ArticleDevelopment (Cambridge, England)2023
A dynamical systems treatment of transcriptomic trajectories in hematopoiesis.
Article in Development (Cambridge, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation.bioRxiv : the preprint server for biology · 2026Article
- Unifying theories in high-dimensional biophysics: approaches, challenges and opportunities.NPJ systems biology and applications · 2026Article
- Identification of Distinct Topological Structures From High-Dimensional Data.bioRxiv : the preprint server for biology · 2025Article
- FatePredictor: Cell fate decision-making prediction with an ensemble deep learning model.Innovation (Cambridge (Mass.)) · 2025Article
- Quantifying Landscape and Flux from Single-Cell Omics: Unraveling the Physical Mechanisms of Cell Function.JACS Au · 2025Review
- Fluctuation structure predicts genome-wide perturbation outcomes.Research square · 2025Article
- Dynamical systems theory as an organizing principle for single-cell biology.NPJ systems biology and applications · 2025Review
- Fluctuation structure predicts genome-wide perturbation outcomes.bioRxiv : the preprint server for biology · 2025Article
- Discovering governing equations of biological systems through representation learning and sparse model discovery.NAR genomics and bioinformatics · 2025Article
- Fokker-Planck diffusion maps of microglial transcriptomes reveal radial differentiation into substates associated with Alzheimer's pathology.Communications biology · 2025Article
- A statistical approach for systematic identification of transition cells from scRNA-seq data.Cell reports methods · 2024Article
- FateNet: an integration of dynamical systems and deep learning for cell fate prediction.Bioinformatics (Oxford, England) · 2024Article
- Fokker-Planck diffusion maps of multiple single cell microglial transcriptomes reveals radial differentiation into substates associated with Alzheimer's pathology.bioRxiv : the preprint server for biology · 2024Article
- Edge-based relative entropy as a sensitive indicator of critical transitions in biological systems.Journal of translational medicine · 2024Article
- Review
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Authors and funding
4 authors.
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Abstract
Inspired by Waddington's illustration of an epigenetic landscape, cell-fate transitions have been envisioned as bifurcating dynamical systems, wherein exogenous signaling dynamics couple to the enormously complex signaling and transcriptional machinery of a cell to elicit qualitative transitions in its collective state. Single-cell RNA sequencing (scRNA-seq), which measures the distributions of possible transcriptional states in large populations of differentiating cells, provides an alternate view, in which development is marked by the variations of a myriad of genes. Here, we present a mathematical formalism for rigorously evaluating, from a dynamical systems perspective, whether scRNA-seq trajectories display statistical signatures consistent with bifurcations and, as a case study, pinpoint regions of multistability along the neutrophil branch of hematopoeitic differentiation. Additionally, we leverage the geometric features of linear instability to identify the low-dimensional phase plane in gene expression space within which the multistability unfolds, highlighting novel genetic players that are crucial for neutrophil differentiation. Broadly, we show that a dynamical systems treatment of scRNA-seq data provides mechanistic insights into the high-dimensional processes of cellular differentiation, taking a step toward systematic construction of mathematical models for transcriptomic dynamics.
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