The Yeast Cell-Cycle Network Is Robustly Designed
arXiv:q-bio/0310010 · doi:10.1073/pnas.0305937101
Abstract
The interactions between proteins, DNA, and RNA in living cells constitute molecular networks that govern various cellular functions. To investigate the global dynamical properties and stabilities of such networks, we studied the cell-cycle regulatory network of the budding yeast. With the use of a simple dynamical model, it was demonstrated that the cell-cycle network is extremely stable and robust for its function. The biological stationary state--the G1 state--is a global attractor of the dynamics. The biological pathway--the cell-cycle sequence of protein states--is a globally attracting trajectory of the dynamics. These properties are largely preserved with respect to small perturbations to the network. These results suggest that cellular regulatory networks are robustly designed for their functions.
24 pages, 7 figures, 3 tables; minor changes; journal version; higher resolution figures at http://www.neci.nj.nec.com/homepages/tang/publication/
References in corpus (2)
Cited by in corpus (150)
- Analyzing and Modeling Real-World Phenomena with Complex Networks: A Survey of Applications
- Colloquium: Criticality and dynamical scaling in living systems
- Boolean network model predicts cell cycle sequence of fission yeast
- Nonequilibrium Physics in Biology
- Topology of biological networks and reliability of information processing
- Evolution of Robustness to Noise and Mutation in Gene Expression Dynamics
- Optimal signal processing in small stochastic biochemical networks
- Logic and connectivity jointly determine criticality in biological gene regulatory networks
- Control of complex networks requires both structure and dynamics
- Information capacity of genetic regulatory elements
- Motifs emerge from function in model gene regulatory networks
- Function Constrains Network Architecture and Dynamics: A Case Study on the Yeast Cell Cycle Boolean Network
- Complex and Adaptive Dynamical Systems: A Primer
- Stochastic Model of Yeast Cell Cycle Network
- Stability of Boolean Multilevel Networks
- Identification of control targets in Boolean molecular network models via computational algebra
- Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development
- Outer-totalistic cellular automata on graphs
- Emergent Criticality from Co-evolution in Random Boolean Networks
- Epistasis can lead to fragmented neutral spaces and contingency in evolution
- Chaotic Gene Regulatory Networks Can Be Robust Against Mutations and Noise
- The effect of scale-free topology on the robustness and evolvability of genetic regulatory networks
- The basis of easy controllability in Boolean networks
- Regulatory patterns in molecular interaction networks
- On the basic computational structure of gene regulatory networks
- Parameter estimation for Boolean models of biological networks
- Statistical Indicators of Collective Behavior and Functional Clusters in Gene Networks of Yeast
- Evolution of Canalizing Boolean Networks
- A Novel Antifragility Measure Based on Satisfaction and Its Application to Random and Biological Boolean Networks
- The phase diagram of random threshold networks
- Molecular Network Control Through Boolean Canalization
- The Influence of Canalization on the Robustness of Boolean Networks
- Entropy of complex relevant components of Boolean networks
- Perturbation propagation in random and evolved Boolean networks
- CANA: A python package for quantifying control and canalization in Boolean Networks
- Funnel landscape and mutational robustness as a result of evolution under thermal noise
- Functional alignment of regulatory networks: A study of temperate phages
- Experiments on autonomous Boolean networks
- Critical Kauffman networks under deterministic asynchronous update
- Stable stochastic dynamics in yeast cell cycle
- Selective control of the apoptosis signaling network in heterogeneous cell populations
- Emergence of robustness against noise: A structural phase transition in evolved models of gene regulatory networks
- Boolean versus continuous dynamics on simple two-gene modules
- Impact of individual nodes in Boolean network dynamics
- Binary threshold networks as a natural null model for biological networks
- Regulatory networks and connected components of the neutral space
- Distribution of essential interactions in model gene regulatory networks under mutation-selection balance
- Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems
- Generic Properties of Random Gene Regulatory Networks
- Kauffman networks with threshold functions
- Robustness under functional constraint: The genetic network for temporal expression in Drosophila neurogenesis
- Stability of Boolean networks: The joint effects of topology and update rules
- Collective Chaos Induced by Structures of Complex Networks
- Funneled Potential and Flux Landscapes Dictate the Stabilities of both the States and the Flow: Fission Yeast Cell Cycle
- Reliability of genetic networks is evolvable
- Relevant components in critical random Boolean networks
- Computational core and fixed-point organisation in Boolean networks
- Antifragility Predicts the Robustness and Evolvability of Biological Networks through Multi-class Classification with a Convolutional Neural Network
- The Regularizing Capacity of Metabolic Networks
- Shaping Robust System through Evolution
- Boolean networks with robust and reliable trajectories
- Robustness Leads Close to the Edge of Chaos in Coupled Map Networks: toward the understanding of biological networks
- Biological control networks suggest the use of biomimetic sets for combinatorial therapies
- Stability of Boolean and continuous dynamics
- Boolean networks with reliable dynamics
- Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks
- Knockouts, Robustness and Cell Cycles
- Evolution in the Debian GNU/Linux software network: analogies and differences with gene regulatory networks
