CHRIS TSUYOSHI AMEMIYA

Summary

Affiliation: Benaroya Research Institute
Country: USA

Publications

  1. ncbi request reprint Animal evolution: when did the 'Hox system' arise?
    Chris T Amemiya
    Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA
    Curr Biol 16:R546-8. 2006
  2. ncbi request reprint Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus
    Steven Q Irvine
    Yale University, Department of Molecular, Cellular and Developmental Biology, New Haven, Connecticut 06520 8103, USA
    J Exp Zool 294:47-62. 2002
  3. pmc Resolution of the novel immune-type receptor gene cluster in zebrafish
    Jeffrey A Yoder
    Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
    Proc Natl Acad Sci U S A 101:15706-11. 2004
  4. ncbi request reprint BAC libraries and comparative genomics of aquatic chordate species
    Tsutomu Miyake
    Molecular Genetics Department, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA
    Comp Biochem Physiol C Toxicol Pharmacol 138:233-44. 2004
  5. pmc Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC
    Yuanyuan Cheng
    Faculty of Veterinary Science, University of Sydney, Sydney, NSW, Australia
    BMC Genomics 13:87. 2012
  6. pmc The African coelacanth genome provides insights into tetrapod evolution
    Chris T Amemiya
    Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA
    Nature 496:311-6. 2013
  7. pmc Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position
    Michael Lang
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    Evodevo 1:11. 2010
  8. pmc Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans
    An Mannaert
    Biology Department, ECOL, Vrije Universiteit Brussel, Belgium
    BMC Genomics 11:658. 2010
  9. pmc Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)
    Lucile Soler
    CIRAD PERSYST, Aquaculture Research Unit, TA B 20 A, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
    BMC Genomics 11:636. 2010
  10. pmc Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus
    Larry J Dishaw
    All Children s Hospital, Department of Molecular Genetics, 801 Sixth Street South, St, Petersburg, FL 33701, USA
    BMC Genet 9:78. 2008

Research Grants

Detail Information

Publications39

  1. ncbi request reprint Animal evolution: when did the 'Hox system' arise?
    Chris T Amemiya
    Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA
    Curr Biol 16:R546-8. 2006
    ....
  2. ncbi request reprint Genomic analysis of Hox clusters in the sea lamprey Petromyzon marinus
    Steven Q Irvine
    Yale University, Department of Molecular, Cellular and Developmental Biology, New Haven, Connecticut 06520 8103, USA
    J Exp Zool 294:47-62. 2002
    ..marinus has a total of either three or four Hox clusters. We also identify four highly conserved non-coding sequence motifs shared with higher vertebrates in a genomic comparison of Hox 10 genes...
  3. pmc Resolution of the novel immune-type receptor gene cluster in zebrafish
    Jeffrey A Yoder
    Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, 4700 Hillsborough Street, Raleigh, NC 27606, USA
    Proc Natl Acad Sci U S A 101:15706-11. 2004
    ..These studies resolve a complete immune gene cluster in zebrafish and indicate that the NITRs represent the most complex family of activating/inhibitory surface receptors thus far described...
  4. ncbi request reprint BAC libraries and comparative genomics of aquatic chordate species
    Tsutomu Miyake
    Molecular Genetics Department, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA
    Comp Biochem Physiol C Toxicol Pharmacol 138:233-44. 2004
    ..It is not intended to be an exhaustive treatise; rather our goal is to provide a primer of the BAC technology in order to make readers aware of these resources and how they may utilize them in their own research programs...
  5. pmc Antigen-presenting genes and genomic copy number variations in the Tasmanian devil MHC
    Yuanyuan Cheng
    Faculty of Veterinary Science, University of Sydney, Sydney, NSW, Australia
    BMC Genomics 13:87. 2012
    ..DFTD is caused by a clonal tumour cell line that is transmitted between unrelated individuals as an allograft without triggering immune rejection due to low levels of Major Histocompatibility Complex (MHC) diversity in Tasmanian devils...
  6. pmc The African coelacanth genome provides insights into tetrapod evolution
    Chris T Amemiya
    Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA
    Nature 496:311-6. 2013
    ..Functional assays of enhancers involved in the fin-to-limb transition and in the emergence of extra-embryonic tissues show the importance of the coelacanth genome as a blueprint for understanding tetrapod evolution...
  7. pmc Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position
    Michael Lang
    Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    Evodevo 1:11. 2010
    ..An insight into the molecular evolution that may explain the unchanged character of Latimeria morphology requires the analysis of the expression patterns of developmental regulator genes and their cis-regulatory modules (CRMs)...
  8. pmc Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans
    An Mannaert
    Biology Department, ECOL, Vrije Universiteit Brussel, Belgium
    BMC Genomics 11:658. 2010
    ..A frog and a caecilian were included in the study to compare coding sequences as well as to determine the gain and loss of putative regulatory sequences...
  9. pmc Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)
    Lucile Soler
    CIRAD PERSYST, Aquaculture Research Unit, TA B 20 A, Campus International de Baillarguet, 34398 Montpellier Cedex 5, France
    BMC Genomics 11:636. 2010
    ..Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species...
  10. pmc Genomic complexity of the variable region-containing chitin-binding proteins in amphioxus
    Larry J Dishaw
    All Children s Hospital, Department of Molecular Genetics, 801 Sixth Street South, St, Petersburg, FL 33701, USA
    BMC Genet 9:78. 2008
    ..In this report, we describe VCBP genomic organization and characterize adjacent and intervening genetic features which may influence both their polymorphism and complex transcriptional repertoire...
  11. pmc Sequence and organization of coelacanth neurohypophysial hormone genes: evolutionary history of the vertebrate neurohypophysial hormone gene locus
    Pai Chung Gwee
    Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, 138673, Singapore
    BMC Evol Biol 8:93. 2008
    ..The coelacanths occupy a unique phylogenetic position close to the divergence of the mammalian and ray-finned fish lineages...
  12. ncbi request reprint Comparative genomics in vertebrate evolution and development
    Chris T Amemiya
    Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington 98101, USA
    J Exp Zool A Comp Exp Biol 305:672-82. 2006
    ..In addition, we briefly discuss the application of genomic approaches to problems in comparative endocrinology...
  13. pmc No more than 14: the end of the amphioxus Hox cluster
    Carolina Minguillon
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona Av Diagonal, 645 E 08028, Barcelona, Spain
    Int J Biol Sci 1:19-23. 2005
    ..We suggest that 14 is the end...
  14. pmc Variable lymphocyte receptors in hagfish
    Zeev Pancer
