ReviewPhilosophical transactions of the Royal Society of London. Series B, Biological sciences2011
Systems biology of stem cells: three useful perspectives to help overcome the paradigm of linear pathways.
Review in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
39 citing papers in PubMed.
- AI-Guided Inference of Morphodynamic Attractor-like States in Glioblastoma.Diagnostics (Basel, Switzerland) · 2026Article
- Beyond metaphor: quantitative reconstruction of Waddington landscape and exploration of cellular behavior.Briefings in bioinformatics · 2025Review
- Artificial intelligence and systems biology analysis in stem cell research and therapeutics development.Stem cells translational medicine · 2025Review
- A method for in silico exploration of potential glioblastoma multiforme attractors using single-cell RNA sequencing.Scientific reports · 2024Article
- Metabolic adaptation pilots the differentiation of human hematopoietic cells.Life science alliance · 2024Article
- Unveiling the Dynamics behind Glioblastoma Multiforme Single-Cell Data Heterogeneity.International journal of molecular sciences · 2024Article
- CRIPTO-based micro-heterogeneity of mouse muscle satellite cells enables adaptive response to regenerative microenvironment.Developmental cell · 2023Article
- Global genome decompaction leads to stochastic activation of gene expression as a first step toward fate commitment in human hematopoietic cells.PLoS biology · 2022Article
- Reconstructing Boolean network ensembles from single-cell data for unraveling dynamics in the aging of human hematopoietic stem cells.Computational and structural biotechnology journal · 2021Article
- Behavior-related gene regulatory networks: A new level of organization in the brain.Proceedings of the National Academy of Sciences of the United States of America · 2020Review
- Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation.Journal of the Royal Society, Interface · 2020Article
- Hierarchy and levels: analysing networks to study mechanisms in molecular biology.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- A Darwinian and Physical Look at Stem Cell Biology Helps Understanding the Role of Stochasticity in Development.Frontiers in cell and developmental biology · 2020Article
- Time-dependent saddle-node bifurcation: Breaking time and the point of no return in a non-autonomous model of critical transitions.Physica D. Nonlinear phenomena · 2019Article
- Memory and relatedness of transcriptional activity in mammalian cell lineages.Nature communications · 2019Article
- Mesenchymal stem cell perspective: cell biology to clinical progress.NPJ Regenerative medicine · 2019Review
- Structural robustness of mammalian transcription factor networks reveals plasticity across development.Scientific reports · 2018Article
- The CD4+ T cell regulatory network mediates inflammatory responses during acute hyperinsulinemia: a simulation study.BMC systems biology · 2017Article
- Single-Cell-Based Analysis Highlights a Surge in Cell-to-Cell Molecular Variability Preceding Irreversible Commitment in a Differentiation Process.PLoS biology · 2016Article
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Abstract
Stem cell behaviours, such as stabilization of the undecided state of pluripotency or multipotency, the priming towards a prospective fate, binary fate decisions and irreversible commitment, must all somehow emerge from a genome-wide gene-regulatory network. Its unfathomable complexity defies the standard mode of explanation that is deeply rooted in molecular biology thinking: the reduction of observables to linear deterministic molecular pathways that are tacitly taken as chains of causation. Such culture of proximate explanation that uses qualitative arguments, simple arrow-arrow schemes or metaphors persists despite the ceaseless accumulation of 'omics' data and the rise of systems biology that now offers precise conceptual tools to explain emergent cell behaviours from gene networks. To facilitate the embrace of the principles of physics and mathematics that underlie such systems and help to bridge the gap between the formal description of theorists and the intuition of experimental biologists, we discuss in qualitative terms three perspectives outside the realm of their familiar linear-deterministic view: (i) state space (ii), high-dimensionality and (iii) heterogeneity. These concepts jointly offer a new vista on stem cell regulation that naturally explains many novel, counterintuitive observations and their inherent inevitability, obviating the need for ad hoc explanations of their existence based on natural selection. Hopefully, this expanded view will stimulate novel experimental designs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.