- Motifs in Triadic Random Graphs based on Steiner Triple Systems
- Dynamics of Boolean networks - an exact solution
- Morphogenesis by coupled regulatory networks: Reliable control of positional information and proportion regulation
- Optimal Stabilization of Boolean Networks through Collective Influence
- Phase transition between synchronous and asynchronous updating algorithms
- Representing perturbed dynamics in biological network models
- Estimating Propensity Parameters using Google PageRank and Genetic Algorithms
- Boolean networks with veto functions
- Boolean function metrics can assist modelers to check and choose logical rules
- Harmonic Analysis of Boolean Networks: Determinative Power and Perturbations
- Bounds on the Average Sensitivity of Nested Canalizing Functions
- Edge usage, motifs and regulatory logic for cell cycling genetic networks
- Robustness and modular design of the Drosophila segment polarity network
- Attractor and Basin Entropies of Random Boolean Networks Under Asynchronous Stochastic Update
- Quantifying the Total Effect of Edge Interventions in Discrete Multistate Networks
- Replica symmetry breaking in an adiabatic spin-glass model of adaptive evolution
- Response of Boolean networks to perturbations
- Inferring Biologically Relevant Models: Nested Canalyzing Functions
- Limits and trade-offs of topological network robustness
- A Multilayer Structure Facilitates the Production of Antifragile Systems in Boolean Network Models
- Synchronized Dynamics and Nonequilibrium Steady States in a Stochastic Yeast Cell-Cycle Network
- Set-based complexity and biological information
- From statistical mechanics to information theory: understanding biophysical information-processing systems
- Selective pressure on metabolic network structures as measured from the random blind-watchmaker network
- Nonlinear signaling on biological networks: the role of stochasticity and spectral clustering
- Partial Order on the set of Boolean Regulatory Functions
- Effect of memory in non-Markovian Boolean networks
- Attractor landscapes in Boolean networks with firing memory
- Synchronization in discrete-time, discrete-state Random Dynamical Systems
- Critical slowing down and attractive manifold: a mechanism for dynamic robustness in yeast cell-cycle process
- A spin glass approach to the directed feedback vertex set problem
- Characterizing short-term stability for Boolean networks over any distribution of transfer functions
- SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
- Symmetry in Critical Random Boolean Network Dynamics
- Core regulatory network motif underlies the ocellar complex patterning in Drosophila melanogaster
- SVEN: Informative Visual Representation of Complex Dynamic Structure
- Feedback arcs and node hierarchy in directed networks
- Reduction of Boolean Networks
- From differential equations to Boolean networks: A Case Study in modeling regulatory networks
- Cell biology: Networks, regulation, pathways
- Coherent regulation in yeast cell cycle network
- Prediction of lethal and synthetically lethal knock-outs in regulatory networks
- Coherent organization in gene regulation: a study on six networks
- A statistical-mechanical study of evolution of robustness in noisy environment
- Master Stability Functions for metacommunities with two types of habitats
- A unified model for informetrics based on the wave and heat equations
- Phase transitions and memory effects in the dynamics of Boolean networks
- Nonlinear signal transduction network with multistate
- Interplay between degree and Boolean rules in the stability of Boolean networks
- Partial annealing of a coupled mean-field spin-glass model with an embedded pattern
- A SAT-Based Algorithm for Computing Attractors in Synchronous Boolean Networks
- Stratification and enumeration of Boolean functions by canalizing depth
- Canalization in the Critical States of Highly Connected Networks of Competing Boolean Nodes
- Inhibition as a determinant of activity and criticality in dynamical networks
- A tractable genotype-phenotype map for the self-assembly of protein quaternary structure
- A Monte Carlo Approach to Measure the Robustness of Boolean Networks
- Dimension Reduction of Large AND-NOT Network Models
- Cancer Genesis and Progression as Dynamics in Functional Landscape of Endogenous Molecular-Cellular Network
- Piecewise linear and Boolean models of chemical reaction networks
- Recursive Network Estimation From Binary-Valued Observation Data
- Integration of cellular signals in chattering environments
- Nested canalyzing depth and network stability
- Exact Analysis of Intrinsic Qualitative Features of Phosphorelays using Mathematical Models
- MCA: Boolean Networks Control Algorithm
- A Review of Mathematical Models for Muscular Dystrophy: A Systems Biology Approach
- Constructing backbone network by using tinker algorithm
- Metanetworks of artificially evolved regulatory networks
- On Simplicity and Complexity in the Brave New World of Large-Scale Neuroscience
- Data-Driven Learning of Boolean Networks and Functions by Optimal Causation Entropy Principle (BoCSE)
- A stylised view on structural and functional connectivity in dynamical processes in networks
- Synthetic Biology in Leishmaniasis: Design,simulation and validation of constructed Genetic circuit
- The Structure and Dynamics of Gene Regulation Networks
- Looking for Signs: Reasoning About FOBNNs Using SAT
- Anomalies in the transcriptional regulatory network of the yeast Saccharomyces cerevisiae
- Combinatorial Algorithms for Control of Biological Regulatory Networks
- An Extensive Study of Two-Node McCulloch-Pitts Networks
- Dynamical Stability of Threshold Networks over Undirected Signed Graphs
- A discrete inhomogeneous model for the yeast cell cycle
- Study of the structure and dynamics of complex biological networks
- Global View of Bionetwork Dynamics: Adaptive Landscape
- Predicting attractors from spectral properties of stylized gene regulatory networks
- Scale- free networks in cell biology