Kyle Awayan

gene2fish arranges 53,595 Thisse in situ hybridization images of 8,263 zebrafish genes into a gene-by-stage grid, with anatomy-term search for validating scRNA-seq markers.

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

inTRACKtive provides a web-based tool for interactive visualization and sharing of large 3D cell tracking datasets without requiring software installation or data downloads.

The paper presents Zebrahub-Multiome, a single-cell multiomic atlas of zebrafish embryogenesis, revealing gene regulatory network dynamics and cis-regulatory elements across developmental stages.

Zebrafish embryos sequenced individually across ten developmental stages, paired with light-sheet lineage reconstruction, form an atlas and browser for in silico fate mapping.

The paper compares MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing in mouse liver and kidney, finding MERFISH provides comparable results and robust cell type identification without needing integration with scRNA-seq atlases.

Portal integrates large-scale single-cell datasets efficiently and accurately by preserving biological variation across samples, platforms, and species.

The paper creates an organism-wide hormone signaling atlas in mouse lemurs, identifying hormone-producing and -target cells and revealing species-specific rewiring and conservation compared to humans and mice.