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Literature DB >> 21353651

The emergence of modularity in biological systems.

Dirk M Lorenz¹, Alice Jeng, Michael W Deem.

Abstract

In this review, we discuss modularity and hierarchy in biological systems. We review examples from protein structure, genetics, and biological networks of modular partitioning of the geometry of biological space. We review theories to explain modular organization of biology, with a focus on explaining how biology may spontaneously organize to a structured form. That is, we seek to explain how biology nucleated from among the many possibilities in chemistry. The emergence of modular organization of biological structure will be described as a symmetry-breaking phase transition, with modularity as the order parameter. Experimental support for this description will be reviewed. Examples will be presented from pathogen structure, metabolic networks, gene networks, and protein-protein interaction networks. Additional examples will be presented from ecological food networks, developmental pathways, physiology, and social networks.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
Proteins

Year: 2011 PMID： 21353651 PMCID： PMC4477837 DOI： 10.1016/j.plrev.2011.02.003

Source DB: PubMed Journal: Phys Life Rev ISSN： 1571-0645 Impact factor: 11.025

87 in total

10. A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines.

Authors: Eirini Tsirvouli; Vasundra Touré; Barbara Niederdorfer; Miguel Vázquez; Åsmund Flobak; Martin Kuiper
Journal: Front Mol Biosci Date: 2020-10-09

The emergence of modularity in biological systems.

1. Modularity, evolvability, and adaptive radiations: a comparison of the hemi- and holometabolous insects.

Review 2. Environmental regulation of mutation rates at specific sites.

3. On the origin of modular variation.

4. Functional modularity of background activities in normal and epileptic brain networks.

5. Modularity of stress response evolution.

6. Modular epistasis in yeast metabolism.

7. Cluster analysis and display of genome-wide expression patterns.

8. Emergent gene order in a model of modular polyketide synthases.

9. Uncoupling of the autonomic and cardiovascular systems in acute brain injury.

10. An analytically solvable model for rapid evolution of modular structure.

1. A multi-scale model for correlation in B cell VDJ usage of zebrafish.

2. Penicillin Trunk Injection Affects Bacterial Community Structure in Citrus Trees.

Review 3. Diverse array-designed modes of combination therapies in Fangjiomics.

Review 4. Spatiotemporal positioning of multipotent modules in diverse biological networks.

5. Identify bilayer modules via pseudo-3D clustering: applications to miRNA-gene bilayer networks.

6. Hierarchy in gene expression is predictive of risk, progression, and outcome in adult acute myeloid leukemia.

7. Exploring modularity in biological networks.

8. On the emergence of cognition: from catalytic closure to neuroglial closure.

9. Hierarchy of gene expression data is predictive of future breast cancer outcome.

10. A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines.