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

S Domcke, J Shendure - Cell, 2023 - cell.com
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 …

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

CE Hinchliff, SA Smith, JF Allman… - Proceedings of the …, 2015 - National Acad Sciences
Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a
grand challenge. The paucity of homologous character data across disparately related …

Phylodynamics for cell biologists

T Stadler, OG Pybus, MPH Stumpf - Science, 2021 - science.org
BACKGROUND The birth, death, and diversification of individuals are events that drive
biological processes across all scales. This is true whether the individuals in question …

Supervised classification enables rapid annotation of cell atlases

HA Pliner, J Shendure, C Trapnell - Nature methods, 2019 - nature.com
Single-cell molecular profiling technologies are gaining rapid traction, but the manual
process by which resulting cell types are typically annotated is labor intensive and rate …

A periodic table of cell types

B Xia, I Yanai - Development, 2019 - journals.biologists.com
Single cell biology is currently revolutionizing developmental and evolutionary biology,
revealing new cell types and states in an impressive range of biological systems. With the …

Broadly sampled multigene analyses yield a well-resolved eukaryotic tree of life

LW Parfrey, J Grant, YI Tekle… - Systematic …, 2010 - academic.oup.com
An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations
underlying the diversity of microbial and macroscopic (eg, plants and animals) eukaryotes …

[HTML][HTML] Evolutionary informatics: unifying knowledge about the diversity of life

CS Parr, R Guralnick, N Cellinese… - Trends in ecology & …, 2012 - cell.com
The accelerating growth of data and knowledge in evolutionary biology is indisputable.
Despite this rapid progress, information remains scattered, poorly documented and in …

Tree thinking for all biology: the problem with reading phylogenies as ladders of progress

KE Omland, LG Cook, MD Crisp - BioEssays, 2008 - Wiley Online Library
Phylogenies are increasingly prominent across all of biology, especially as DNA sequencing
makes more and more trees available. However, their utility is compromised by widespread …

Common cell type nomenclature for the mammalian brain

JA Miller, NW Gouwens, B Tasic, F Collman… - Elife, 2020 - elifesciences.org
The advancement of single-cell RNA-sequencing technologies has led to an explosion of
cell type definitions across multiple organs and organisms. While standards for data and …

The origin and evolution of model organisms

SB Hedges - Nature Reviews Genetics, 2002 - nature.com
The phylogeny and timescale of life are becoming better understood as the analysis of
genomic data from model organisms continues to grow. As a result, discoveries are being …