David Kimelman

Embryo-scale single-cell chemical transcriptomics reveals dependencies between cell types and signaling pathways

The paper uses single-cell RNA-seq to study signaling pathway dependencies in zebrafish pectoral fin development, identifying new cell types and signaling relationships.

A statistical framework for inferring genetic requirements from embryo-scale single-cell sequencing experiments

This paper introduces two tools to infer genetic requirements from single-cell sequencing data of perturbed embryos, revealing new roles for transcription factors in zebrafish development.

A single-cell transcriptional timelapse of mouse embryonic development, from gastrula to pup

12.4 million single-nucleus transcriptomes from 83 staged mouse embryos (E8 to P0) yield 190 cell types, a zygote-to-pup cell-type tree, and rapid postnatal transcriptional shifts.

Proteostasis governs differential temperature sensitivity across embryonic cell types

The paper uses single-cell RNA-seq to study temperature sensitivity in zebrafish embryos, finding that notochord sheath cells are particularly vulnerable due to protein misfolding.

Deep molecular, cellular and temporal phenotyping of developmental perturbations at whole organism scale

The paper presents single cell transcriptomic data from zebrafish embryos with genetic perturbations to analyze developmental variation and cell type composition.