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Modular co-evolution of metabolic networks

Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, Zhi-Wei Cao, Yi-Xue Li
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
However, how the modular topology of the molecular network affects the evolution of its member proteins remains unclear.  ...  architecture of metabolic networks.  ...  However, little has been known about how network modularity affects protein evolution.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-311">doi:10.1186/1471-2105-8-311</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17723146">pmid:17723146</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2001200/">pmcid:PMC2001200</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yuworlgzyfe7fom3glas7cgrty">fatcat:yuworlgzyfe7fom3glas7cgrty</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830080755/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-8-311?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/71/e5/71e55dac322cf620737449c2f2b69d544ad9a6fd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-311"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2001200" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Evolutionary design principles in metabolism

Gayathri Sambamoorthy, Himanshu Sinha, Karthik Raman
<span title="2019-03-13">2019</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f4dvulqgv5hongx66rijauzrt4" style="color: black;">Proceedings of the Royal Society of London. Biological Sciences</a> </i> &nbsp;
In this review, we discuss the design principles that are known to exist in metabolic networks, such as functional redundancy, modularity, flux coupling and exaptations.  ...  Therefore, studying adaptations in metabolic networks is crucial to understand the emergence of novel metabolic capabilities.  ...  In summary, FCA is crucial to identifying essential genes and reactions in metabolic networks, and can provide information about the co-occurrence of genes, co-expression of genes and the evolution of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspb.2019.0098">doi:10.1098/rspb.2019.0098</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30836874">pmid:30836874</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6458322/">pmcid:PMC6458322</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uytbj6de4zavvmsdw5zpafjkyu">fatcat:uytbj6de4zavvmsdw5zpafjkyu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191026222004/https://royalsocietypublishing.org/doi/pdf/10.1098/rspb.2019.0098" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspb.2019.0098"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458322" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The origins and evolution of functional modules: lessons from protein complexes

J. B. Pereira-Leal, E. D. Levy, S. A. Teichmann
<span title="2006-03-29">2006</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p7stgfom7rbkheuw5cc6avanwu" style="color: black;">Philosophical Transactions of the Royal Society of London. Biological Sciences</a> </i> &nbsp;
We also provide a perspective on the evolutionary mechanisms driving the growth of other modular cellular networks such as transcriptional regulatory and metabolic networks.  ...  The protein complexes in physical protein interaction networks are a good example of this, and here we focus on their origins and evolution.  ...  There are many anecdotal examples of protein complexes, metabolic and signalling pathways and sets of co-expressed genes that are conserved in evolution.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rstb.2005.1807">doi:10.1098/rstb.2005.1807</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16524839">pmid:16524839</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1609335/">pmcid:PMC1609335</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l2kqz552gja7xkbiefmyc6f2re">fatcat:l2kqz552gja7xkbiefmyc6f2re</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191017000126/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC1609335&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ec/60/ec60b0f656f64985ac2943da5fa76475f12323ce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rstb.2005.1807"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1609335" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modularity and Centrality in Metabolic Network Evolution

Craig C. Jolley, Aurélien Mazurie, Mark Young, Trevor Douglas
<span title="">2010</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
We exploit the property of positive semi-definiteness of the stochastic covariance structure of a biochemical network of arbitrary stoichiometry.  ...  The dynamics of stochastic biochemical networks are often modeled using Langevin equations as an approximation to the underlying Chemical Master Equation.  ...  The capacity of probing dynamical characteristics from the response function is also explored. 3850-Pos Modularity and Centrality in Metabolic Network Evolution Craig C.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.12.4058">doi:10.1016/j.bpj.2009.12.4058</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hhgqglxat5ew7eqvpn5t7a5myq">fatcat:hhgqglxat5ew7eqvpn5t7a5myq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170930054115/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/88b/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAwNjM0OTUwOTA1ODYzOQ%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ad/66/ad6655724eaff15d24c2a04e083e1418eb627243.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2009.12.4058"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Specialization Can Drive the Evolution of Modularity

Carlos Espinosa-Soto, Andreas Wagner, M. Madan Babu
<span title="2010-03-26">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
We show that modularity can increase in gene regulatory networks as a byproduct of specialization in gene activity.  ...  We also show how modularity can facilitate co-option, the utilization of existing gene activity to build new gene activity patterns, a frequent feature of evolutionary innovations.  ...  A prominent example is metabolic networks, whose phenotypes are patterns of metabolic fluxes through network reactions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000719">doi:10.1371/journal.pcbi.1000719</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20360969">pmid:20360969</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2847948/">pmcid:PMC2847948</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4f6wfubssvgidepzbcso3pubpi">fatcat:4f6wfubssvgidepzbcso3pubpi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130805070711/http://www.ieu.uzh.ch:80/wagner/papers/Soto_Wagner_PloS2010.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/20/c2/20c259d9fec86c95a421296a919087f684462b2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000719"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847948" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Network-based approaches for linking metabolism with environment

