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

Methods in molecular biology (Clifton, N.J.), 2017-01, Vol.1611, p.147

Uchiyama, Ikuo

2017

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Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex

Nature communications, 2020-05, Vol.11 (1), p.2481-2481, Article 2481

2020

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

Nucleic acids research, 2015-01, Vol.43 (Database issue), p.D270-D276

2015

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

Nucleic acids research, 2019-01, Vol.47 (D1), p.D382-D389

2019

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

BMC genomics, 2008-10, Vol.9 (1), p.515-515

Uchiyama, Ikuo

2008

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Genome sequence and analysis of the Japanese morning glory Ipomoea nil

Nature communications, 2016-11, Vol.7 (1), p.13295-13295, Article 13295

2016

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

Nature plants, 2019-08, Vol.5 (8), p.890-901

2019

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

Nucleic acids research, 2013-01, Vol.41 (Database issue), p.D631-D635

2013

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

PloS one, 2015-07, Vol.10 (7), p.e0132994-e0132994

2015

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Molecular phylogeny of fucoxanthin‐chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

Physiologia plantarum, 2022-01, Vol.174 (1), p.e13598-n/a

2022

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

BMC bioinformatics, 2014-05, Vol.15 (1), p.148-148, Article 148

2014

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

PloS one, 2015-04, Vol.10 (4), p.e0122802-e0122802

2015

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

Molecular biology and evolution, 2013-06, Vol.30 (6), p.1454-1464

2013

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

Nucleic acids research, 2010-01, Vol.38 (Database issue), p.D361-D365

2010

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

PloS one, 2011-04, Vol.6 (4), p.e18819-e18819

2011

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

Frontiers in microbiology, 2019-07, Vol.10, p.1764

2019

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Complete Genome Sequence of Macrococcus caseolyticus Strain JSCS5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci

Journal of Bacteriology, 2009-02, Vol.191 (4), p.1180-1190

2009

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A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology

DNA research, 2019-06, Vol.26 (3), p.217-229

2019

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A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem

PloS one, 2012-01, Vol.7 (1), p.e30559-e30559

2012

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A simple and practical workflow for genotyping of CRISPR–Cas9‐based knockout phenotypes using multiplexed amplicon sequencing

Genes to cells : devoted to molecular & cellular mechanisms, 2020-07, Vol.25 (7), p.498-509

2020

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Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

BMC microbiology, 2011-05, Vol.11 (1), p.104-104

2011

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

PloS one, 2016-08, Vol.11 (8), p.e0159419-e0159419

2016

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Artificial acceleration of mammalian cell reprogramming by bacterial proteins

Genes to cells : devoted to molecular & cellular mechanisms, 2017-10, Vol.22 (10), p.918-928

2017

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

Developmental biology, 2015-10, Vol.406 (2), p.271-282

2015

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Comparative Genomics of Physcomitrella patens Gametophytic Transcriptome and Arabidopsis thaliana: Implication for Land Plant Evolution

Proceedings of the National Academy of Sciences - PNAS, 2003-06, Vol.100 (13), p.8007-8012

2003

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

Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex

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

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

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

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

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

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

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

Molecular phylogeny of fucoxanthin‐chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity

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

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

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

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

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

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

Complete Genome Sequence of Macrococcus caseolyticus Strain JSCS5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci

A comprehensive reference transcriptome resource for the Iberian ribbed newt Pleurodeles waltl, an emerging model for developmental and regeneration biology

A deeply branching thermophilic bacterium with an ancient acetyl-CoA pathway dominates a subsurface ecosystem

A simple and practical workflow for genotyping of CRISPR–Cas9‐based knockout phenotypes using multiplexed amplicon sequencing

Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes

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

Artificial acceleration of mammalian cell reprogramming by bacterial proteins

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

Comparative Genomics of Physcomitrella patens Gametophytic Transcriptome and Arabidopsis thaliana: Implication for Land Plant Evolution

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