Cell type evolution reconstruction across species through cell phylogenies of single-cell RNA sequencing data

JL Mah, CW Dunn - Nature Ecology & Evolution, 2024 - nature.com
The origin and evolution of cell types has emerged as a key topic in evolutionary biology.
Driven by rapidly accumulating single-cell datasets, recent attempts to infer cell type …

ALES: cell lineage analysis and mapping of developmental events

V Braun, RBR Azevedo, M Gumbel, PM Agapow… - …, 2003 - academic.oup.com
Motivation: Animals build their bodies by altering the fates of cells. The way in which they do
so is reflected in the topology of cell lineages and the fates of terminal cells. Cell lineages …

[PDF][PDF] Next-generation lineage tracing and fate mapping to interrogate development

S VanHorn, SA Morris - Developmental cell, 2021 - cell.com
Lineage tracing and fate mapping, overlapping yet distinct disciplines to follow cells and
their progeny, have evolved rapidly over the last century. Lineage tracing aims to identify all …

Quantitative fate mapping: reconstructing progenitor field dynamics via retrospective lineage barcoding

W Fang, CM Bell, A Sapirstein, S Asami, K Leeper… - bioRxiv, 2022 - biorxiv.org
Natural and induced somatic mutations that accumulate in the genome during development
record the phylogenetic relationships of cells; however, whether these lineage barcodes can …

[PDF][PDF] Single-cell multi-omics and lineage tracing to dissect cell fate decision-making

L Haghverdi, LS Ludwig - Stem Cell Reports, 2023 - cell.com
The concept of cell fate relates to the future identity of a cell, and its daughters, which is
obtained via cell differentiation and division. Understanding, predicting, and manipulating …

Different lineage contexts direct common pro-neural factors to specify distinct retinal cell subtypes

M Wang, L Du, AC Lee, Y Li, H Qin, J He - Journal of Cell Biology, 2020 - rupress.org
How astounding neuronal diversity arises from variable cell lineages in vertebrates remains
mostly elusive. By in vivo lineage tracing of∼ 1,000 single zebrafish retinal progenitors, we …

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

JA Briggs, C Weinreb, DE Wagner, S Megason… - Science, 2018 - science.org
INTRODUCTION Metazoan development represents a big jump in complexity compared
with unicellular life in two aspects: cell-type differentiation and cell spatial organization. In …

[PDF][PDF] The independent probabilistic firing of transcription factors: a paradigm for clonal variability in the zebrafish retina

H Boije, S Rulands, S Dudczig, BD Simons… - Developmental cell, 2015 - cell.com
Early retinal progenitor cells (RPCs) in vertebrates produce lineages that vary greatly both in
terms of cell number and fate composition, yet how this variability is achieved remains …

A novel view on stem cell development: analysing the shape of cellular genealogies

I Glauche, R Lorenz, D Hasenclever… - Cell …, 2009 - Wiley Online Library
Objectives: The analysis of individual cell fates within a population of stem and progenitor
cells is still a major experimental challenge in stem cell biology. However, new monitoring …

Deciphering cell fate decision by integrated single-cell sequencing analysis

Sagar, D Grün - Annual review of biomedical data science, 2020 - annualreviews.org
Cellular differentiation is a common underlying feature of all multicellular organisms through
which naïve cells progressively become fate restricted and develop into mature cells with …