    Division of Developmental and Clinical Immunology, Department of Medicine, University of Alabama, Birmingham, AL 35294, USA
    Proc Natl Acad Sci U S A 102:9224-9. 2005
    ..The development of two very different strategies for receptor diversification at the dawn of vertebrate evolution approximately 500 million years ago attests to the fitness value of a lymphocyte-based system of anticipatory immunity...
  15. pmc Ancient divergence of a complex family of immune-type receptor genes
    John P Cannon
    Department of Pediatrics, University of South Florida College of Medicine, and USF ACH Children s Research Institute, 830 First Street South, St Petersburg, FL, 33701, USA
    Immunogenetics 58:362-73. 2006
    ....
  16. ncbi request reprint Tuatara (Sphenodon) genomics: BAC library construction, sequence survey, and application to the DMRT gene family
    Zhenshan Wang
    Department of Biology, University of Washington, Seattle, WA 98195, USA
    J Hered 97:541-8. 2006
    ..A deep coverage contig spanning nearly 300 kb was generated, supporting the deep coverage and utility of the library for exploring tuatara genomics...
  17. pmc Evolutionary constraint on Otx2 neuroectoderm enhancers-deep conservation from skate to mouse and unique divergence in teleost
    Daisuke Kurokawa
    Laboratory for Vertebrate Body Plan, RIKEN Center for Developmental Biology, 2 2 3 Minatojima minamimachi, Chuo Ku, Kobe 650 0047, Japan
    Proc Natl Acad Sci U S A 103:19350-5. 2006
    ....
  18. pmc Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin cluster
    Wei Ping Yu
    Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore
    Proc Natl Acad Sci U S A 105:3819-24. 2008
    ..The small and "stable" genome of the elephant shark is a valuable reference for understanding the evolution of vertebrate genomes...
  19. doi request reprint The amphioxus Hox cluster: characterization, comparative genomics, and evolution
    Chris T Amemiya
    Benaroya Research Institute at Virginia Mason, Seattle, Washington, USA
    J Exp Zool B Mol Dev Evol 310:465-77. 2008
    ....
  20. ncbi request reprint Evolution of microRNAs located within Hox gene clusters
    Andrea Tanzer
    Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Kreuzstrasse 7b, D 04103 Leipzig, Germany
    J Exp Zool B Mol Dev Evol 304:75-85. 2005
    ..Here we describe their evolution in detail. We show that the micro RNAs closely follow the patterns of protein evolution in the Hox clusters, which is characterized by cluster duplications followed by differential gene loss...
  21. ncbi request reprint Genomics of the HOX gene cluster
    Pedro Martinez
    Department of Anatomy and Cell Biology, University of Bergen, Aarstadveien, 19, 5009, Bergen, Norway
    Comp Biochem Physiol B Biochem Mol Biol 133:571-80. 2002
    ..Moreover, a comprehensive study of Hox target genes in tissues and organisms promises, in the long term, to give us a clear idea of the role that Hox genes play during development and how they have evolved over time...
  22. ncbi request reprint Positive Darwinian selection operating on the immunoglobulin heavy chain of Antarctic fishes
    Tatsuya Ota
    Center for Human Genetics, Boston University School of Medicine, Boston, MA 02118, USA
    J Exp Zool B Mol Dev Evol 295:45-58. 2003
    ..Results of Southern blot hybridization experiments were consistent with a translocon type of IgH gene organization reminiscent of bony fishes and tetrapods...
  23. pmc Lineage-restricted retention of a primitive immunoglobulin heavy chain isotype within the Dipnoi reveals an evolutionary paradox
    Tatsuya Ota
    Department of Biosystems Science, The Graduate University for Advanced Studies Sokendai, Hayama, Kanagawa 240 0193, Japan
    Proc Natl Acad Sci U S A 100:2501-6. 2003
    ..Moreover, its absence in other gnathostome lineages implies paradoxically that the IgW-type genes were lost from teleost and tetrapod lineages...
  24. ncbi request reprint Phylogenetic analysis of the mammalian Hoxc8 non-coding region
    Chang Bae Kim
    Department of Molecular, Cellular, and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520, USA
    J Struct Funct Genomics 3:195-9. 2003
    ..This study demonstrates usefulness of a comparative approach employing non-coding regions of Hox gene complexes...
  25. pmc Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution
    Chi hua Chiu
    Department of Genetics, Rutgers University, Piscataway, New Jersey 08854, USA
    Genome Res 14:11-7. 2004
    ..Hence, in the earliest actinopterygians, evolution of the single HoxA cluster was already more dynamic than in human and shark. This tendency peaked among teleosts after HoxA cluster duplication...
  26. ncbi request reprint The shark HoxN cluster is homologous to the human HoxD cluster
    Sonja J Prohaska
    Bioinformatik, Institut fur Informatik, Universitat Leipzig, Kreuzstrassse 7b, D 04103 Leipzig, Germany
    J Mol Evol 58:212-7. 2004
    ..This finding implies that the most recent common ancestor of jawed vertebrates had at least four Hox clusters, including those which are orthologous to the four mammalian Hox clusters...
