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

The Human Pangenome Project: a global resource to map genomic diversity

(2022) Ting Wang et al.   NATURE

Systematic reconstruction of cellular trajectories across mouse embryogenesis

(2022) Chengxiang Qiu et al.   NATURE GENETICS

Genetic mosaicism in the human brain: from lineage tracing to neuropsychiatric disorders

(2022) Sara Bizzotto et al.   NATURE REVIEWS NEUROSCIENCE

What is a cell type and how to define it?

(2022) Hongkui Zeng   CELL

A time-resolved, multi-symbol molecular recorder via sequential genome editing

(2022) Junhong Choi et al.   NATURE

The continuum of Drosophila embryonic development at single-cell resolution

(2022) Diego Calderon et al.   SCIENCE

Quantitative fate mapping: A general framework for analyzing progenitor state dynamics via retrospective lineage barcoding

(2022) Weixiang Fang et al.   CELL

Phylodynamics for cell biologists

(2021) T. Stadler et al.   SCIENCE

Automated methods for cell type annotation on scRNA-seq data

(2021) Giovanni Pasquini et al.   Computational and Structural Biotechnology Journal

Tracing cell-type evolution by cross-species comparison of cell atlases

(2021) Jingjing Wang et al.   Cell Reports

A single-embryo, single-cell time-resolved model for mouse gastrulation

(2021) Markus Mittnenzweig et al.   CELL

Molecular topography of an entire nervous system

(2021) Seth R. Taylor et al.   CELL

RNA velocity—current challenges and future perspectives

(2021) Volker Bergen et al.   Molecular Systems Biology

Mapping single-cell data to reference atlases by transfer learning

(2021) Mohammad Lotfollahi et al.   NATURE BIOTECHNOLOGY

Lineage tracing on transcriptional landscapes links state to fate during differentiation

(2020) Caleb Weinreb et al.   SCIENCE

Sci-fate characterizes the dynamics of gene expression in single cells

(2020) Junyue Cao et al.   NATURE BIOTECHNOLOGY

Lineage tracing meets single-cell omics: opportunities and challenges

(2020) Daniel E. Wagner et al.   NATURE REVIEWS GENETICS

The Source and Dynamics of Adult Hematopoiesis: Insights from Lineage Tracing

(2020) Joseph N. Pucella et al.   Annual Review of Cell and Developmental Biology

An in vitro model of early anteroposterior organization during human development

(2020) Naomi Moris et al.   NATURE

Alignment of Cell Lineage Trees Elucidates Genetic Programs for the Development and Evolution of Cell Types

(2020) Meng Yuan et al.   iScience

Combinatorial Action of Temporally Segregated Transcription Factors

(2020) Julien Charest et al.   DEVELOPMENTAL CELL

Common cell type nomenclature for the mammalian brain

(2020) Jeremy A Miller et al.   eLife

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Recording development with single cell dynamic lineage tracing

(2019) Aaron McKenna et al.   DEVELOPMENT

The evolving concept of cell identity in the single cell era

(2019) Samantha A. Morris   DEVELOPMENT

A periodic table of cell types

(2019) Bo Xia et al.   DEVELOPMENT

A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution

(2019) Jonathan S. Packer et al.   SCIENCE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

The dynamics of gene expression in vertebrate embryogenesis at single-cell resolution

(2018) James A. Briggs et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Emerging applications for DNA writers and molecular recorders

(2018) Fahim Farzadfard et al.   SCIENCE

What Is Your Conceptual Definition of “Cell Type” in the Context of a Mature Organism?

(2017)   Cell Systems

Revisiting Neuronal Cell Type Classification in Caenorhabditis elegans

(2016) Oliver Hobert et al.   CURRENT BIOLOGY

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Intrinsically different retinal progenitor cells produce specific types of progeny

(2014) Connie Cepko   NATURE REVIEWS NEUROSCIENCE

Quantifying the Waddington landscape and biological paths for development and differentiation

(2011) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA