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Why don't the modules dominate?

Zhenyue Qin, Tom Gedeon, R I (Bob) McKay
2018 Proceedings of the Genetic and Evolutionary Computation Conference Companion on - GECCO '18  
In nature, modular solutions generally dominate populations, whereas in this domain, modularity, when it emerges, is a relatively rare variant.  ...  Wagner's modularity inducing problem domain is a key contribution to the study of the evolution of modularity, including both evolutionary theory and evolutionary computation.  ...  Espinosa-Soto and Wagner 1 studied the emergence of modularity in an artificial environment requiring gene specialization [8] , in which gene regulatory networks need to be able to regulate toward multiple  ... 
doi:10.1145/3205651.3205737 dblp:conf/gecco/QinGM18 fatcat:zqjp43blwzfb3ogrjzouqtpo34

Applications of Biological Cell Models in Robotics [article]

Michele Braccini
2017 arXiv   pre-print
In particular, this work represents a survey of some models inspired, or making use of concepts, by gene regulatory networks (GRNs): these networks describe the complex interactions that affect gene expression  ...  This gives rise to genetic regulatory systems structured by networks of regulatory interactions between DNA, RNA, proteins and other molecules [3] : a complex network termed as a gene regulatory network  ...  morphogenesis, that uses a hierarchical gene regulatory network (EH-GRN) evolved using network motifs.  ... 
arXiv:1712.02303v1 fatcat:w5j7oi2shnfn7l5i27ny6d4dzu

Robust Detection of Hierarchical Communities from Escherichia coli Gene Expression Data

Santiago Treviño, Yudong Sun, Tim F. Cooper, Kevin E. Bassler, Satoru Miyano
2012 PLoS Computational Biology  
One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to environmental and genetic perturbations.  ...  Further, analysis of the most significantly enriched communities identified several candidate new regulatory interactions.  ...  Introduction Gene regulation networks represent the set of regulatory interactions between all genes of an organism.  ... 
doi:10.1371/journal.pcbi.1002391 pmid:22383870 pmcid:PMC3285575 fatcat:puucuet7hbf63fjhzebm3yiryi

Complex Networks

Carlos Gershenson, Mikhail Prokopenko
2011 Artificial Life  
Introduction to the Special Issue on Complex Networks, Artificial Life journal.  ...  We are also grateful for the support provided by the organizers of the ALife XII conference for facilitating the organization of the session on complex networks.  ...  of gene regulatory networks [11] , carried out by Wang et al  ... 
doi:10.1162/artl_e_00037 pmid:21762018 fatcat:4vlzcgkkm5ehxbjfw5ruzhhrxa

A scalable solution to n-bit parity via artificial development

Tuze Kuyucu, Martin A. Trefzer, Julian F. Miller, Andy M. Tyrrell
2009 2009 Ph.D. Research in Microelectronics and Electronics  
As a candidate solution to the scalability issue, an artificial developmental system is presented.  ...  The result obtained further supports the artificial developmental system as a good candidate solution to the scalability problem in evolvable hardware.  ...  via the regulatory network present within that cell.  ... 
doi:10.1109/rme.2009.5201348 fatcat:qbxs5y4sdrhindlwuz3ufvzvya

Are network motifs the spandrels of cellular complexity?

R SOLE, S VALVERDE
2006 Trends in Ecology & Evolution  
Motifs and modules Life is modular [1] and selection for function has shaped cellular networks, such as metabolic pathways or gene regulatory webs, to perform efficiently.  ...  Kuo et al. recently explored this approach in detail by extending previous work on artificial transcriptional regulatory networks lacking real functionality [10] .  ... 
doi:10.1016/j.tree.2006.05.013 pmid:16764967 fatcat:2itvq3ztmngxxhwpmz6y2y5miq

Artificial Gene Regulatory Networks—A Review

Sylvain Cussat-Blanc, Kyle Harrington, Wolfgang Banzhaf
2019 Artificial Life  
In Engineering, modeling and implementations of artificial gene regulatory 1 networks has been an expanding field of research and development over the past few decades.  ...  This review discusses the concept of gene regulation, the current state-of-the-art in gene regulatory networks, including modeling and simulation, and reviews their use in artificial evolutionary settings  ...  That shows the capacity of gene regulatory networks to produce modular patterns.  ... 
doi:10.1162/artl_a_00267 fatcat:kmshnduj7bap5nezctik63uvae

Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules

James T. Lim, Chen Chen, Adam D. Grant, Megha Padi
2021 Frontiers in Genetics  
CRANE can be used to generate a null distribution of gene regulatory networks that can in turn be used to rank the most significant changes in candidate disease communities.  ...  The use of biological networks such as protein–protein interaction and transcriptional regulatory networks is becoming an integral part of genomics research.  ...  cancer (BC), and used them to infer two gene regulatory networks, BCN1 and BCN2.  ... 
doi:10.3389/fgene.2020.603264 pmid:33519907 pmcid:PMC7841433 fatcat:3ml47okt5ve4dkjgd4h2q3tslu

Chemical crosshairs on the central dogma

Aseem Z Ansari
2007 Nature Chemical Biology  
cascades within gene regulatory networks.  ...  The insights from such studies of cellular networks will lay the foundation for devising molecules that will, in principle, be used to regulate artificial genomes in artificial cells, thereby opening the  ... 
doi:10.1038/nchembio0107-2 pmid:17173017 fatcat:ncjxefrwangubnpq6avw66vcpu

Specialization Can Drive the Evolution of Modularity

Carlos Espinosa-Soto, Andreas Wagner, M. Madan Babu
2010 PLoS Computational Biology  
We show that modularity can increase in gene regulatory networks as a byproduct of specialization in gene activity.  ...  Such specialization occurs after gene regulatory networks are selected to produce new gene activity patterns that appear in a specific body structure or under a specific environmental condition.  ...  We here show that modularity can arise in gene regulatory networks as a byproduct of specialization in gene activity.  ... 
doi:10.1371/journal.pcbi.1000719 pmid:20360969 pmcid:PMC2847948 fatcat:4f6wfubssvgidepzbcso3pubpi

Modeling Stress-Induced Regulatory Cascades With Artificial Neural Networks

Maria E. Manioudaki, Panayiota Poirazi
2009 Zenodo  
These findings suggest that the combination of gene expression and protein-DNA interaction data with artificial neural networks can successfully mo [...]  ...  ) and the output layer corresponds to the expression of genes within each module.  ...  Other methods include biclustering algorithms where data from microarray experiments are organized in matrices and genes Modeling Stress-Induced Regulatory Cascades with Artificial Neural Networks Maria  ... 
doi:10.5281/zenodo.1074669 fatcat:tdgvboyto5g3fgw7uq3c26oyra

Generating Ensembles of Gene Regulatory Networks to Assess Robustness of Disease Modules [article]

James T Lim, Chen Chen, Adam D Grant, Megha Padi
2020 bioRxiv   pre-print
The use of biological networks such as protein-protein interaction and transcriptional regulatory networks is becoming an integral part of biological research in the genomics era.  ...  However, these networks are not static, and during phenotypic transitions like disease onset, they can acquire new "communities" of genes that carry out key cellular processes.  ...  cancer (BC), and used them to infer two gene regulatory networks, BCN1 and BCN2.  ... 
doi:10.1101/2020.07.12.198747 fatcat:j62cfgq67vdpfcydmtv6bvnxaa

Generating Realistic In Silico Gene Networks for Performance Assessment of Reverse Engineering Methods

Daniel Marbach, Thomas Schaffter, Claudio Mattiussi, Dario Floreano
2009 Journal of Computational Biology  
DREAM challenge | reverse engineering | gene regulatory networks | modularity | network motifs  ...  Our method was selected to generate the "gold standard" networks for the gene network reverse engineering challenge of the third DREAM conference (Dialogue on Reverse Engineering Assessment and Methods  ...  blocks of modules in gene regulatory networks.  ... 
doi:10.1089/cmb.2008.09tt pmid:19183003 fatcat:y5mt5mca7zby5j5oxar64psl7y

Evolutionary-Based Control Approaches for Multirobot Systems [chapter]

Jekanthan Thangavelautham, Timothy D., Gabriele M.T.
2008 Frontiers in Evolutionary Robotics  
The growth program within many of these morphogenetic systems is controlled through artificial gene regulation.  ...  Artificial Neural Tissues (ANT) includes a coarsecoding-based neural regulatory system that is similar to the network modularity evident in fixed-topology ensemble approaches.  ...  How to learn such behaviors is a central issue of Distributed Artificial Intelligence (DAI), which has recently attracted much attention.  ... 
doi:10.5772/5447 fatcat:yynfj2bgundmdkz3qvu2bfobpe

Evolved Modular Epistasis in Artificial Organisms

Sergi Valverde, Ricard V. Solé
2012 Artificial Life 13  
A central concept within genetic systems is epistasis, namely the modulation of the effects of a given gene by one or several other genes.  ...  How does complexity evolve in artificial and natural systems?  ...  Within the context of regulatory gene networks, it has been shown the presence of complex interactions between epistasis, network redundancy and degeneracy (Macía et al., 2012) .  ... 
doi:10.7551/978-0-262-31050-5-ch016 dblp:conf/alife/ValverdeSE12 fatcat:nsci2sw3gzfqhhwmxewd3ndxea
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