  27. ncbi request reprint Hoxc8 early enhancer of the Indonesian coelacanth, Latimeria menadoensis
    Cooduvalli Shashikant
    Department of Dairy and Animal Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, 324 Henning Building, University Park, PA 16802, USA
    J Exp Zool B Mol Dev Evol 302:557-63. 2004
    ..The divergence of teleost (actinopterygii) Hoxc8 early enhancer may reflect a case of relaxed selection or other forms of instability induced by genome duplication events...
  28. pmc Coelacanth genome sequence reveals the evolutionary history of vertebrate genes
    James P Noonan
    Department of Genetics, Stanford University School of Medicine, Stanford, California 94305 5120, USA
    Genome Res 14:2397-405. 2004
    ..Our results indicate that coelacanth provides the ideal outgroup sequence against which tetrapod genomes can be measured. We therefore present L. menadoensis as a candidate for whole-genome sequencing...
  29. ncbi request reprint Evolution of isotype switching
    Janet Stavnezer
    Department of Molecular Genetics and Microbiology, Program in Immunology and Virology, University of Massachusetts Medical School, 55 Lake Ave N, Worcester, MA 01655 0122, USA
    Semin Immunol 16:257-75. 2004
    ..Although at least some fishes are likely to undergo SHM, CSR is highly unlikely to occur in this group. We discuss the first appearance of CSR in amphibians and how it differs in birds and mammals...
  30. pmc Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes
    Elliott H Margulies
    Genome Technology Branch and NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    Proc Natl Acad Sci U S A 102:3354-9. 2005
    ..Our results confirm that genomic sequence from noneutherian mammals can contribute uniquely to unraveling the functional and evolutionary histories of the mammalian genome...
  31. ncbi request reprint A BAC library of the East African haplochromine cichlid fish Astatotilapia burtoni
    Michael Lang
    Lehrstuhl fur Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
    J Exp Zool B Mol Dev Evol 306:35-44. 2006
    ....
  32. pmc Divergence of Hoxc8 early enhancer parallels diverged axial morphologies between mammals and fishes
    Sanjay Anand
    Department of Dairy and Animal Science, College of Agricultural Sciences, Pennsylvania State University, University Park, PA 16802, USA
    Proc Natl Acad Sci U S A 100:15666-9. 2003
    ....
  33. ncbi request reprint Echinoderms
    Chris T Amemiya
    Molecular Genetics Program, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA
    Curr Biol 15:R944-6. 2005
  34. ncbi request reprint The zebrafish as a model organism to study development of the immune system
    David Traver
    Division of Hematology, Children s Hospital, 320, Longwood Avenue, Boston, MA 02115, USA
    Adv Immunol 81:253-330. 2003
  35. ncbi request reprint Evidence for a Hox14 paralog group in vertebrates
    Thomas P Powers
    Curr Biol 14:R183-4. 2004
  36. ncbi request reprint Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 447:167-77. 2007
    ..A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation...
  37. ncbi request reprint An ancient Fox gene cluster in bilaterian animals
    Francoise Mazet
    Curr Biol 16:R314-6. 2006
  38. ncbi request reprint Comparative cis-regulatory analyses identify new elements of the mouse Hoxc8 early enhancer
    Wayne C H Wang
    Department of Dairy and Animal Science, College of Agricultural Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
    J Exp Zool B Mol Dev Evol 302:436-45. 2004
    ....
  39. ncbi request reprint Comparative genomics, cis-regulatory elements, and gene duplication
    Allan Force
    Molecular Genetics Program, Benaroya Research Institute, Seattle, Washington 98101, USA
    Methods Cell Biol 77:545-61. 2004

Research Grants9

  1. GENOMICS RESOURCES AND INFRASTRUCTURE FOR THE ZEBRAFISH
    Chris Amemiya; Fiscal Year: 2003
    ..In addition, the libraries so generated will be an integral component for future large-scale physical mapping and sequencing of the zebrafish genome, as well as functional genomics experiments. ..
  2. Genomics Resources and Infrastucture for the Zebrafish
    Chris Amemiya; Fiscal Year: 2009
    ..In addition in keeping with the educational mission of NCRR, science outreach will be established for undergraduates and science teachers through partnerships with local educational and science outreach programs. ..
  3. Genomics Resources and Infrastucture for the Zebrafish
    CHRIS TSUYOSHI AMEMIYA; Fiscal Year: 2010
    ..In addition in keeping with the educational mission of NCRR, science outreach will be established for undergraduates and science teachers through partnerships with local educational and science outreach programs. ..
  4. Emergence of developmental and genomic complexity in a basal vertebrate
    Marianne Bronner Fraser; Fiscal Year: 2010
    ..The VLRs are also of biotechnological [and possibly clinical] relevance since the molecules can be manipulated to encompass many of the same features as conventional monoclonal antibodies. ..