Joachim Wittbrodt

The paper investigates how temperature cycles affect medaka embryonic development, revealing temperature-insensitive spatial patterns that compensate for temperature-sensitive temporal oscillations.

The paper investigates how morphogen gradients remain robust under temperature-induced changes in developmental tempo in medaka embryos, finding that reaction kinetics, not diffusion, drive this robustness.

The paper shows microglia phagocytose medaka retinal stem cells under homeostasis, but Ccl25b-Ccr9a signaling is not essential for their maintenance.

The paper introduces faster variants of the Caprola tool for calcium-dependent fluorescent labeling, enabling more sensitive and efficient recording of neuronal activity in zebrafish.

The paper maps heterochrony in zebrafish and medaka using single-cell genomics, revealing cell-level timing shifts that contribute to species-specific phenotypes.

This study shows that extrinsic polarity cues determine whether retinal organoids develop a laminated epithelium or cluster-based organization, revealing plasticity in vertebrate retinal development.

This paper uses deep learning to predict tissue outcomes in retinal organoids before they are visually discernible, improving understanding of developmental trajectories.

This paper introduces a high-throughput optomotor response platform for analyzing vision in medaka and zebrafish, finding that albino medaka show heightened sensitivity to visual stimuli.

The paper establishes an auxin-inducible system to acutely knock down Pmm2 protein in medaka, mimicking hypomorphic mutations seen in PMM2-CDG patients.

The paper uses Nanopore duplex sequencing to analyze 5hmC and 5mC distribution in medaka brain DNA, revealing strand-specific patterns in CpG dinucleotides.

The paper develops a behavioral assay and uses a Hidden Markov Model to analyze bold-shy behaviors in medaka fish, identifying direct and social genetic effects on behavior.

The paper maps and validates key genetic loci influencing heart rate and function in fish, identifying potential targets for cardiac disease treatment.

The paper uses medaka fish to study genetic and environmental interactions in heart rate, identifying QTLs and validating genes, while showing limitations of GWAS in capturing complex genetic effects.

This study generates fish ocular organoids with lens and retina, showing lens forms via an 'inside-out' process instead of the in vivo 'outside-in' mode.

FEHAT automatically detects heart rates in Medaka fish embryos from high-resolution videos, showing reliable performance across temperature perturbations.

This paper introduces DNA microbeads to control morphogen release in organoids, enabling spatio-temporal regulation of development and improving tissue mimicry.

This study shows that spatial and temporal control of axis segmentation in medaka fish are dissociable modules, identified through devQTL mapping and CRISPR validation.

This paper develops a multimodal approach combining X-ray computed tomography and light-sheet fluorescence microscopy to visualize gene expression in 3D tissue context, applicable to in vitro models and model organisms.

This study develops a high-throughput optomotor response assay in medaka larvae to quantify visual traits and detect strain-specific differences.

The paper presents a platform for minimal-invasive 3D laser printing of microimplants in vivo using synthetic polymer inks, demonstrating biological responses in teleost fish and fruit fly embryos.

This paper develops a 2-photon printing method to create 3D microstructures for mechanically stimulating multicellular systems, showing cells change morphology under cyclic stretch.

The paper develops a multi-species brain atlas platform for comparative neuroscience in teleost fish, revealing species-specific neural structures and enabling gene expression and activity comparisons.

The paper evaluates genotype imputation in F2 crosses of inbred medaka lines, finding that imputation performance plateaus with increased sequencing coverage and develops a computational pipeline for cost-benefit analysis.

This paper introduces an approach called 'inception' that allows base editing at previously inaccessible sites by generating new PAM sequences through sequential combinatorial base editing.

This study demonstrates that 5-biotinylation of donor DNA enhances single-copy HDR in mice, achieving 19-26% efficiency in generating conditional alleles.

The paper identifies Zic1's role in epaxial myotome morphogenesis by regulating Wnt11r to guide dorsal movement and neural tube coverage.

The paper develops a base editing framework in medaka and zebrafish to functionally validate SNVs, demonstrating its application in recreating cardiac phenotypes and validating candidate genes for congenital heart disease.

The paper introduces hei-tag, a tag that enhances CRISPR/Cas9 and base editor efficiency across multiple species and applications.

The paper introduces the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel, a vertebrate genetic resource for genotype-to-phenotype studies, enabling controlled experiments on complex traits.

The paper analyzes genomic and epigenomic variation in the MIKK panel using long-read sequencing and pan-genome graphs, revealing novel structural variants and methylation patterns.