Ikuo Uchiyama

Ikuo Uchiyama

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Ikuo Uchiyama

Ikuo Uchiyama

Publications by authors named "Ikuo Uchiyama"

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Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.

Nat Plants 2019 08 29;5(8):890-901. Epub 2019 Jul 29.

Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan.

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http://dx.doi.org/10.1038/s41477-019-0477-xDOI Listing
August 2019

RNA-Seq Analysis Reveals Genes Related to Photoreception, Nutrient Uptake, and Toxicity in a Noxious Red-Tide Raphidophyte .

Front Microbiol 2019 31;10:1764. Epub 2019 Jul 31.

Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.

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http://dx.doi.org/10.3389/fmicb.2019.01764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685483PMC
July 2019

MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons.

Nucleic Acids Res 2019 Jan;47(D1):D382-D389

Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.

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http://dx.doi.org/10.1093/nar/gky1054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6324027PMC
January 2019

Ortholog Identification and Comparative Analysis of Microbial Genomes Using MBGD and RECOG.

Authors:
Ikuo Uchiyama

Methods Mol Biol 2017 ;1611:147-168

Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.

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http://dx.doi.org/10.1007/978-1-4939-7015-5_12DOI Listing
February 2018

Artificial acceleration of mammalian cell reprogramming by bacterial proteins.

Genes Cells 2017 Oct 4;22(10):918-928. Epub 2017 Aug 4.

Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.

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http://dx.doi.org/10.1111/gtc.12519DOI Listing
October 2017

A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands.

PLoS One 2016 9;11(8):e0159419. Epub 2016 Aug 9.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159419PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4978471PMC
July 2017

An acid-tolerant ammonia-oxidizing γ-proteobacterium from soil.

ISME J 2017 05 10;11(5):1130-1141. Epub 2017 Jan 10.

Yokohama Institute, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokohama, Kanagawa, Japan.

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http://dx.doi.org/10.1038/ismej.2016.191DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5437925PMC
May 2017

SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

BMC Bioinformatics 2017 Feb 8;18(1):93. Epub 2017 Feb 8.

National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi, 444-8585, Japan.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/s12859-017-1531-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5299738PMC
February 2017

The Orthology Ontology: development and applications.

J Biomed Semantics 2016 06 4;7(1):34. Epub 2016 Jun 4.

National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, 444-8585, Aichi, Japan.

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http://dx.doi.org/10.1186/s13326-016-0077-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893294PMC
June 2016

Complete Genome Sequence of Aurantimicrobium minutum Type Strain KNCT, a Planktonic Ultramicrobacterium Isolated from River Water.

Genome Announc 2016 Jun 30;4(3). Epub 2016 Jun 30.

Genetic Strains Research Center, National Institute of Genetics, Mishima, Japan The Graduate University for Advanced Studies (SOKENDAI), Mishima, Japan.

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http://genomea.asm.org/lookup/doi/10.1128/genomeA.00616-16
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http://dx.doi.org/10.1128/genomeA.00616-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4929513PMC
June 2016

Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System.

PLoS One 2015 21;10(7):e0132994. Epub 2015 Jul 21.

Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan; Advanced Science & Innovation Group, Mitsubishi Research Institute Inc. (MRI), Nagata-cho, Chiyoda-ku, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0132994PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510362PMC
April 2016

Construction of an ortholog database using the semantic web technology for integrative analysis of genomic data.

PLoS One 2015 13;10(4):e0122802. Epub 2015 Apr 13.

Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0122802PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4395280PMC
January 2016

Epigenetic modification maintains intrinsic limb-cell identity in Xenopus limb bud regeneration.

Dev Biol 2015 Oct 14;406(2):271-82. Epub 2015 Aug 14.

Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Hirosaki, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.ydbio.2015.08.013DOI Listing
October 2015

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes.

Environ Microbiol Rep 2015 Apr 23;7(2):341-50. Epub 2015 Jan 23.

Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Monobe B200, Nankoku, Kochi, 783-8502, Japan.

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http://dx.doi.org/10.1111/1758-2229.12254DOI Listing
April 2015

Diofenolan induces male offspring production through binding to the juvenile hormone receptor in Daphnia magna.

Aquat Toxicol 2015 Feb 24;159:44-51. Epub 2014 Nov 24.

Environmental Quality Measurement Section, Research Center for Environmental Risk, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba 305-8506, Ibaraki, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.aquatox.2014.11.015DOI Listing
February 2015

MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data.

Nucleic Acids Res 2015 Jan 14;43(Database issue):D270-6. Epub 2014 Nov 14.

Laboratory of Genome Informatics, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.

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http://dx.doi.org/10.1093/nar/gku1152DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383954PMC
January 2015

Molecular impact of juvenile hormone agonists on neonatal Daphnia magna.

J Appl Toxicol 2014 May 5;34(5):537-44. Epub 2013 Sep 5.

Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan; Department of Basic Biology, Faculty of Life Science, Graduate University for Advanced Studies (SOKENDAI), 5-1 Higashiyama, Myodaiji, Okazaki, Aichi, 444-8787, Japan.

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http://dx.doi.org/10.1002/jat.2922DOI Listing
May 2014

Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score.

BMC Bioinformatics 2014 May 18;15:148. Epub 2014 May 18.

National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan.

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http://dx.doi.org/10.1186/1471-2105-15-148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035852PMC
May 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://dx.doi.org/10.1186/2041-1480-5-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Chromosome painting in silico in a bacterial species reveals fine population structure.

