A reference cell tree will serve science better than a reference cell atlas

Cell. 2023 Mar 16;186(6):1103-1114. doi: 10.1016/j.cell.2023.02.016.


Single-cell biology is facing a crisis of sorts. Vast numbers of single-cell molecular profiles are being generated, clustered and annotated. However, this is overwhelmingly ad hoc, and we continue to lack a principled, unified, and well-moored system for defining, naming, and organizing cell types. In this perspective, we argue against an atlas or periodic table-like discretization as the right metaphor for a reference taxonomy of cell types. In its place, we advocate for a data-driven, tree-based nomenclature that is rooted in a "consensus ontogeny" spanning the life cycle of a given species. We explore how such a reference cell tree, inclusive of both lineage histories and molecular states, could be constructed, represented, and segmented in practice. Analogous to the taxonomic classification of species, a consensus ontogeny would provide a universal, stable, and extendable framework for precise scientific communication, both contemporaneously and across the ages.

Publication types

  • Review

MeSH terms

  • Communication
  • Cytology*
  • Life Cycle Stages
  • Phylogeny
  • Single-Cell Analysis