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Spontaneous evolution of modularity and network motifs

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Modularity in development and evolution

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A review of evolutionary artificial neural networks

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Evolvable systems : from biology to hardware : 7th International Conference, ICES 2007, Wuhan, China, September 21-23, 2007 : proceedings

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Genetic programming II: Automatic discovery of reusable programs

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Evolvable hardware: genetic search in a physical realm

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Pattern Recognition and Neural Networks

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Chemotaxis in Escherichia coli analysed by Three-dimensional Tracking

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From molecular to modular cell biology

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Protein molecules as computational elements in living cells

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Natural engineering principles of electron tunnelling in biological oxidation–reduction

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A coherent feed‐forward loop with a SUM input function prolongs flagella expression in Escherichia coli

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The evolutionary origin of complex features

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Functional cartography of complex metabolic networks

inferredcites →https://doi.org/10.1038/ng1181openalex-snapshot

Convergent evolution of gene circuits

inferredcites →https://doi.org/10.1038/ng881openalex-snapshot

Network motifs in the transcriptional regulation network of Escherichia coli

inferredcites →https://doi.org/10.1073/pnas.2133841100openalex-snapshot

Structure and function of the feed-forward loop network motif

inferredcites →https://doi.org/10.1093/bioinformatics/bth163openalex-snapshot

Efficient sampling algorithm for estimating subgraph concentrations and detecting network motifs

inferredcites →https://doi.org/10.1103/physreve.68.026127openalex-snapshot

Subgraphs in random networks

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Finding and evaluating community structure in networks

inferredcites →https://doi.org/10.1103/physreve.69.066133openalex-snapshot

Fast algorithm for detecting community structure in networks

inferredcites →https://doi.org/10.1103/physreve.70.031909openalex-snapshot

Topological generalizations of network motifs

inferredcites →https://doi.org/10.1103/physreve.71.016127openalex-snapshot

Coarse-graining and self-dissimilarity of complex networks

inferredcites →https://doi.org/10.1103/physrevlett.92.188701openalex-snapshot

Networks, Dynamics, and Modularity

inferredcites →https://doi.org/10.1109/20.952626openalex-snapshot

Improvements in genetic algorithms

inferredcites →https://doi.org/10.1109/54.785838openalex-snapshot

Unveiling the ISCAS-85 benchmarks: a case study in reverse engineering

inferredcites →https://doi.org/10.1109/robot.2001.933266openalex-snapshot

Evolution of generative design systems for modular physical robots

inferredcites →https://doi.org/10.1111/j.0014-3820.2002.tb01466.xopenalex-snapshot

ON THE ORIGIN OF MODULAR VARIATION

inferredcites →https://doi.org/10.1111/j.1558-5646.1996.tb02339.xopenalex-snapshot

PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY

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Rewiring MAP Kinase Pathways Using Alternative Scaffold Assembly Mechanisms

inferredcites →https://doi.org/10.1126/science.1089072openalex-snapshot

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inferredcites →https://doi.org/10.1126/science.1089167openalex-snapshot

Superfamilies of Evolved and Designed Networks

inferredcites →https://doi.org/10.1126/science.283.5400.381openalex-snapshot

Emergent Properties of Networks of Biological Signaling Pathways

inferredcites →https://doi.org/10.1126/science.298.5594.824openalex-snapshot

Network Motifs: Simple Building Blocks of Complex Networks

inferredcites →https://doi.org/10.1128/mcb.19.4.2435openalex-snapshot

Mitogen-Activated Protein Kinases: Specific Messages from Ubiquitous Messengers

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Chemotaxis

inferredcites →https://doi.org/10.7551/mitpress/1090.001.0001openalex-snapshot

Adaptation in Natural and Artificial Systems

inferredcites →https://doi.org/10.7551/mitpress/3927.001.0001openalex-snapshot

An Introduction to Genetic Algorithms

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Crosstalk and the Dynamical Modularity of Feed-Forward Loops in Transcriptional Regulatory Networks

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Bridging single cells to organs: Mesoscale modules as fundamental units of tissue function

inferred← citeshttps://doi.org/10.1016/j.celrep.2018.02.020openalex-snapshot

Quantitative Operating Principles of Yeast Metabolism during Adaptation to Heat Stress

inferred← citeshttps://doi.org/10.1016/j.celrep.2021.110032openalex-snapshot

The diversity and multiplexity of edge communities within and between brain systems

inferred← citeshttps://doi.org/10.1016/j.cels.2015.08.006openalex-snapshot

Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome

inferred← citeshttps://doi.org/10.1016/j.cels.2016.02.014openalex-snapshot

Cross-Disciplinary Network Comparison: Matchmaking between Hairballs

inferred← citeshttps://doi.org/10.1016/j.cels.2016.06.010openalex-snapshot

Switch-like Transitions Insulate Network Motifs to Modularize Biological Networks

inferred← citeshttps://doi.org/10.1016/j.cels.2025.101446openalex-snapshot

Integrating synthetic biology to understand and engineer the heart, lung, blood, and sleep systems

inferred← citeshttps://doi.org/10.1016/j.cels.2025.101514openalex-snapshot

Genetic resonance in the p53 signaling network

inferred← citeshttps://doi.org/10.1016/j.ces.2011.10.068openalex-snapshot

Designing biological systems: Systems Engineering meets Synthetic Biology

inferred← citeshttps://doi.org/10.1016/j.cobeha.2015.11.008openalex-snapshot

Using robots to investigate the evolution of adaptive behavior

inferred← citeshttps://doi.org/10.1016/j.cobme.2020.100252openalex-snapshot

Synthetic regulation of multicellular systems for regenerative engineering

inferred← citeshttps://doi.org/10.1016/j.copbio.2013.04.008openalex-snapshot

Optimality in evolution: new insights from synthetic biology

inferred← citeshttps://doi.org/10.1016/j.cub.2021.06.047openalex-snapshot

Ensemble synchronization in the reassembly of Hydra’s nervous system

inferred← citeshttps://doi.org/10.1016/j.dcn.2015.01.011openalex-snapshot

The use of functional and effective connectivity techniques to understand the developing brain

inferred← citeshttps://doi.org/10.1016/j.ecolind.2026.114644openalex-snapshot

Soil properties rather than climate dominate the variation of leaf trait network structure in desert ecosystems: a case study from the Hexi Corridor, Northwestern China

inferred← citeshttps://doi.org/10.1016/j.febslet.2008.02.069openalex-snapshot

Targeting and tinkering with interaction networks

inferred← citeshttps://doi.org/10.1016/j.febslet.2008.06.023openalex-snapshot

Modularity in the genetic disease‐phenotype network

inferred← citeshttps://doi.org/10.1016/j.fooweb.2022.e00246openalex-snapshot

Trophic hierarchy in a marine community revealed by network analysis on co-occurrence data

inferred← citeshttps://doi.org/10.1016/j.heliyon.2021.e06997openalex-snapshot

Self-selection of evolutionary strategies: adaptive versus non-adaptive forces

inferred← citeshttps://doi.org/10.1016/j.ifacol.2019.09.136openalex-snapshot

A Control Perspective on the Evolution of Biological Modularity

inferred← citeshttps://doi.org/10.1016/j.ifacol.2019.12.193openalex-snapshot

Optimal sparse network topology under sparse control in Laplacian networks

inferred← citeshttps://doi.org/10.1016/j.ins.2009.08.019openalex-snapshot

Periodical switching between related goals for improving evolvability to a fixed goal in multi-objective problems

inferred← citeshttps://doi.org/10.1016/j.isci.2020.101731openalex-snapshot

Evolving the Behavior of Machines: From Micro to Macroevolution

inferred← citeshttps://doi.org/10.1016/j.jedc.2013.04.009openalex-snapshot

Stability of the World Trade Web over time – An extinction analysis

inferred← citeshttps://doi.org/10.1016/j.jes.2024.01.051openalex-snapshot

Evaluating complementaries among urban water, energy, infrastructure, and social Sustainable Development Goals in China

inferred← citeshttps://doi.org/10.1016/j.jrmge.2024.02.044openalex-snapshot

Graph theoretical analysis of limestone fracture network damage patterns based on uniaxial compression test

inferred← citeshttps://doi.org/10.1016/j.jtbi.2006.10.003openalex-snapshot

Asymptotic states and topological structure of an activation–deactivation chemical network

inferred← citeshttps://doi.org/10.1016/j.jtbi.2012.08.020openalex-snapshot

Phenotype–genotype relation in Wagner's canalization model

inferred← citeshttps://doi.org/10.1016/j.jtbi.2012.12.012openalex-snapshot

Network modularity promotes cooperation

inferred← citeshttps://doi.org/10.1016/j.jtbi.2019.06.007openalex-snapshot

Novelty detection improves performance of reinforcement learners in fluctuating, partially observable environments

inferred← citeshttps://doi.org/10.1016/j.mbs.2011.02.001openalex-snapshot

To signal a conjunction of many inputs negative regulation is likely

inferred← citeshttps://doi.org/10.1016/j.mbs.2011.02.005openalex-snapshot

Methods for and results from the study of design principles in molecular systems

inferred← citeshttps://doi.org/10.1016/j.neunet.2012.01.001openalex-snapshot

Evolving neural fields for problems with large input and output spaces

inferred← citeshttps://doi.org/10.1016/j.neunet.2014.07.013openalex-snapshot

Mathematical modeling for evolution of heterogeneous modules in the brain

inferred← citeshttps://doi.org/10.1016/j.neunet.2021.09.009openalex-snapshot

Parallel and hierarchical neural mechanisms for adaptive and predictive behavioral control

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2008.09.062openalex-snapshot

Age-related changes in modular organization of human brain functional networks

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2009.05.032openalex-snapshot

Generic aspects of complexity in brain imaging data and other biological systems

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2011.01.010openalex-snapshot

Age-related alterations in the modular organization of structural cortical network by using cortical thickness from MRI

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2014.03.041openalex-snapshot

Modular structure of functional networks in olfactory memory

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2014.12.046openalex-snapshot

Is functional integration of resting state brain networks an unspecific biomarker for working memory performance?

