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Gene Duplication Models and Reconstruction of Gene Regulatory Network Evolution from Network Structure

Juris Viksna, David Gilbert
2016 Baltic Journal of Modern Computing  
In this paper we study evolution of gene regulatory networks from the graph-theoretic perspective.  ...  Our aims are to assess the biological appropriateness of the proposed models and to study the possibilities of reconstruction of the evolution history of networks solely on the basis of network topology  ...  Models of network evolution We consider two gene duplication models for gene regulatory network evolution.  ... 
doi:10.22364/bjmc.2016.4.4.18 fatcat:kqtrxdk4lzguhfpcxegwirwi6y

Refining transcriptional regulatory networks using network evolutionary models and gene histories

Xiuwei Zhang, Bernard ME Moret
2010 Algorithms for Molecular Biology  
Results: In this paper, we extend the evolutionary model so as to take into account gene duplications and losses, which are viewed as major drivers in the evolution of regulatory networks.  ...  In this paper we present evolutionary approaches to improve the inference of regulatory networks for a family of organisms by developing an evolutionary model for these networks and taking advantage of  ...  Acknowledgements A preliminary version of this paper appeared in the proceedings of the 9 th Workshop on Algorithms in Bioinformatics WABI'09 [30] .  ... 
doi:10.1186/1748-7188-5-1 pmid:20047657 pmcid:PMC2823753 fatcat:jv33yc5jafdjxc3uysqnqslhhu

Improving Inference of Transcriptional Regulatory Networks Based on Network Evolutionary Models [chapter]

Xiuwei Zhang, Bernard M. E. Moret
2009 Lecture Notes in Computer Science  
In this paper, we extend the evolutionary model so as to take into account gene duplications and losses, which are viewed as major drivers in the evolution of regulatory networks.  ...  In this paper we present evolutionary approaches to improve the inference of regulatory networks for a family of organisms by developing an evolutionary model for these networks and taking advantage of  ...  In this paper we present a model of network evolution that takes into account gene duplications and losses and their effect on regulatory network structures.  ... 
doi:10.1007/978-3-642-04241-6_34 fatcat:mn6gzi6t6vhyvjxpovek5nh4iy

ProPhyC: A Probabilistic Phylogenetic Model for Refining Regulatory Networks [chapter]

Xiuwei Zhang, Bernard M. E. Moret
2011 Lecture Notes in Computer Science  
the duplications and losses of genes.  ...  We demonstrate its applicability with two different network evolutionary models: one that considers only the gains and losses of regulatory connections during evolution, and one that also takes into account  ...  While the gene content of the leaf networks is known, we need to reconstruct the gene content for ancestral networks, that is, to reconstruct the history of gene duplications and losses.  ... 
doi:10.1007/978-3-642-21260-4_33 fatcat:yc5byj4jnrdyxa4zgf2jcgbusy

The Phenotype Paradox: Lessons From Natural Transcriptome Evolution on How to Engineer Plants

Justin Law, Kangbo Ng, Oliver P. F. Windram
2020 Frontiers in Plant Science  
Plants have evolved genome complexity through iterative rounds of single gene and whole genome duplication.  ...  This has led to substantial expansion in transcription factor numbers following preferential retention and subsequent functional divergence of these regulatory genes.  ...  To reconstruct directed networks, inference approaches such as Dynamic Bayesian Models, ordinary differential equation (ODE)-based models and machine learning-based models are often used (Delgado and  ... 
doi:10.3389/fpls.2020.00075 pmid:32133018 pmcid:PMC7040092 fatcat:uibk3htqxndahohfand4bscd7u

Refining Regulatory Networks through Phylogenetic Transfer of Information

Xiuwei Zhang, B. M. E. Moret
2012 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In this paper, we describe ProPhyC, a probabilistic phylogenetic model and associated inference algorithms, designed to improve the inference of regulatory networks for a family of organisms by using known  ...  The experimental determination of transcriptional regulatory networks in the laboratory remains difficult and timeconsuming, while computational methods to infer these networks provide only modest accuracy  ...  Jaebum Kim for providing much of the data we used for the Drosophila networks.  ... 
doi:10.1109/tcbb.2012.62 pmid:22547434 fatcat:6m7jtvfelfakvpajfoydppom4q

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

Dawn Thompson, Aviv Regev, Sushmita Roy
2015 Annual Review of Cell and Developmental Biology  
of gene regulatory processes and their adaptive contribution.  ...  Although reconstruction of regulatory circuits from genomic data alone is therefore desirable, this remains a major computational challenge.  ...  ACKNOWLEDGMENTS We thank Leslie Gaffney for help with preparation of figures. D.T. is supported by the NIH (R01CA119176-01).  ... 
doi:10.1146/annurev-cellbio-100913-012908 pmid:26355593 fatcat:sryxj3e2gvapnnnkmnzdhnyzr4

Towards understanding how molecular networks evolve in plants

Lee Chae, Insuk Lee, Junha Shin, Seung Yon Rhee
2012 Current opinion in plant biology  
Residing beneath the phenotypic landscape of a plant are intricate and dynamic networks of genes and proteins.  ...  In this review, we discuss progress being made to elucidate the nature of these forces and their impact on the composition and structure of molecular networks.  ...  Evolution of network composition Gene duplication as a driving force for node evolution How do nodes evolve and what evolutionary forces shape their divergence?  ... 
doi:10.1016/j.pbi.2012.01.006 pmid:22280840 fatcat:u36zefokafc3zm7gu545bdiivi

