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List of works by Hidemasa U. Bono

A chromosome-level genome sequence of Chrysanthemum seticuspe, a model species for hexaploid cultivated chrysanthemum

scientific article published on 07 October 2021

All of gene expression (AOE): An integrated index for public gene expression databases

scientific article published on 24 January 2020

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

scientific article (publication date: 2011)

Analysis of molecular mechanism for acceleration of polyembryony using gene functional annotation pipeline in Copidosoma floridanum

scientific article published on 11 February 2020

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

scientific article (publication date: 5 December 2002)

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

scientific article

Apoptosis-mediated vasa down-regulation controls developmental transformation in Japanese Copidosoma floridanum female soldiers

scientific article published on 19 September 2019

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

scientific article published on January 2008

BioHackJP 2023 Report R3: Expand the pathway analysis environment to non-model organisms

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

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

scientific article

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

scientific article

Cancerous phenotypes associated with hypoxia-inducible factors are not influenced by the volatile anesthetic isoflurane in renal cell carcinoma

scientific article published on 15 April 2019

Characterization of brown adipose tissue thermogenesis in the naked mole-rat (Heterocephalus glaber), a heterothermic mammal

scientific article published on 10 November 2020

Cigarette Smoke Extract Activates Hypoxia-Inducible Factors in a Reactive Oxygen Species-Dependent Manner in Stroma Cells from Human Endometrium

scientific article published on 03 January 2021

Comparative analysis of seven types of superoxide dismutases for their ability to respond to oxidative stress in Bombyx mori

scientific article published on 18 February 2019

Comparison of Oxidative and Hypoxic Stress Responsive Genes from Meta-Analysis of Public Transcriptomes

scientific article published in 2021

Comprehensive analysis of the mouse metabolome based on the transcriptome

scientific article published on June 2003

Construction of a simple evaluation system for the intestinal absorption of an orally administered medicine using Bombyx mori larvae

scientific article published in January 2018

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

scientific article published in June 2003

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

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

scientific article

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

scientific article

Differentiated embryo chondrocyte plays a crucial role in DNA damage response via transcriptional regulation under hypoxic conditions.

scientific article published on 21 February 2018

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

scientific article

Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive

scientific article

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

scientific article

FANTOM enters 20th year: expansion of transcriptomic atlases and functional annotation of non-coding RNAs

scientific article published on 19 November 2020

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

scientific article published on 26 January 2021

Functional annotation of a full-length mouse cDNA collection

scientific article (publication date: 8 February 2001)

Functional annotation of human long noncoding RNAs via molecular phenotyping

scientific article published on 27 July 2020

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

scientific article

G protein-coupled receptor genes in the FANTOM2 database

scientific article

GEM: Genome Editing Meta-database, a dataset of genome editing related metadata systematically extracted from PubMed literatures

scientific article published in 2023

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

scientific article

GLIS1, a novel hypoxia-inducible transcription factor, promotes breast cancer cell motility via activation of WNT5A

scientific article published on 12 February 2020

Gateways to the FANTOM5 promoter level mammalian expression atlas

scientific article

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

scientific article published on 04 June 2009

Gene discovery in genetically labeled single dopaminergic neurons of the retina

scholarly article

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

scientific article

Gene expression profiling in multipotent DFAT cells derived from mature adipocytes

scientific article published on 16 March 2011

Genome-scale Gene Expression Analysis and Pathway Reconstruction in KEGG

article

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

scientific article

Human disease genes and their cloned mouse orthologs: exploration of the FANTOM2 cDNA sequence data set

scientific article

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

scientific journal article

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

scientific article

Identification of functional enolase genes of the silkworm Bombyx mori from public databases with a combination of dry and wet bench processes.

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

KEGG: Kyoto Encyclopedia of Genes and Genomes

scientific article from 1999

Meta-Analysis of Hypoxic Transcriptomes from Public Databases

scientific article published on 09 January 2020

Meta-Analysis of Oxidative Transcriptomes in Insects

scientific article published in 2021

Meta-Analysis of RNA Sequencing Data of Arabidopsis and Rice under Hypoxia ⬇️

scientific article published on 19 July 2022

Meta-Analysis of Transcriptomes in Insects Showing Density-Dependent Polyphenism

scientific article published in 2022

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

scientific article published on January 1997

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

scientific article

Promotion of malignant phenotype after disruption of the three-dimensional structure of cultured spheroids from colorectal cancer.

scientific article published on 23 March 2018

Protein-protein interaction panel using mouse full-length cDNAs

scientific article

READ: RIKEN Expression Array Database.

scientific article published on January 2002

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

scientific article published on March 1998

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

scientific article

Resistance to chemical carcinogenesis induction via a dampened inflammatory response in naked mole-rats

scientific article published on 30 March 2022

Revealing Landscapes of Transposable Elements in Apis Species by Meta-Analysis

scientific article published in 2022

SayaMatcher: genome scale organization and systematic analysis of nuclear receptor response elements

scientific article published on 24 August 2005

Superoxide dismutase down-regulation and the oxidative stress is required to initiate pupation in Bombyx mori

scientific article published on 11 October 2019

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

scientific article

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

scientific article

Systematic Functional Annotation Workflow for Insects

scientific article published in 2022

Systematic Prediction of Orthologous Units of Genes in the Complete Genomes

scientific article published on 01 January 1998

Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays

scientific article published on June 2003

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

scientific article

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

scientific article

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

scientific article

The transcriptional landscape of the mammalian genome

scientific article

Thyroid hormone facilitates in vitro decidualization of human endometrial stromal cells via thyroid hormone receptors

scientific article published on 03 April 2020

TogoEx: the integration of gene expression data

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

scientific article

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV

scientific article

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

scientific article published in November 1998

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

scientific article published on 27 October 2016

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