Shinya Oki

Natriuretic Peptide Augmentation Attenuates Renin Cell Hyperactivation and Afferent Arteriolar Hypertrophy During Long-Term Renin-Angiotensin System Inhibition

This study shows that augmenting natriuretic peptide signaling with ARNI reduces renin cell activation and afferent arteriolar hypertrophy during RAS inhibition, preserving therapeutic benefits.

The heterochronic activation of TGF-β signaling drives the diversity of the avian sterna

The paper investigates how differences in TGF-β signaling timing between carinate and ratite embryos lead to distinct sternal morphology.

Identification of stem cell marker-positive subpopulations in the vocal fold of the larynx through transcriptomic analyses

The paper identifies stem cell marker-positive subpopulations in the mouse larynx using scRNA-seq and spatial transcriptomics, revealing new insights into laryngeal tissue composition and stem cell biology.

Uncertainty-aware transcription factor activity and perturbation inference without additional training

TFActProfiler improves TF activity inference and perturbation prediction using pre-trained TF-mRNA interactions and RNA-seq data without additional training.

Self-organized mechanochemical instabilities drive the emergence of digit tissue morphogenesis

The paper develops a limb-mesenchymal organoid system and models to show that digit-like structures form through mechanochemical instabilities involving cell adhesion, chemotaxis, and convergent-extension.

Extraction of biological terms using large language models enhances the usability of metadata in the BioSample database

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

Biallelic null variants in PNPLA8 cause microcephaly through the reduced abundance of basal radial glia

This study identifies biallelic PNPLA8 variants causing microcephaly by reducing basal radial glia in cerebral organoids and disrupting phospholipid metabolism.

Trans-ancestry genome-wide analysis of atrial fibrillation provides new insights into disease biology and enables polygenic prediction of cardioembolic risk

This paper identifies new genetic loci for atrial fibrillation through a trans-ancestry meta-analysis and develops a polygenic risk score linked to cardioembolic risk.

High resolution spatial transcriptome analysis by photo-isolation chemistry

This paper introduces PIC, a method for high-resolution spatial transcriptome analysis, and shows it detects gene expression in small regions of mouse embryos.

Paternal age affects offspring's behavior possibly via an epigenetic mechanism recruiting a transcriptional repressor REST

The paper shows that paternal age affects offspring behavior through epigenetic changes in sperm DNA methylation, leading to altered gene expression and neuronal abnormalities.

Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions

The paper integrates public ChIP-seq and DNase-seq data to identify transcription factor interactions and their association with disease risk loci in noncoding regions.

SraTailor: GUI software for visualizing high-throughput sequence read archives

SraTailor converts SRA files into BigWig format and allows graphical visualization, making SRAs accessible to biologists without command-line expertise.