Hierarchy and feedback in the evolution of the Escherichia coli transcription network

M. Cosentino Lagomarsino, P. Jona, B. Bassetti, H. Isambert
2007 Proceedings of the National Academy of Sciences of the United States of America  
These findings highlight the important evolutionary roles of both duplication and selective deletion of crosstalks between autoregulators in the emergence of the hierarchical transcription network of E.coli  ...  We also argue that rewiring of regulatory links due to mutation/selection of novel transcription factor/DNA binding interactions appears not to significantly affect the network global hierarchy, and that  ...  Lercher for generously providing and illustrating data from ref. 14 , H. Salgado for help with the regulonDB dataset, B. Vischioni, U. Alon, F. Poelwijk, P. ten Wolde, J. Widom, M.  ... 
doi:10.1073/pnas.0609023104 pmid:17372223 pmcid:PMC1838485 fatcat:fe7mnhq46rff5jtmcgar6nr36q

Evolutionary Context Improves Regulatory Network Predictions

Jonathan L. Gordon, Brigida Gallone, Steven Maere, Kevin J. Verstrepen
2017 Cell Systems  
However, our understanding of how regulatory networks function and evolve is still limited and confounded by their sheer complexity, with a large number of regulatory proteins interacting with each other  ...  and/or with specific binding sequences that can be physically distant from their respective target genes.  ...  Ultimately, accurate and complete network reconstructions will allow the tracing of the evolution of expression dynamics for any given gene or pathway across a phylogeny.  ... 
doi:10.1016/j.cels.2017.05.004 pmid:28544878 pmcid:PMC5467721 fatcat:qlghaypnxzddrinpaczbf6psyi

Signal Correlations in Ecological Niches Can Shape the Organization and Evolution of Bacterial Gene Regulatory Networks [chapter]

Yann S. Dufour, Timothy J. Donohue
2012 Advances in Microbial Physiology  
Nevertheless, the mechanisms and constraints driving the evolution of regulatory networks have been the subjects of numerous analyses, and several models have been proposed.  ...  Conversely, the characteristics of environmental niches determine the selective pressures and can shape the structure of regulatory network accordingly.  ...  College of Agricultural and Life Sciences, and the William H.  ... 
doi:10.1016/b978-0-12-394423-8.00001-9 pmid:23046950 pmcid:PMC4540341 fatcat:3ktp2n6vvzaztgraeap4pxzoxq

Research proposal: Evolution of the Dorsal-Ventral gene regulatory network in Drosophila species

Randy Olson, David Arnosti, Christoph Adami
2013 Figshare  
Often, single genes are regulated by a complex network of genes with activators, repressors, attenuators and the like, and the elucidation of these networks has taken molecular and develop- mental biologists  ...  Animal body plans, their structures and in particular the functions that the animal morphology provides, are the consequence over time and space of successive regulatory and developmental processes.  ...  Are certain types of changes common for a particular adaptive purpose? This way, perhaps we can come up with better models of how gene regulatory networks actually evolve.  ... 
doi:10.6084/m9.figshare.247214.v1 fatcat:wtup5zkr2vfkjeuoyuvqdplliy

Reconstruction of microbial transcriptional regulatory networks

Markus J Herrgård, Markus W Covert, Bernhard Ø Palsson
2004 Current Opinion in Biotechnology  
Reconstruction of regulatory networks Herrgå rd, Covert and Palsson 71  ...  Large-scale regulatory network reconstructions can be converted to in silico models that allow systematic analysis of network behavior in response to changes in environmental conditions.  ...  of reconstructed regulatory network structures in E. coli and S. cerevisiae.  ... 
doi:10.1016/j.copbio.2003.11.002 pmid:15102470 fatcat:zzadypbtcbchzdtwz7xyzbgaq4

Molecular Evolution, Networks in [chapter]

Andreas Wagner
2009 Encyclopedia of Complexity and Systems Science  
The reason is that the evolution of metabolic enzymes can be better reconstructed through gene sequence and protein structure comparisons.  ...  That is, the available data is either derived from comparisons of protein content and/or network structure of very distantly related organisms, or from within one genome, such as from gene duplicates (  ... 
doi:10.1007/978-0-387-30440-3_336 fatcat:rl5u3k5nwbhwbopik7e6tg446m

Effects of Signalling on the Evolution of Gene Regulatory Networks

Dafyd J. Jenkins, Dov J. Stekel
2008 Workshop on the Synthesis and Simulation of Living Systems  
We investigate whether observed transcription network structures and network motifs are a byproduct of the mechanisms by which DNA strands evolve, or if they are fundamental to the function of the network  ...  Comparing the evolved networks with neutrally evolved populations indicates that networks evolve to lose most regulatory activity, due to loss of binding sites and transcription factor activity, including  ...  We investigate the effects of dynamics in the evolution of transcription network structure using models with and without energy signalling.  ... 
dblp:conf/alife/JenkinsS08 fatcat:nupnmkxe5vf4pmhajkkjtslevu
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