Affiliation: University of Tokyo
- The human intestinal microbiome: a new frontier of human biologyMasahira Hattori
Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kasiwanoha, Kashiwa, Chiba 277 8561, Japan
DNA Res 16:1-12. 2009....
- Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomesMikihiko Kawai
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo, 108 8639, Japan
BMC Microbiol 11:104. 2011..We used newly developed comparative methods to follow the evolution of East Asian H. pylori genomes using 20 complete genome sequences from Japanese, Korean, Amerind, European, and West African strains...
- Comparative genomic analyses of Streptococcus mutans provide insights into chromosomal shuffling and species-specific contentFumito Maruyama
Division of Bacteriology, Department of Infectious Diseases Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 108 8639, Japan
BMC Genomics 10:358. 2009..While the pathogenicity of this species is distinct from other human pathogenic streptococci, the species-specific evolution of the genus Streptococcus and its genomic diversity are poorly understood...
- The identification and functional implications of human-specific "fixed" amino acid substitutions in the glutamate receptor familyHiroki Goto
Division of Human Moelcular Genetics, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812 8582, Japan
BMC Evol Biol 9:224. 2009..To clarify the evolutionary dynamics and mechanisms of the GluR genes in the lineage leading to humans, we determined the complete sequences of the coding regions and splice sites of 26 chimpanzee GluR genes...
- Birth and death of genes linked to chromosomal inversionYoshikazu Furuta
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato ku, Tokyo 108 8639, Japan
Proc Natl Acad Sci U S A 108:1501-6. 2011..These results will guide the interpretation of extensive DNA sequencing results for understanding long- and short-term genome evolution in various organisms and in cancer cells...
- Complete genome sequence of the denitrifying and N2O-reducing bacterium Azoarcus sp. strain KH32CTomoyasu Nishizawa
Department of Applied Biological Chemistry, The University of Tokyo, Yayoi, Bunkyo ku, Tokyo, Japan
J Bacteriol 194:1255. 2012..strain KH32C. The genome is composed of one chromosome and one megaplasmid and contains genes for plant-microbe interactions and the gene clusters for aromatic-compound degradations...
- Analysis of early bacterial communities on volcanic deposits on the island of Miyake (Miyake-jima), Japan: a 6-year study at a fixed siteReiko Fujimura
United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu shi, Tokyo, Japan
Microbes Environ 27:19-29. 2012..The detection of known 16S rRNA gene sequences from Fe(III)-reducing acidophiles promoted us to propose the acidity-driven iron cycle for the early microbial ecosystem on the deposit...
- Complete genome sequence of the serotype k Streptococcus mutans strain LJ23Chihiro Aikawa
Section of Bacterial Pathogenesis, Tokyo Medical and Dental University Graduate School of Medical and Dental Sciences, Tokyo, Japan
J Bacteriol 194:2754-5. 2012..Here we report the complete genome sequence of serotype k S. mutans strain LJ23, which was recently isolated from the oral cavity of a Japanese patient...
- Genome-wide profiling of DNA methylation in human cancer cellsKatsumi Ogoshi
Department of Molecular Preventive Medicine, Graduate School of Medicine, The University of Tokyo, 7 3 1 Hongo, Bunkyo ku, Tokyo 113 0033, Japan
Genomics 98:280-7. 2011..The MSDS method has the potential to provide novel insight into the functional complexity of the human genome...
- Microbial populations responsive to denitrification-inducing conditions in rice paddy soil, as revealed by comparative 16S rRNA gene analysisSatoshi Ishii
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1 1 1 Yayoi, Bunkyo ku, Tokyo 113 8657, Japan
Appl Environ Microbiol 75:7070-8. 2009..Therefore, OTUs related to Herbaspirillum are potential key players in nitrate respiration and denitrification under the conditions used...
- [Disease and metagenomics of intestinal microbiomes]Masahira Hattori
Graduate School of Frontier Sciences, The University of Tokyo
Nihon Rinsho 67:1214-8. 2009..The International Human Microbiome Project was recently launched to further promote this newly developing field, which will provide new strategies for the maintenance of human health...
- A large-scale full-length cDNA analysis to explore the budding yeast transcriptomeFumihito Miura
Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa 277 8561, Japan
Proc Natl Acad Sci U S A 103:17846-51. 2006..The budding yeast will serve as a versatile model for the studies on these aspects of transcriptome, and the full-length cDNA clones can function as an invaluable resource in such studies...
- Complete genome sequence of the wild-type commensal Escherichia coli strain SE15, belonging to phylogenetic group B2Hidehiro Toh
Advanced Science Institute, RIKEN, Yokohama, Kanagawa, Japan
J Bacteriol 192:1165-6. 2010..coli phylogenetic group B2, which includes the majority of extraintestinal pathogenic E. coli. Here, we report the finished and annotated genome sequence of this organism...