The main reference for citing zebrahub is:
Lange et al., Cell, 2024.
Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis
Multi-omic zebrafish atlas by jointly profiling single-cell RNA-seq and ATAC-seq for early developmental stages, allowing for time-resolved gene regulatory networks and in silico genetic perturbation. More information can be found in the epigenomics tab.
Kim et al., bioRxiv, 2024.
DaXi - high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy
Single-objective light-sheet microscope that allows for fast, high quality imaging of large volumes. More information can be found in the instruments tab.
Yang et al., Nat Methods, 2022.
Ultrack: pushing the limits of cell tracking across biological scales
Versatile and scalable cell-tracking method that achieves state-of-the-art performance on large developmental time-lapses of several different organisms. More information can be found in the software tab.
Bragantini et al., Nat Methods, 2025.
inTRACKtive: a web-based tool for interactive cell tracking visualization
A browser-based platform for exploring 2D and 3D cell tracking datasets, enabling users to trace lineages, share interactive views, and access the Virtual Embryo Zoo without requiring software installation or large data downloads. There is a Zebrahub inTRACKtive instance available as well.
Huijben et al., Nat Methods, 2025.
Maximizing single cell dissociation protocol for individual zebrafish embryo
Optimized protocol for isolating single cells from individual zebrafish embryos, allowing for exploration of inter-individual genetic differences and embryo-specific lineage tracing. More information can be found in the protocols tab.
VijayKumar et al., MethodsX, 2024.
Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts
Benchmark study comparing several different RNA velocity methods, focusing on accuracy, stability, and more. Our RNA velocity can be downloaded from the data tab.
Ancheta et al., bioRxiv, 2024.