Sarath Janga, M Madan Babu
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
genome-wide metabolic maps has led to the development of network-based computational approaches for linking an organism with its biochemical habitat.  ...  d a ap pp pr ro oa ac ch he es s f fo or r l li in nk ki in ng g m me et ta ab bo ol li is sm m w wi it th h e en nv vi ir ro on nm me en nt t A Ab bs st tr ra ac ct t Progress in the reconstruction of  ...  Although several studies have provided insights into the structure and evolution of a metabolic network, very few have addressed the influence of environment on metabolic network structure in species from  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-11-239">doi:10.1186/gb-2008-9-11-239</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19040774">pmid:19040774</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2614483/">pmcid:PMC2614483</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/owyq662qcvhybn6seuzo56ijhq">fatcat:owyq662qcvhybn6seuzo56ijhq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719144605/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2008-9-11-239?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4c/e7/4ce7afb62daa48b3411e92485bc31f6072246c9e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2008-9-11-239"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614483" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modularity: a new perspective in biology

Diksha N Dani, Jayashree K Sainis
<span title="">2007</span> <i title="NISCAIR"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cqeng3mdajaybpzg34aajalnru" style="color: black;">Indian Journal of Biochemistry &amp; Biophysics</a> </i> &nbsp;
A module can be defined as an organization of macromolecules performing a synchronous function in a given metabolic pathway.  ...  to modular biology.  ...  Acknowledgement DD was a recipient of Department of Atomic Energy graduate fellowship.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17650580">pmid:17650580</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c53mowh6gnd2ppggi3iqlcb4ve">fatcat:c53mowh6gnd2ppggi3iqlcb4ve</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813111901/http://nopr.niscair.res.in/bitstream/123456789/104/1/IJBB%2044%283%29%20%282007%29%20133-139.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/83/ce/83cefcf94e6d4d25bf6848bb9de3355fedb130f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Biological networks

E Alm
<span title="">2003</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/uzv6ve6frfevrcjkqzfvw36bfu" style="color: black;">Current Opinion in Structural Biology</a> </i> &nbsp;
de novo design of networks.  ...  Instead of viewing the genetic parts list of an organism as a loose collection of biochemical activities, in the best case, we anticipate discrete networks of function to bridge the gap between genotype  ...  Acknowledgements We are grateful to the Howard Hughes Medical Institute and the Department of Energy for the support of research particular to this review.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0959-440x(03)00031-9">doi:10.1016/s0959-440x(03)00031-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12727512">pmid:12727512</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nkjtcq22onf3dfq5sziuzbvhc4">fatcat:nkjtcq22onf3dfq5sziuzbvhc4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100610003357/http://www.cs.tufts.edu/comp/167/arkinreview.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/13/c81395caca8ad732bb6e7161070f2a00fb9e4ddb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0959-440x(03)00031-9"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Evolution of Complex Modular Biological Networks

Arend Hintze, Christoph Adami
<span title="">2008</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Here, we investigate the in silico evolution of modularity and robustness in complex artificial metabolic networks that encode an increasing amount of information about their environment while acquiring  ...  The combination of network modularity tools together with genetic interaction data constitutes a powerful approach to study and dissect the role of modularity in the evolution and function of biological  ...  Discussion Evolution shapes our artificial metabolic networks into complex tightly connected pathways that are modular in nature, and that share many of the well-known properties of biological networks  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.0040023">doi:10.1371/journal.pcbi.0040023</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18266463">pmid:18266463</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2233666/">pmcid:PMC2233666</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e6tggizy3zedrhlojlbaw7jlym">fatcat:e6tggizy3zedrhlojlbaw7jlym</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130927214505/http://adamilab.msu.edu/wp-content/uploads/Reprints/2008/HintzeAdami2008.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/77/31/773191bea21f21baa1ab6dc7b979f09e06ba29c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.0040023"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2233666" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A metabolic network in the evolutionary context: Multiscale structure and modularity

V. Spirin, M. S. Gelfand, A. A. Mironov, L. A. Mirny
<span title="2006-05-26">2006</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
The enormous complexity of biological networks has led to the suggestion that networks are built of modules that perform particular functions and are "reused" in evolution in a manner similar to reusable  ...  by mapping the metabolic network and genomic associations (2, 26) on a graph with vertices representing reactions and two types of edges: metabolic ones that connect  ...  In summary, the observed discrepancy between modules and pathways in not because of limitations of the algorithm but rather reflect the complex modular structure and evolution of the metabolic network.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0510258103">doi:10.1073/pnas.0510258103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16731630">pmid:16731630</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1482654/">pmcid:PMC1482654</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cyogebewmfbndcumehk52lqcay">fatcat:cyogebewmfbndcumehk52lqcay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060829023950/http://www.rtcb.iitp.ru:80/PDF/16731630.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/90/31/903141d050c96f3c869e279bb28fd542b89506df.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.0510258103"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1482654" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Evolution of complex modular biological networks

