiya, C. T., and Litman, G. W. 1999. A novel multigene family encodes diversified variable regions. Proceedings of the National Academy of Sciences USA 96: 15080-15085.
Kim, C.-B., Amemiya, C., Bailey, W., Kawasaki, K., Mezey, J., Miller, W., Minoshima, S., Shimizu, N., Wagner, G., and Ruddle, F. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proceedings of the National Academy of Sciences USA 97: 1655-1660.
Zapata, A. and Amemiya, C. T. 2000. Phylogeny of lower vertebrates and their immunological structures. Current Topics in Microbiology and Immunology 248: 67-110.
Kim, C. B., Amemiya, C. T., Bailey, W., Kawasaki, K., Mezey, J., Miller, W., Minoshima, S., Shimizu, N., Wagner, G., and Ruddle, F. H. 2000. Hox cluster genomics in the horn shark, Heterodontus francisci. Proceedings of the National Academy of Sciences USA 97: 1655-1660.
Amemiya, C. T., Ota, T., Mueller, G. and Litman, G. W. 2001. Generation and characterization of a PAC genomic library of the Southern pufferfish, Spheroides nephelus. GENE 272: 283-289.
Amemiya, C. T. and Ikuta, T. 2001. Large-insert cloning and its applications for studying the developmental biology of hematopoiesis. In: Zon, L. I., ed. Hematopoiesis: A developmental approach, pp 663-671. Oxford University Press.
Irvine, S. Q., Carr, J. L., Shimizu, N., Bailey, Amemiya, C., and Ruddle, F. H. 2002. Genomic analysis of the Hox clusters in the sea lamprey Petromyzon marinus, Journal of Experimental Zoology (Molecular and Developmental Evolution) 294: 47-62.
Kim, C.-H., Shashikant, C. S., Sumiyama, K., Wang, W. C. H., Amemiya, C. T. and Ruddle, F. H. 2003. Phylogenetic analysis of the mammalian Hoxc8 non-coding region. Journal of Structural and Functional Genomics 3: 195-199.
Ota, T., Nguyen, T., Huang, E., Detrich, W., and Amemiya, C. T. 2003. Positive Darwinian selection operating on immunoglobulin heavy chain of antarctic fishes, Journal of Experimental Zoology (Molecular and Developmental Evolution) 295B: 45-58.
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. Proceedings of the National Academy of Sciences USA 100: 2501-2506.