zebrafish

The paper investigates how B chromosomes in maize affect chromatin accessibility and gene expression in pollen nuclei using ATAC-seq and RNA-seq.

This study shows that combining apple pectin and cellulose in zebrafish diets leads to non-additive gut microbiome changes and lasting intestinal barrier effects.

The paper introduces LADD to measure lineage path deviations from inferred developmental dynamics in single-cell RNA-seq data and finds lineages move faster than optimal paths.

This study identifies the endothelial protein C receptor (EPCR) as the entry receptor for Langya virus and reveals the molecular basis of its interaction with the viral attachment glycoprotein.

The paper investigates plumage diversity in Capuchino Seedeaters by analyzing gene expression and variants, finding that pigmentation differences arise from regulatory changes rather than differential gene expression.

The paper identifies a novel epithelial cell type in zebrafish fins, spike cells, and shows their role in maintaining immune cell niche homeostasis through interactions with mpeg1+ immune cells.

This study characterizes the MHC genomic architecture in the Midas cichlid using integrated genomic and transcriptomic analyses, revealing gene diversity, evolutionary patterns, and tissue-specific expression.

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

This study maps genome-wide chromatin accessibility in A. calliptera embryos across three stages, revealing dynamic changes in regulatory elements and transcription factor activity during early development.

This study examines parallel evolution of nuclear OXPHOS genes in threespine stickleback across freshwater populations and identifies mitonuclear evolutionary coupling in specific functional modules.

The paper shows that basal ganglia output in zebrafish destabilizes neural activity states to guide decision-making in a Go/No-go task.

This study identifies DPYD's role in sleep regulation through glial lipid metabolism and myelination across species, linking genetic variants to oligodendrocyte-specific control.

This study shows UCS in zebrafish alters exploratory behavior patterns, with method-dependent identification of resilient-like archetypes.

The paper investigates gene-gene interactions in Duchenne muscular dystrophy using human and zebrafish data, finding interaction effects for six gene pairs and rescue of muscle organization in zebrafish for MAN1A1 and ACTN3.

The paper identifies MIRINE, a small ORF-encoded polypeptide that promotes neuronal differentiation in vertebrate brain development by regulating the balance between proliferation and maturation.

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

This study identifies a conserved Foxp1-Pde4d regulatory axis that preserves inflammatory responsiveness by controlling cAMP signaling across vertebrate species.

This study examines how different dietary fibre regimes affect the gut microbiome, SCFA profiles, and immune responses in zebrafish, showing context-specific effects influenced by sex and dietary context.

This study identifies SVEP1 as a mediator of ANG2-TIE1 binding, leading to TIE1 phosphorylation and downstream signaling in lymphatic endothelial cells.

The paper investigates how inflammation alters cell type-specific glucocorticoid responsiveness through single-cell RNA sequencing in zebrafish.

Zebrafish larva infection experiments plus pharmacokinetic-pharmacodynamic (PKPD) modelling gave bedaquiline's in vivo Emax and EC50 against M. marinum in about 2 months; waterborne clarithromycin barely entered larvae.

Region-stratified scRNA-seq of 607,370 cells plus 500-gene MERFISH maps adult Danionella cerebrum cell types body-wide, revealing fibroblast Hox and limb-identity programs and telencephalon regeneration dynamics.

This study uses drift-diffusion modeling on larval zebrafish to show that evidence integration dynamics develop during early stages and are altered by disease-linked mutations.

The paper compares saccadic suppression strength between macaques and zebrafish, showing it reflects differences in sensory and motor noise levels and computational resource allocation.

This study identifies a conserved post-embryonic gene network in teleost fish that is responsive to thyroid hormone and ecological variation, showing how it evolves through gene copy number changes.

This study quantifies spatial asymmetry in zebrafish pectoral fin regeneration, revealing differential gene expression and signaling dynamics between anterior and posterior regions.

The paper identifies 61,243 phenologs between human diseases and model organism phenotypes, using a hypergeometric method to rank candidate genes and validate their predictive power.

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

This study identifies DHX30 as an R-loop helicase that resolves RNA:DNA hybrids, prevents replication stress, and maintains genome stability in human and zebrafish cells.