Arend Hintze, Chris Adami
<span title="">2005</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
Here, we investigate the in silico evolution of modularity and robustness in complex artificial metabolic networks that encode an increasing amount of information about their environment while acquiring  ...  Citation: Hintze A, Adami C (2008) Evolution of complex modular biological networks. PLoS Comput Biol 4(2): e23.  ...  Discussion Evolution shapes our artificial metabolic networks into complex tightly connected pathways that are modular in nature, and that share many of the well-known properties of biological networks  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.0040023.eor">doi:10.1371/journal.pcbi.0040023.eor</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yz4dshhrwbe4pmmjhb5v3wu2tu">fatcat:yz4dshhrwbe4pmmjhb5v3wu2tu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015125916/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0040023&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/14/e6/14e6e92c71ecb001f630827faaefdca66b456abd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.0040023.eor"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

The conservation and evolutionary modularity of metabolism

José M Peregrín-Alvarez, Chris Sanford, John Parkinson
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Metabolic modularity A novel evolutionary analysis of metabolic networks across 26 taxa reveals a highly-conserved but flexible core of metabolic enzymes.  ...  Applying a novel co-conservation analysis, KEGG defined pathways did not generally display evolutionary coherence. Instead, such modularity appears restricted to smaller subsets of enzymes.  ...  Similarly Freilich and colleagues [33] looked at the evolution of the human metabolic network from the perspective of vertebrate evolution.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2009-10-6-r63">doi:10.1186/gb-2009-10-6-r63</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19523219">pmid:19523219</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2718497/">pmcid:PMC2718497</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/joxdaqwg2rc5bax5jf5eeepuiu">fatcat:joxdaqwg2rc5bax5jf5eeepuiu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809230423/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2009-10-6-r63?site=genomebiology.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5e/65/5e65860cc6e9d438ae12eecd80e0039cdc52267b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2009-10-6-r63"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2718497" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

Gustavo Caetano-Anollés, M Fayez Aziz, Fizza Mughal, Frauke Gräter, Ibrahim Koç, Kelsey Caetano-Anollés, Derek Caetano-Anollés
<span title="2019-09-05">2019</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/if2lxezisvecpgymxjdulyfwky" style="color: black;">Evolutionary Bioinformatics</a> </i> &nbsp;
Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism  ...  The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels.  ...  The early evolution of metabolic networks.  ... 
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<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210525181514/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6728656&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/84/c7/84c76b7949a3a3f83869f869035620565e9a5305.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1177/1176934319872980"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> sagepub.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6728656" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria

Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yuanyuan Li, Jing Hou, Yixue Li, Lei Liu
<span title="2006-04-30">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones.  ...  The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation.  ...  Nunes Amaral for kindly providing us the software Modul-w and the usage of the software for module discovery. We would like to thank Dr. Carl Woese, Dr. Hans Bohnert, and Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-7-100">doi:10.1186/1471-2164-7-100</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16646993">pmid:16646993</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1524952/">pmcid:PMC1524952</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/syata44srvae5jvqohrgv5lyay">fatcat:syata44srvae5jvqohrgv5lyay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426091701/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-7-100" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3c/7f/3c7f8e249da2f857d56d1cdee991f2b30c535e46.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-7-100"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1524952" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Phylogenetic Profiling for Probing the Modular Architecture of the Human Genome

Gautam Dey, Tobias Meyer
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eqzh5s6rlnf5hginbk2cz4aatm" style="color: black;">Cell Systems</a> </i> &nbsp;
Importantly, groups of co-evolving genes reveal widespread modularity in the underlying genetic network, facilitating experimental analyses in human cells as well as comparative studies of conserved functional  ...  evolutionary approach to the functional analysis of gene interaction networks.  ...  ACKNOWLEDGMENTS G.D. and T.M. thank members of the Meyer lab for many helpful discussions and suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cels.2015.08.006">doi:10.1016/j.cels.2015.08.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27135799">pmid:27135799</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5m5gfoefbzevvddj42atf7yzda">fatcat:5m5gfoefbzevvddj42atf7yzda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225190359/https://core.ac.uk/download/pdf/81994950.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/18/44/184494d98a1f80be910955aaf4e7e70a4a1c2832.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cels.2015.08.006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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