Literature DB >> 17626003

Spontaneous emergence of modularity in cellular networks.

Ricard V Solé1, Sergi Valverde.   

Abstract

Modularity is known to be one of the most relevant characteristics of biological systems and appears to be present at multiple scales. Given its adaptive potential, it is often assumed to be the target of selective pressures. Under such interpretation, selection would be actively favouring the formation of modular structures, which would specialize in different functions. Here we show that, within the context of cellular networks, no such selection pressure is needed to obtain modularity. Instead, the intrinsic dynamics of network growth by duplication and diversification is able to generate it for free and explain the statistical features exhibited by small subgraphs. The implications for the evolution and evolvability of both biological and technological systems are discussed.

Mesh:

Year:  2008        PMID: 17626003      PMCID: PMC2605507          DOI: 10.1098/rsif.2007.1108

Source DB:  PubMed          Journal:  J R Soc Interface        ISSN: 1742-5662            Impact factor:   4.118


  28 in total

1.  Duplication of modules facilitates the evolution of functional specialization.

Authors:  R Calabretta; S Nolfi; D Parisi; G P Wagner
Journal:  Artif Life       Date:  2000       Impact factor: 0.667

2.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

3.  On the origin of modular variation.

Authors:  Hod Lipson; Jordan B Pollack; Nam P Suh
Journal:  Evolution       Date:  2002-08       Impact factor: 3.694

4.  Hierarchical organization of modularity in metabolic networks.

Authors:  E Ravasz; A L Somera; D A Mongru; Z N Oltvai; A L Barabási
Journal:  Science       Date:  2002-08-30       Impact factor: 47.728

5.  Modeling gene and genome duplications in eukaryotes.

Authors:  Steven Maere; Stefanie De Bodt; Jeroen Raes; Tineke Casneuf; Marc Van Montagu; Martin Kuiper; Yves Van de Peer
Journal:  Proc Natl Acad Sci U S A       Date:  2005-03-30       Impact factor: 11.205

6.  Network motifs in computational graphs: a case study in software architecture.

Authors:  Sergi Valverde; Ricard V Solé
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-08-08

7.  Duplication-divergence model of protein interaction network.

Authors:  I Ispolatov; P L Krapivsky; A Yuryev
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2005-06-22

8.  Are network motifs the spandrels of cellular complexity?

Authors:  Ricard V Solé; Sergi Valverde
Journal:  Trends Ecol Evol       Date:  2006-06-09       Impact factor: 17.712

9.  Network growth models and genetic regulatory networks.

Authors:  D V Foster; S A Kauffman; J E S Socolar
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-03-14

10.  An evolutionary and functional assessment of regulatory network motifs.

Authors:  Aurélien Mazurie; Samuel Bottani; Massimo Vergassola
Journal:  Genome Biol       Date:  2005-03-24       Impact factor: 13.583

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  26 in total

Review 1.  Network inference and network response identification: moving genome-scale data to the next level of biological discovery.

Authors:  Diogo F T Veiga; Bhaskar Dutta; Gábor Balázsi
Journal:  Mol Biosyst       Date:  2009-12-11

2.  On the origins of hierarchy in complex networks.

Authors:  Bernat Corominas-Murtra; Joaquín Goñi; Ricard V Solé; Carlos Rodríguez-Caso
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-29       Impact factor: 11.205

Review 3.  Lineage-specific transcription factors and the evolution of gene regulatory networks.

Authors:  Katja Nowick; Lisa Stubbs
Journal:  Brief Funct Genomics       Date:  2010-01-16       Impact factor: 4.241

4.  Distributed robustness in cellular networks: insights from synthetic evolved circuits.

Authors:  Javier Macia; Ricard V Solé
Journal:  J R Soc Interface       Date:  2008-09-16       Impact factor: 4.118

5.  Evolving complexity: how tinkering shapes cells, software and ecological networks.

Authors:  Ricard Solé; Sergi Valverde
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-02-24       Impact factor: 6.237

Review 6.  The emergence of modularity in biological systems.

Authors:  Dirk M Lorenz; Alice Jeng; Michael W Deem
Journal:  Phys Life Rev       Date:  2011-02-25       Impact factor: 11.025

Review 7.  The sociobiology of molecular systems.

Authors:  Kevin R Foster
Journal:  Nat Rev Genet       Date:  2011-02-08       Impact factor: 53.242

8.  Limitations of gene duplication models: evolution of modules in protein interaction networks.

Authors:  Frank Emmert-Streib
Journal:  PLoS One       Date:  2012-04-18       Impact factor: 3.240

9.  Extinctions in heterogeneous environments and the evolution of modularity.

Authors:  Nadav Kashtan; Merav Parter; Erez Dekel; Avi E Mayo; Uri Alon
Journal:  Evolution       Date:  2009-03-10       Impact factor: 3.694

10.  The architecture of mutualistic networks as an evolutionary spandrel.

Authors:  Sergi Valverde; Jordi Piñero; Bernat Corominas-Murtra; Jose Montoya; Lucas Joppa; Ricard Solé
Journal:  Nat Ecol Evol       Date:  2017-11-20       Impact factor: 15.460

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