Hidemasa U. Bono

tWhEEL quantifies CRISPR knockout feasibility by integrating transcriptome data with guide RNA design and functional annotations to prioritize tractable biological functions and organisms.

The paper presents a high-quality genome assembly of Ascogaster reticulata, providing a reference for comparative studies and evolutionary research in Braconidae wasps.

This study uses transcriptome data to analyze hybridization dynamics and genetic structure in Japanese and Chinese giant salamanders, identifying hybrid groups and genetic contributions.

The paper identifies transcriptional start sites and candidate enhancers regulating worker metamorphosis in honeybees using CAGE, revealing lineage-specific regulatory relationships.

The paper evaluates open-weight large language models for screening RNA-seq metadata in public databases, finding they significantly improve classification performance over keyword searches.

The paper identifies a miR-3260 mutation in the loop structure of Bombyx mori and shows it does not affect dicing activity or phenotypic outcomes.

This study generates a new genome assembly for Japanese-reared naked mole rats, identifies novel gene models and genomic variations, and provides functional annotations.

This study develops a fungal-specific functional annotation workflow for RNA-seq data, achieving high annotation accuracy and applicability to Iso-Seq data without requiring reference genomes.

The paper functionally annotates heat stress-responsive genes in rice by integrating transcriptome data with structural information from AlphaFold, identifying genes related to metal homeostasis.

This study uses CRISPR-Cas9 to edit the F3H gene in Perilla, resulting in green plants with increased luteolin accumulation and reduced anthocyanin production.

The paper presents a high-quality genome assembly and functional annotation of Hiroshima-derived Pacific oyster Magallana gigas, providing a genomic resource for studying genetic diversity and environmental adaptations.

The paper investigates how the metabolic system of Papilio memnon larvae transforms host plant components into bioactive substances, identifying two chlorophyll catabolites with anti-cancer and anti-amyloid properties.

This study analyzes gene expression changes in domesticated and wild relatives of rice, tomato, and soybean to understand domestication effects on stress tolerance and other traits.

PtWAVE improves detection of large indels in genome editing by extending deconvolution range and enhancing accuracy and sensitivity.

The paper develops PiCTURE and machine learning models to predict RNA off-target effects of CRISPR base editors in tissue-specific transcriptomes, finding higher risks in colon and lungs compared to brain and ovaries.

This study develops a data-driven workflow for gene expression analysis in complex microbiomes using metagenomic and metatranscriptomic data, showing metagenomic contigs are better than conventional references.

The paper develops a method to extract genome editing information using large language models and applies it to prioritize genes for future research.

This study performs a meta-analysis of RNA-Seq data from Oryza sativa under drought and salt stress to identify stress-responsive genes and compare them with Arabidopsis thaliana.

This paper evaluates using large language models to extract biological terms from BioSample metadata, improving data findability and reusability.

The paper constructs comprehensive expression datasets for two honey bee species, Apis mellifera and Apis cerana japonica, using RNA-Seq data and reference transcript sequences.

This study identifies gene mutations associated with pyrethroid resistance in bed bugs by comparing genomes of resistant and susceptible strains.

The paper develops Triterpene RDF, a manually curated database of plant enzymes and transcription factors involved in triterpene biosynthesis, to improve functional annotation of genomes and transcriptomes.

The paper identifies two unexploited genes related to oxidative stress in Parkinson's disease using a pipeline to address missing data in disease-associated gene databases.

The paper identifies gene expression changes associated with domestication by comparing pigs, chickens, wild boars, and red junglefowl using RNA-seq data and meta-analysis.

The paper reports the long-read genome assembly of the Japanese strain of Copidosoma floridanum, identifying genomic differences between Japanese and US strains that may underlie caste determination.

The paper provides time-course transcriptome data of silk glands in Bombyx mori larvae from day 0 to 7, supporting molecular biology and genetic research.

This study uses transcriptome analysis to show SNPiP enhances cardiogenesis-related pathways and improves cardiac function in mice.

The paper improves the genome assembly of the Japanese honey bee using homology-based methods and nanopore long-reads, resulting in a more contiguous and complete genome.

The paper performs a meta-analysis of heat-stressed transcriptomes from human and mouse samples to identify common upregulated and downregulated genes.

DANGER analysis assesses on/off-target effects of CRISPR editing using RNA-seq data without a reference genome, identifying deleterious off-target sites and quantifying their phenotypic impact.