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Cell lineage and communication network inference via optimization for single-cell transcriptomics
Abstract The use of single-cell transcriptomics has become a major approach to delineate cell subpopulations and the transitions between them. While various computational tools using differentExpand
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A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions
TLDR
We study a minimal gene regulatory network permissive of multi-lineage MSC differentiation into four cell fates. Expand
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Feedback mechanisms control coexistence in a stem cell model of acute myeloid leukaemia
Haematopoietic stem cell dynamics regulate healthy blood cell production and are disrupted during leukaemia. Competition models of cellular species help to elucidate stem cell dynamics in the boneExpand
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Exploring intermediate cell states through the lens of single cells
As our catalog of cell states expands, appropriate characterization of these states and the transitions between them is crucial. Here we discuss the roles of intermediate cell states (ICSs) in thisExpand
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Mathematical and Statistical Techniques for Systems Medicine: The Wnt Signaling Pathway as a Case Study.
TLDR
We use the Wnt pathway to showcase current mathematical and statistical techniques that enable modelers to gain insight into (models of) gene regulation and generate testable predictions. Expand
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An Ovol2‐Zeb1 transcriptional circuit regulates epithelial directional migration and proliferation
Directional migration is inherently important for epithelial tissue regeneration and repair, but how it is precisely controlled and coordinated with cell proliferation is unclear. Here, we reportExpand
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The ecology in the hematopoietic stem cell niche determines the clinical outcome in chronic myeloid leukemia
Significance Three contrasting models of the ecological interactions in the hematopoietic stem cell niche explain clinical progression of chronic myeloid leukemia equally well, but do so in differentExpand
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Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled
Haematopoietic stem cells (HSCs) are responsible for maintaining immune cells, red blood cells and platelets throughout life. HSCs must be located in their ecological niche (the bone marrow) toExpand
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Bayesian inference of agent-based models: a tool for studying kidney branching morphogenesis
The adult mammalian kidney has a complex, highly-branched collecting duct epithelium that arises as a ureteric bud sidebranch from an epithelial tube known as the nephric duct. Subsequent branchingExpand
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Single cell transcriptomics of human epidermis reveals basal stem cell transition states
How stem cells give rise to human interfollicular epidermis is unclear despite the crucial role the epidermis plays in barrier and appendage formation. Here we use single cell-RNA sequencing toExpand
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