The main reference for citing zebrahub is:
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.
Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis
Single-objective light-sheet microscope that allows for fast, high quality imaging of large volumes. More information can be found in the instruments tab.
DaXi - high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy
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.
Ultrack: pushing the limits of cell tracking across biological scales
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.
Maximizing single cell dissociation protocol for individual zebrafish embryo
Benchmark study comparing several different RNA velocity methods, focusing on accuracy, stability, and more. Our RNA velocity can be downloaded from the data tab.
Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts