List of works - Hidemasa U. Bono

The transcriptional landscape of the mammalian genome

scientific article

KEGG: Kyoto Encyclopedia of Genes and Genomes

scientific article from 1999

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

scientific article (publication date: 5 December 2002)

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.

scientific article

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

Protein-protein interaction panel using mouse full-length cDNAs

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

scholarly article

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia

scientific article

Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.

scientific article published on March 1998

Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling

scientific article

Two-component response regulators from Arabidopsis thaliana contain a putative DNA-binding motif.

scientific article published in November 1998

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

scientific article published on June 2003

Gene discovery in genetically labeled single dopaminergic neurons of the retina

scholarly article

The mouse secretome: functional classification of the proteins secreted into the extracellular environment

scientific article

Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation

scientific journal article

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

scientific article published on 27 October 2016

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

scientific article

Organizing and computing metabolic pathway data in terms of binary relations.

scientific article published on January 1997

Tumour resistance in induced pluripotent stem cells derived from naked mole-rats.

scientific article

Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation

scientific article

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

scientific article (publication date: 5 February 2014)

Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure

scientific article

Analysis of the mouse transcriptome for genes involved in the function of the nervous system.

scientific article

READ: RIKEN Expression Array Database.

scientific article published on January 2002

Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG

article

Gene expression profiling in multipotent DFAT cells derived from mature adipocytes

scientific article published on 16 March 2011

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

scientific article published in June 2003

Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data.

scientific article

Development and evaluation of an automated annotation pipeline and cDNA annotation system

scientific article

Gendoo: functional profiling of gene and disease features using MeSH vocabulary.

scientific article published on 04 June 2009

Identification and functional analysis of consensus androgen response elements in human prostate cancer cells.

scientific article

Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

scientific article published on October 22, 2013

Allie: a database and a search service of abbreviations and long forms

scientific article (publication date: 2011)

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library

scientific article

G protein-coupled receptor genes in the FANTOM2 database

scientific article

Identification of key uric acid synthesis pathway in a unique mutant silkworm Bombyx mori model of Parkinson's disease

scientific article

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes.

scientific article published on January 2008

Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data

scientific article

Can the silkworm (Bombyx mori) be used as a human disease model?

scientific article

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

scientific article

Comprehensive analysis of the mouse metabolome based on the transcriptome

scientific article published on June 2003

Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice.

scientific article

HIF-1-mediated suppression of mitochondria electron transport chain function confers resistance to lidocaine-induced cell death.

scientific article

Superoxide dismutases, SOD1 and SOD2, play a distinct role in the fat body during pupation in silkworm Bombyx mori

scientific article

Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts.

scientific article

Suppression of mitochondrial oxygen metabolism mediated by the transcription factor HIF-1 alleviates propofol-induced cell toxicity

scientific article

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

scientific article

The study of metabolic pathways in tumors based on the transcriptome.

scientific article

List of works by Hidemasa U. Bono

The transcriptional landscape of the mammalian genome

KEGG: Kyoto Encyclopedia of Genes and Genomes

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Functional annotation of a full-length mouse cDNA collection

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.

Gateways to the FANTOM5 promoter level mammalian expression atlas

Protein-protein interaction panel using mouse full-length cDNAs

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia

Reconstruction of amino acid biosynthesis pathways from the complete genome sequence.

Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling

Two-component response regulators from Arabidopsis thaliana contain a putative DNA-binding motif.

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

Gene discovery in genetically labeled single dopaminergic neurons of the retina

The mouse secretome: functional classification of the proteins secreted into the extracellular environment

Id4, a new candidate gene for senile osteoporosis, acts as a molecular switch promoting osteoblast differentiation

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones.

Organizing and computing metabolic pathway data in terms of binary relations.

Tumour resistance in induced pluripotent stem cells derived from naked mole-rats.

Identification of novel PPARgamma target genes by integrated analysis of ChIP-on-chip and microarray expression data during adipocyte differentiation

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

Detection of genes with tissue-specific expression patterns using Akaike's information criterion procedure

Analysis of the mouse transcriptome for genes involved in the function of the nervous system.

READ: RIKEN Expression Array Database.

Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG

Gene expression profiling in multipotent DFAT cells derived from mature adipocytes

Continued discovery of transcriptional units expressed in cells of the mouse mononuclear phagocyte lineage

Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data.

Development and evaluation of an automated annotation pipeline and cDNA annotation system

Gendoo: functional profiling of gene and disease features using MeSH vocabulary.

Identification and functional analysis of consensus androgen response elements in human prostate cancer cells.

Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

Allie: a database and a search service of abbreviations and long forms

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library

G protein-coupled receptor genes in the FANTOM2 database

Identification of key uric acid synthesis pathway in a unique mutant silkworm Bombyx mori model of Parkinson's disease

BioCompass: a novel functional inference tool that utilizes MeSH hierarchy to analyze groups of genes.

Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data

Can the silkworm (Bombyx mori) be used as a human disease model?

RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes

Comprehensive analysis of the mouse metabolome based on the transcriptome

Gene expression profile of normal lungs predicts genetic predisposition to lung cancer in mice.

HIF-1-mediated suppression of mitochondria electron transport chain function confers resistance to lidocaine-induced cell death.

Superoxide dismutases, SOD1 and SOD2, play a distinct role in the fat body during pupation in silkworm Bombyx mori

Functional transcriptomes: comparative analysis of biological pathways and processes in eukaryotes to infer genetic networks among transcripts.

Suppression of mitochondrial oxygen metabolism mediated by the transcription factor HIF-1 alleviates propofol-induced cell toxicity

GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.

The study of metabolic pathways in tumors based on the transcriptome.