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2017.08.044openalex-snapshot

Fluctuations between high- and low-modularity topology in time-resolved functional connectivity

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2018.01.037openalex-snapshot

Predicting future learning from baseline network architecture

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2018.06.057openalex-snapshot

Similarity in functional brain architecture between rest and specific task modes: A model of genetic and environmental contributions to episodic memory

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2018.11.003openalex-snapshot

Modular architecture of metabolic brain network and its effects on the spread of perturbation impact

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2020.117632openalex-snapshot

Connectome-based evidence for creative thinking as an emergent property of ordinary cognitive operations

inferred← citeshttps://doi.org/10.1016/j.neuroimage.2021.118177openalex-snapshot

Brain-environment alignment during movie watching predicts fluid intelligence and affective function in adulthood

inferred← citeshttps://doi.org/10.1016/j.neuropsychologia.2019.05.021openalex-snapshot

Brain network modularity predicts cognitive training-related gains in young adults

inferred← citeshttps://doi.org/10.1016/j.neuroscience.2017.10.033openalex-snapshot

Graph Theoretical Framework of Brain Networks in Multiple Sclerosis: A Review of Concepts

inferred← citeshttps://doi.org/10.1016/j.neuroscience.2019.09.017openalex-snapshot

Mathematical Models to Shed Light on Amyloid-Beta and Tau Protein Dependent Pathologies in Alzheimer’s Disease

inferred← citeshttps://doi.org/10.1016/j.nicl.2019.102060openalex-snapshot

Altered brain connectivity in sudden unexpected death in epilepsy (SUDEP) revealed using resting-state fMRI

inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2013.09.004openalex-snapshot

Systems approaches in understanding evolution and evolvability

inferred← citeshttps://doi.org/10.1016/j.physa.2011.03.036openalex-snapshot

Community structure of complex software systems: Analysis and applications

inferred← citeshttps://doi.org/10.1016/j.physa.2011.06.023openalex-snapshot

Detecting the optimal number of communities in complex networks

inferred← citeshttps://doi.org/10.1016/j.physa.2015.08.001openalex-snapshot

Type-dependent irreversible stochastic spin models for genetic regulatory networks at the level of promotion–inhibition circuitry

inferred← citeshttps://doi.org/10.1016/j.physa.2017.04.084openalex-snapshot

Exploring the evolution of node neighborhoods in Dynamic Networks

inferred← citeshttps://doi.org/10.1016/j.physa.2019.04.199openalex-snapshot

Cooperation of local and collective synchronization in complex networks

inferred← citeshttps://doi.org/10.1016/j.physa.2022.128171openalex-snapshot

Regional operating patterns of world container shipping network: A perspective from motif identification

inferred← citeshttps://doi.org/10.1016/j.physd.2006.09.029openalex-snapshot

Synchronization processes in complex networks

inferred← citeshttps://doi.org/10.1016/j.physleta.2014.08.026openalex-snapshot

Analyzing topological characteristics of neuronal functional networks in the rat brain

inferred← citeshttps://doi.org/10.1016/j.physrep.2020.05.004openalex-snapshot

Networks beyond pairwise interactions: Structure and dynamics

inferred← citeshttps://doi.org/10.1016/j.physrep.2023.07.006openalex-snapshot

The genomic physics of tumor–microenvironment crosstalk

inferred← citeshttps://doi.org/10.1016/j.plrev.2013.07.010openalex-snapshot

Evolution: Life has evolved to evolve

inferred← citeshttps://doi.org/10.1016/j.plrev.2016.06.002openalex-snapshot

Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

inferred← citeshttps://doi.org/10.1016/j.plrev.2016.06.008openalex-snapshot

Simulating the actual and the possible

inferred← citeshttps://doi.org/10.1016/j.plrev.2021.03.004openalex-snapshot

From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics

inferred← citeshttps://doi.org/10.1016/j.plrev.2023.11.015openalex-snapshot

Classification of particles with respect to active inference properties as a path towards formalizing agency Comment on “Path integrals, particular kinds, and strange things” by K. Friston, L. Da Costa, D. A. R. Sakthivadivel, C. Heins, G. A. Pavliotis, M. Ramstead, T. Parr

inferred← citeshttps://doi.org/10.1016/j.pneurobio.2023.102537openalex-snapshot

Cortico-spinal modularity in the parieto-frontal system: A new perspective on action control

inferred← citeshttps://doi.org/10.1016/j.schres.2023.02.007openalex-snapshot

Abnormal brain network community structure related to psychological stress in schizophrenia

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