Systematic identification of cell-fate regulatory programs using a single-cell atlas of mouse development

L Fei, H Chen, L Ma, WE, R Wang, X Fang, Z Zhou… - Nature Genetics, 2022 - nature.com
Waddington's epigenetic landscape is a metaphor frequently used to illustrate cell
differentiation. Recent advances in single-cell genomics are altering our understanding of …

[PDF][PDF] Single-cell landscape of transcriptional heterogeneity and cell fate decisions during mouse early gastrulation

H Mohammed, I Hernando-Herraez, A Savino… - Cell reports, 2017 - cell.com
The mouse inner cell mass (ICM) segregates into the epiblast and primitive endoderm (PrE)
lineages coincident with implantation of the embryo. The epiblast subsequently undergoes …

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination

F Wu, RQ Su, YC Lai, X Wang - Elife, 2017 - elifesciences.org
The process of cell fate determination has been depicted intuitively as cells travelling and
resting on a rugged landscape, which has been probed by various theoretical studies …

Systematic reconstruction of cellular trajectories across mouse embryogenesis

C Qiu, J Cao, BK Martin, T Li, IC Welsh, S Srivatsan… - Nature …, 2022 - nature.com
Mammalian embryogenesis is characterized by rapid cellular proliferation and
diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells …

An atlas of rabbit development as a model for single-cell comparative genomics

MLN Ton, D Keitley, B Theeuwes, C Guibentif… - Nature Cell …, 2023 - nature.com
Traditionally, the mouse has been the favoured vertebrate model for biomedical research,
due to its experimental and genetic tractability. However, non-rodent embryological studies …

A deterministic map of Waddington's epigenetic landscape for cell fate specification

S Bhattacharya, Q Zhang, ME Andersen - BMC systems biology, 2011 - Springer
Background The image of the" epigenetic landscape", with a series of branching valleys and
ridges depicting stable cellular states and the barriers between those states, has been a …

Systems-level dynamic analyses of fate change in murine embryonic stem cells

R Lu, F Markowetz, RD Unwin, JT Leek, EM Airoldi… - Nature, 2009 - nature.com
Molecular regulation of embryonic stem cell (ESC) fate involves a coordinated interaction
between epigenetic,,,, transcriptional,,,,, and translational, mechanisms. It is unclear how …

Deep learning of cross-species single-cell landscapes identifies conserved regulatory programs underlying cell types

J Li, J Wang, P Zhang, R Wang, Y Mei, Z Sun, L Fei… - Nature Genetics, 2022 - nature.com
Despite extensive efforts to generate and analyze reference genomes, genetic models to
predict gene regulation and cell fate decisions are lacking for most species. Here, we …

Parallel evolution of male germline epigenetic poising and somatic development in animals

BJ Lesch, SJ Silber, JR McCarrey, DC Page - Nature genetics, 2016 - nature.com
Abstract Changes in gene regulation frequently underlie changes in morphology during
evolution, and differences in chromatin state have been linked with changes in anatomical …

The single-cell transcriptional landscape of mammalian organogenesis

J Cao, M Spielmann, X Qiu, X Huang, DM Ibrahim… - Nature, 2019 - nature.com
Mammalian organogenesis is a remarkable process. Within a short timeframe, the cells of
the three germ layers transform into an embryo that includes most of the major internal and …