Self-organizing circuitry and emergent computation in mouse embryonic stem cells.
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Summary
A new way of considering regulatory circuitry is presented that describes the expression of each transcription factor (TF) as a branching process that propagates through time, interacting and competing with others, and how this phenomenon provides a valid description of whole genome regulatory circuit dynamics.
- Type
- review
- Published
- 2012-03-01
- Cited by
- 20
- References
- 81
- OpenAlex
- https://openalex.org/W1977358562
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:8854464
Keywords
Biology, Cell fate determination, Transcription factor, Embryonic stem cell, Gene regulatory network
References
- Maximal Information Transfer and Behavior Diversity in Random Threshold Networks
- Flexibility at the Edge of Chaos: a Clear Example from Foraging in Ants
- Toward Self-Organization and Complex Matter
- Complexity: An energetics agenda
- The Theory of critical phenomena
- Design principles of pluripotency
- Self-Organization in nonequilibrium systems
- Less Is More in Modeling Large Genetic Networks
- Evolution of Self-Organized Systems
- Nanog safeguards pluripotency and mediates germline development
- Oct4 kinetics predict cell lineage patterning in the early mammalian embryo
- The cyclic gene Hes1 contributes to diverse differentiation responses of embryonic stem cells.
- Cellular automata as models of complexity
- Critical-like self-organization and natural selection: Two facets of a single evolutionary process?
- Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian conception of evolution by natural law.
- Protein dynamics: implications for nuclear architecture and gene expression.
- Sea Urchin Spines as a Model-System for Permeable, Light-Weight Ceramics with Graceful Failure Behavior. Part II. Mechanical Behavior of Sea Urchin Spine Inspired Porous Aluminum Oxide Ceramics under Compression
- On the concept of attractor
- Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst.
- Mapping Self-Organized Criticality onto Criticality
Cited by
- Adrien Albert Award: How to Mine Chemistry Space for New Drugs and Biomedical Therapies
- Big signals from small particles: regulation of cell signaling pathways by nanoparticles.
- Identification of a Novel Gene Signature of ES Cells Self-Renewal Fluctuation through System-Wide Analysis
- Reprogramming in vivo produces teratomas and iPS cells with totipotency features
- Side Scatter Intensity Is Highly Heterogeneous in Undifferentiated Pluripotent Stem Cells and Predicts Clonogenic Self-Renewal
- Deconstructing transcriptional heterogeneity in pluripotent stem cells
- Jun‐Mediated Changes in Cell Adhesion Contribute to Mouse Embryonic Stem Cell Exit from Ground State Pluripotency
- Physiological controls of large‐scale patterning in planarian regeneration: a molecular and computational perspective on growth and form
- Gap Junctional Signaling in Pattern Regulation: Physiological Network Connectivity Instructs Growth and Form
- Genome-wide mouse embryonic stem cell regulatory network self-organisation : a big data CoSMoS computational modelling approach.
- Nanog Dynamics in Mouse Embryonic Stem Cells: Results from Systems Biology Approaches
- The bioelectric code: An ancient computational medium for dynamic control of growth and form
- A conceptual and computational framework for modelling and understanding the non-equilibrium gene regulatory networks of mouse embryonic stem cells
- Engineering Simulations as Scientific Instruments: A Pattern Language
- Self-Organizing Global Gene Expression Regulated through Criticality: Mechanism of the Cell-Fate Change
- INO80 promotes H2A.Z occupancy to regulate cell fate transition in pluripotent stem cells
- Archetypal Architecture Construction, Patterning, and Scaling Invariance in a 3D Embryoid Body Differentiation Model
- From reinforcement learning to agency: Frameworks for understanding basal cognition
- Self-Organizing Global Gene Expression Regulated Through Criticality: Mechanism of the Cell-Fate Change
- Computational Modeling and Stem Cell Engineering
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