Mol Biol Evol 2013 Jun 16;30(6):1454-64. Epub 2013 Mar 16.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1093/molbev/mst055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3649679PMC
June 2013

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

Nucleic Acids Res 2013 Jan 30;41(Database issue):D631-5. Epub 2012 Oct 30.

Laboratory of Genome Informatics, Data Integration and Analysis Facility, National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.

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http://dx.doi.org/10.1093/nar/gks1006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531178PMC
January 2013

Domain movement within a gene: a novel evolutionary mechanism for protein diversification.

PLoS One 2011 Apr 14;6(4):e18819. Epub 2011 Apr 14.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo, Japan.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0018819PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3077401PMC
April 2011

Birth and death of genes linked to chromosomal inversion.

Proc Natl Acad Sci U S A 2011 Jan 6;108(4):1501-6. Epub 2011 Jan 6.

Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1073/pnas.1012579108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029772PMC
January 2011

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

Nucleic Acids Res 2010 Jan 11;38(Database issue):D361-5. Epub 2009 Nov 11.

National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.

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http://dx.doi.org/10.1093/nar/gkp948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808943PMC
January 2010

Complete genome sequence of Macrococcus caseolyticus strain JCSCS5402, [corrected] reflecting the ancestral genome of the human-pathogenic staphylococci.

J Bacteriol 2009 Feb 12;191(4):1180-90. Epub 2008 Dec 12.

Department of Microbiology and Infection Control Science, Juntendo University, 2-1-1 Hongo, Bunkyo, Tokyo 113-8421, Japan.

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http://dx.doi.org/10.1128/JB.01058-08DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2632007PMC
February 2009

Multiple genome alignment for identifying the core structure among moderately related microbial genomes.

Authors:
Ikuo Uchiyama

BMC Genomics 2008 Oct 31;9:515. Epub 2008 Oct 31.

Department of Theoretical Biology, National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.

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http://dx.doi.org/10.1186/1471-2164-9-515DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615449PMC
October 2008

Genome comparison in silico in Neisseria suggests integration of filamentous bacteriophages by their own transposase.

DNA Res 2005 22;12(6):389-401. Epub 2006 Feb 22.

Department of Medical Genome Sciences, Graduate School of Frontier Science, The University of Tokyo, Japan.

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http://dx.doi.org/10.1093/dnares/dsi021DOI Listing
October 2007

MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.

Authors:
Ikuo Uchiyama

Nucleic Acids Res 2007 Jan 29;35(Database issue):D343-6. Epub 2006 Nov 29.

National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan.

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http://dx.doi.org/10.1093/nar/gkl978DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751538PMC
January 2007

How genomes rearrange: genome comparison within bacteria Neisseria suggests roles for mobile elements in formation of complex genome polymorphisms.

Gene 2006 Nov 28;383:52-63. Epub 2006 Jul 28.

Department of Medical Genome Sciences, Graduate School of Frontier Science, the University of Tokyo, Japan.

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http://dx.doi.org/10.1016/j.gene.2006.07.013DOI Listing
November 2006

CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes.

BMC Bioinformatics 2006 Oct 24;7:472. Epub 2006 Oct 24.

National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan.

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http://www.biomedcentral.com/content/pdf/1471-2105-7-472.pdf
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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-7-472DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1643837PMC
October 2006

Evolution of paralogous genes: Reconstruction of genome rearrangements through comparison of multiple genomes within Staphylococcus aureus.

Mol Biol Evol 2006 Jun 6;23(6):1269-85. Epub 2006 Apr 6.

Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo, Japan.

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http://dx.doi.org/10.1093/molbev/msk013DOI Listing
June 2006

Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.

Authors:
Ikuo Uchiyama

Nucleic Acids Res 2006 25;34(2):647-58. Epub 2006 Jan 25.

National Institute for Basic Biology, National Institutes of Natural Sciences, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585 Japan.

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http://dx.doi.org/10.1093/nar/gkj448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1351371PMC
February 2006

Analysis of expressed sequence tags of the water flea Daphnia magna.

Genome 2005 Aug;48(4):606-9

Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences, Japan.

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http://dx.doi.org/10.1139/g05-038DOI Listing
August 2005

Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5'-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi.

Nucleic Acids Res 2005 Jul 21;33(13):e112. Epub 2005 Jul 21.

Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.

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http://dx.doi.org/10.1093/nar/gni113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1178009PMC
July 2005

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus.

Nucleic Acids Res 2004 1;32(21):6292-303. Epub 2004 Dec 1.

Microbial Genome Research Group, Japan Agency of Marine-Earth Science and Technology, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan.

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http://dx.doi.org/10.1093/nar/gkh970DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC535678PMC
December 2004

[A system for comparative analysis of microbial genomes].

Authors:
Ikuo Uchiyama

Nihon Rinsho 2003 Mar;61 Suppl 3:441-8

Research Center for Computational Science, Okazaki National Research Institutes.

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March 2003

MBGD: microbial genome database for comparative analysis.

Authors:
Ikuo Uchiyama

Nucleic Acids Res 2003 Jan;31(1):58-62

Research Center for Computational Science, Okazaki National Research Institutes, Nishigonaka 38, Myodaiji, Okazaki 444-8585, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165556PMC
http://dx.doi.org/10.1093/nar/gkg109DOI Listing
January 2003

Genome sequence of Oceanobacillus iheyensis isolated from the Iheya Ridge and its unexpected adaptive capabilities to extreme environments.

Nucleic Acids Res 2002 Sep;30(18):3927-35

Japan Marine Science and Technology Center, Microbial Genome Research Group, 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC137110PMC
http://dx.doi.org/10.1093/nar/gkf526DOI Listing
September 2002