Alexander van Oudenaarden

Sharq preprocesses single cell RNA-seq data from fastq files to gene expression tables, addressing amplification biases and providing quality control diagnostics.

The paper traces neuromesodermal progenitors in zebrafish embryos to show they contribute to spinal cord and mesoderm with distinct growth dynamics across species.

The paper proposes the Human Cell Atlas project to catalog all human cell types through molecular profiling and connects this data with classical cellular descriptions.

scartrace uses Cas9-induced genetic scars for clonal analysis in zebrafish, aiming at lineage reconstruction across many cells at once rather than the small subsets imaging covers.