Zebrafish Biomedical Research Applications

A conditional generative model to disentangle morphological variation from batch effects in model organism imaging studies

This paper introduces a conditional latent diffusion model to separate batch effects from morphological features in zebrafish imaging data, enabling accurate genotype classification.

Plug-and-Play automated behavioral tracking of zebrafish larvae with DeepLabCut and SLEAP: pre-trained networks and datasets of annotated poses

The paper provides a pre-trained pose estimation dataset and models for zebrafish larval behavior tracking using DeepLabCut and SLEAP, enabling faster and more efficient behavioral analysis.

Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations

This study identifies diencephalic and neuropeptidergic dysfunction in zebrafish with autism-risk mutations, revealing potential molecular and behavioral mechanisms.

A method for creating custom 3D-printed molds to facilitate zebrafish imaging studies, including of cardiac development.

The paper describes a method to create 3D-printed molds for reproducibly mounting zebrafish embryos for imaging studies, specifically for cardiac development.

Comprehensive 3D imaging of whole zebrafish using a water-based clearing reagent for hard tissues

This paper introduces a new clearing reagent, LUCID, enabling high-resolution 3D imaging of whole zebrafish, including dense tissues like bone and cartilage, without significant distortion or signal loss.

Multi-behavioral phenotyping in early-life-stage zebrafish for identifying disruptors of non-associative learning

The paper develops a multi-behavioral phenotyping approach in larval zebrafish to identify neurotoxic chemicals, finding chlorophene disrupts habituation via GABAARs and resembles Kv7 activator effects.

Robust statistical assessment of Oncogenotype to Organotropism translation in xenografted zebrafish

This paper develops an imaging-based assay using zebrafish larvae to assess organotropism of cancer xenografts and identifies EWSR1::FLI1 and SOX6 as plasticity factors enhancing metastatic adaptability.

Disrupted development of sensory systems and the cerebellum in a zebrafish ebf3a mutant

This study characterizes a zebrafish ebf3a mutant, revealing brain size reduction, functional impairments, and gene expression changes in sensory systems and the cerebellum.

A dual readout embryonic zebrafish xenograft model of rhabdomyosarcoma to assess clinically relevant multi-receptor tyrosine kinase inhibitors

This paper develops an embryonic zebrafish xenograft model to assess the efficacy of multi-receptor tyrosine kinase inhibitors in rhabdomyosarcoma, identifying VEGF-A as a potential biomarker for Regorafenib response.

Bona fide hematopoietic stem cells in zebrafish originate from the supra-intestinal artery

This study shows that in zebrafish, hematopoietic stem cells (HSCs) originate from the supra-intestinal artery, not the dorsal aorta, as previously thought.

Engineering precision zebrafish alleles of human disease

This paper describes the generation of zebrafish models carrying specific human disease variants using CRISPR/Cas9 and ssODNs, with methods to evaluate HDR efficiency and genotype F1 animals.

A Spinal Circuit for Hypoxia-Evoked Motor Output in Zebrafish Larvae

The paper identifies a spinal motor circuit in zebrafish larvae that mediates hypoxia-evoked pectoral fin movements by linking hypoxia detection to motor output through cholinergic spinal motor neurons.

Characterisation of transgenic lines labelling reticulospinal neurons in larval zebrafish

The paper characterizes four existing and three new transgenic lines in larval zebrafish to label reticulospinal neurons and other brainstem neurons, providing genetic access for functional studies.

High-resolution phenotypic screen in zebrafish identifies novel regulators of CNS axon diameter growth

The paper identifies 33 compounds that alter Mauthner axon diameter in zebrafish using a high-resolution imaging-based screen.

Seizure-like behavior and hyperactivity in napb knockout zebrafish as a model for autism and epilepsy

This study creates a zebrafish model of NAPB knockout to study autism and epilepsy, finding hyperactivity and hyperexcitability resembling human epileptic encephalopathy.

A Conserved Venous Remodeling Program Governs Inferior Vena Cava Formation in Zebrafish

This study identifies a conserved venous remodeling program in zebrafish that mirrors mammalian IVC formation, revealing cellular origins and molecular mechanisms of IVC development.

Automated microinjection for zebrafish xenograft models

This paper develops an automated microinjection robot for zebrafish xenograft models, achieving 60% success rate and 70% survival rate, with twice the speed of manual injections.

Tnfrsf10 Signaling is Required to Maintain the Stem Cell Niche in the Zebrafish Lateral Line

This study identifies tnfrsfa as essential for maintaining the stem cell niche in zebrafish neuromasts and supporting hair cell regeneration through NF-κB signaling and Sox2 expression.

Anatomical and Molecular Characterization of the Zebrafish Meninges

This paper characterizes the zebrafish meninges using single-cell transcriptomics, identifying a novel cell type essential for brain development.

Genetic compensation in podocalyxin-like mutants during zebrafish liver development

This study investigates the role of podxl in zebrafish liver development and finds that its loss leads to reduced HSC numbers, with compensation through upregulation of extracellular matrix genes.

The axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish

The paper identifies a new external immune organ in zebrafish, the axillary lymphoid organ, suitable for live imaging of immune cell dynamics.

Zebrafish Avatar-test predicts patient's tumor response to chemotherapy in breast cancer: a co-clinical study towards personalized medicine

The paper develops a zebrafish model to predict breast cancer patient response to chemotherapy, showing perfect correlation between patient and model treatment outcomes.

Optimistic and pessimistic cognitive judgement bias modulates the stress response and cancer progression in zebrafish

The paper shows that optimistic and pessimistic cognitive biases in zebrafish affect stress reactivity and cancer progression, with optimists showing lower tumorigenesis.

Whole-brain, all-optical interrogation of neuronal dynamics underlying gut interoception in zebrafish

The paper develops an all-optical system to study whole-brain neuronal dynamics during gut interoception in zebrafish, revealing how nutrient delivery and sensory stimuli are encoded across brain regions.

Dataset on Temperature Dependency of Zebrafish Early Development

This paper presents a dataset documenting zebrafish early development at 26°C and 28°C, showing temperature-dependent developmental milestones and suggesting revised guidelines for toxicological studies.

Social status in zebrafish modulates the behavioral response to 5-HT2C receptor agonists and antagonists

This study shows that social status in zebrafish affects their behavioral response to 5-HT2C receptor agonists and antagonists in a novel tank test.

Agarose Stamped Device: A simple but effective fixation method for Zebrafish Larvae through Customizable 3D Printed Molds for Danio rerio (Zebrafish)

The paper introduces a novel agarose stamping device for immobilizing zebrafish larvae, improving imaging and behavioral studies through reduced stress and increased throughput.

Whole-brain mapping in adult zebrafish and identification of a novel tank test functional connectome

The paper develops a pipeline for whole-brain activity mapping in adult zebrafish and identifies a novel functional connectome during the novel tank test.

Transient Vascular Occlusions in a Zebrafish Model of Tuberculous Meningitis

This study uses a zebrafish model to show mycobacteria cause transient vascular occlusions and ischemia during early brain infection, establishing a model for TBM vascular complications.

Leveraging zebrafish embryo phenotypic observations to advance data-driven analyses in toxicology

A structured zebrafish embryo toxicity database (INTOB, 638 experiments) enabled control-quality tests, dose-response modeling and phenotype-fingerprint clustering of 47 substances (133 experiments); literature data proved unsuitable for meta-analysis.