HopLand: single-cell pseudotime recovery using continuous Hopfield network-based modeling of Waddington's epigenetic landscape

J Guo, J Zheng - Bioinformatics, 2017 - academic.oup.com
… It reveals from the single-cell data the combinatorial regulatory interactions among … from
single-cell gene expression data by mapping cells to the Waddington’s epigenetic landscape. By …

Quantifying Waddington's epigenetic landscape: a comparison of single-cell potency measures

J Shi, AE Teschendorff, W Chen… - Briefings in …, 2020 - academic.oup.com
… In summary, by performing a comprehensive analysis over 11 … robust single-cell potency
measures, revealing that their robustness is driven by a correlation between mRNA expression

Universality of cell differentiation trajectories revealed by a reconstruction of transcriptional uncertainty landscapes from single-cell transcriptomic data

NP Gao, O Gandrillon, A Páldi, U Herbach, R Gunawan - bioRxiv, 2020 - biorxiv.org
… on single-cell transcriptomic data that conforms with the Waddington’s epigenetic landscape
… studies reconstructed the epigenetic landscape from single-cell gene expression data using …

Transition states and cell fate decisions in epigenetic landscapes

N Moris, C Pina, AM Arias - Nature Reviews Genetics, 2016 - nature.com
epigenetic landscape and genetic programmes in the light of recent advances in genomics
and, specifically, single-cell … does not only lie in their potential to reveal structures within …

Mathematical modeling and simulation of stem cell differentiation and reprogramming by Waddington's epigenetic landscape

J Guo - 2018 - dr.ntu.edu.sg
… Dynamical systems modeling has revealed the complexity of the regulation of … genes
constitute a kinetic model which can be calibrated by learning from single-cell gene expression data

Distance covariance entropy reveals primed states and bifurcation dynamics in single-cell RNA-Seq data

Q Luo, AK Maity, AE Teschendorff - Iscience, 2022 - cell.com
… In summary, by studying the dynamic changes of expression covariation entropy, DICE can
… primed states and bifurcation dynamics without the need for single-cell epigenomic data. …

[HTML][HTML] Noise distorts the epigenetic landscape and shapes cell-fate decisions

MA Coomer, L Ham, MPH Stumpf - Cell Systems, 2022 - cell.com
Summary The Waddington epigenetic landscape has become an iconic representation of …
Recent single-cell transcriptomic data provide new opportunities for quantifying this originally …

Shaping the epigenetic landscape: Complexities and consequences

MA Coomer, L Ham, MPH Stumpf - bioRxiv, 2020 - biorxiv.org
… Recent single-cell transcriptomic data provide new … , which shows the fixed points of the
deterministic landscape U(x) … not be amenable to the bifurcation analysis presented above. The …

[HTML][HTML] Single-cell transcriptional uncertainty landscape of cell differentiation

NP Gao, O Gandrillon, A Páldi, U Herbach… - …, 2023 - ncbi.nlm.nih.gov
… Although the epigenetic landscape was originally proposed only as … epigenetic landscape
the valley naturally widens around the branching point in the cell lineage, our analysis shows

Reprogramming, oscillations and transdifferentiation in epigenetic landscapes

B Kaity, R Sarkar, B Chakrabarti, MK Mitra - Scientific reports, 2018 - nature.com
epigenetic landscape which represent the two differentiated states. A comprehensive phase
space and bifurcation analysis … Since the bifurcation diagram shows two distinct dynamical …