List of works - Ikuo Uchiyama

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

scientific article

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

scientific article published on 01 June 2019

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

scientific article (publication date: 2012)

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

scientific article published on 23 April 2020

A system for comparative analysis of microbial genomes

scientific article published on 01 March 2003

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

scientific article

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

scientific article published on August 2005

Artificial acceleration of mammalian cell reprogramming by bacterial proteins

scientific article

BioHackathon 2015: Semantics of data for life sciences and reproducible research

scientific article published on 24 February 2020

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

scientific article (publication date: 5 February 2014)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

scientific article

Birth and death of genes linked to chromosomal inversion.

scientific article

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

scientific article

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

scientific article published on 16 March 2013

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution

scientific article

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

scientific article published on 30 June 2016

Complete Genome Sequence of Macrococcus caseolyticus Strain JCSC5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci

scientific article published in May 2009

Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1

scientific article

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

scientific article published on 12 December 2008

Construction of a dictionary of sequence motifs that characterize groups of related proteins ⬇️

scientific article published on 01 September 1992

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

scientific article

Development of new PCR primers by comparative genomics for the detection of Helicobacter suis in gastric biopsy specimens

scientific article published on 28 March 2014

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

scientific article published on 24 November 2014

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

scientific article

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

scientific article

Draft Genome Sequence of Helicobacter suis Strain SNTW101, Isolated from a Japanese Patient with Nodular Gastritis

scientific article published on 08 September 2016

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

scientific article published on 14 August 2015

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

scientific article

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

scientific article published on 06 April 2006

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

scientific article published on 21 July 2015

Genetic diversity of staphylocoagulase genes (coa): insight into the evolution of variable chromosomal virulence factors in Staphylococcus aureus

scientific article

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

scientific article published on 01 January 2005

Genome sequence and analysis of the Japanese morning glory Ipomoea nil.

scientific article

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

scientific article

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

scientific article published on 8 March 2016

Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species

scientific article

Helicobacter suis KB1 derived from pig gastric lymphoid follicles induces the formation of gastric lymphoid follicles in mice through the activation of B cells and CD4 positive cells

scientific article published on 21 March 2011

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

scientific article

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

scientific article published on 03 March 2014

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

scientific article published on 28 July 2006

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

scientific article

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes

scientific article published on 23 January 2015

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

scientific article

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

scientific article

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

scientific article

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

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

scientific article published on 29 November 2006

MBGD: microbial genome database for comparative analysis

scientific article

Molecular impact of juvenile hormone agonists on neonatal Daphnia magna.

scientific article published on 05 September 2013

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

scientific article

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

scientific article published on January 2017

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

scientific article published on 31 July 2019

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

scientific article

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

scientific article published on 18 May 2020

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

scientific article published on 29 July 2019

Ten Years of Collaborative Progress in the Quest for Orthologs

scientific article published on 2 April 2021

The Orthology Ontology: development and applications

scientific article

The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution

scientific article published on 28 May 2008

The physiological potential of anammox bacteria as revealed by their core genome structure

scientific article published on 24 December 2020

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus

scientific article

List of works by Ikuo Uchiyama

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

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

A system for comparative analysis of microbial genomes

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

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

Artificial acceleration of mammalian cell reprogramming by bacterial proteins

BioHackathon 2015: Semantics of data for life sciences and reproducible research

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

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Birth and death of genes linked to chromosomal inversion.

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

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

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution

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

Complete Genome Sequence of Macrococcus caseolyticus Strain JCSC5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci

Complete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1

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

Construction of a dictionary of sequence motifs that characterize groups of related proteins ⬇️

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

Development of new PCR primers by comparative genomics for the detection of Helicobacter suis in gastric biopsy specimens

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

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

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

Draft Genome Sequence of Helicobacter suis Strain SNTW101, Isolated from a Japanese Patient with Nodular Gastritis

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

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

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

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

Genetic diversity of staphylocoagulase genes (coa): insight into the evolution of variable chromosomal virulence factors in Staphylococcus aureus

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

Genome sequence and analysis of the Japanese morning glory Ipomoea nil.

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

Genome-wide survey of codons under diversifying selection in a highly recombining bacterial species, Helicobacter pylori

Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species

Helicobacter suis KB1 derived from pig gastric lymphoid follicles induces the formation of gastric lymphoid follicles in mice through the activation of B cells and CD4 positive cells

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

High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

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

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

Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes

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

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

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

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

MBGD: microbial genome database for comparative analysis

Molecular impact of juvenile hormone agonists on neonatal Daphnia magna.

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

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

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

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

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

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

Ten Years of Collaborative Progress in the Quest for Orthologs

The Orthology Ontology: development and applications

The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution

The physiological potential of anammox bacteria as revealed by their core genome structure

Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacillus kaustophilus

Towards the Semantic Standardization of Orthology Content ⬇️