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Emergent Network Structure, evolvable Robustness and non-linear Effects of Point Mutations in an Artificial Genome Model [article]

Thimo Rohlf, Christopher R. Winkler
<span title="2009-08-25">2009</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We analyze statistical properties of randomly generated genomes both on the sequence- and network level, and show that this model correctly predicts the frequency of genes in genomes as found in experimental  ...  Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand.  ...  By binding to specific regions of the genome, the protein produced by one gene can affect the activity of other genes, and those genes may in turn express proteins that enhance or inhibit still more genes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0908.3610v1">arXiv:0908.3610v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3trunj5oabfqvlmno2kf3jp2tm">fatcat:3trunj5oabfqvlmno2kf3jp2tm</a> </span>
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Gene Expression Is Not Random: Scaling, Long-Range Cross-Dependence, and Fractal Characteristics of Gene Regulatory Networks

Mahboobeh Ghorbani, Edmond A. Jonckheere, Paul Bogdan
<span title="2018-10-22">2018</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/evju7ot335gbrctgmomg4gg6je" style="color: black;">Frontiers in Physiology</a> </i> &nbsp;
Unlike previous studies, which report the fractal and long-range dependency of DNA structure, we investigate the individual gene expression dynamics as well as the cross-dependency between them in the  ...  Here, we report the scaling properties of gene expression time series in Escherichia coli and Saccharomyces cerevisiae.  ...  ACKNOWLEDGMENTS We thank our reviewers for extremely insightful comments and feedback on our work that contributed to the significant improvement of the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphys.2018.01446">doi:10.3389/fphys.2018.01446</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30459629">pmid:30459629</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6232942/">pmcid:PMC6232942</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l3grzijzjzh3ppigj3f75jnfe4">fatcat:l3grzijzjzh3ppigj3f75jnfe4</a> </span>
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Mathematical Modelling of Gene Regulatory Networks [chapter]

Ana Tuek, elimir Kurtanjek
<span title="2012-03-23">2012</span> <i title="InTech"> Applied Biological Engineering - Principles and Practice </i> &nbsp;
Due to the fact that number of events occurring in the cells is not large and events are dependent, it is not possible to use deterministic rate equations for description of the gene network (gene expression  ...  Every gene 114 has one or more activators and one or more inhibitors that are regulating the specific gene expression, depending on the situation in the cell and cell environment.  ...  Mathematical Modelling of Gene Regulatory Networks, Applied Biological Engineering -Principles and Practice, Dr. Ganesh R.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/31388">doi:10.5772/31388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vbvytqbmnra7ndxtnb6fjofye4">fatcat:vbvytqbmnra7ndxtnb6fjofye4</a> </span>
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A Novel Method for Identifying Essential Genes by Fusing Dynamic Protein–Protein Interactive Networks

Fengyu Zhang, Wei Peng, Yunfei Yang, Wei Dai, Junrong Song
<span title="2019-01-08">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/githwx23ynaxdoftesby3jya3y" style="color: black;">Genes</a> </i> &nbsp;
Finally, a novel centrality method was designed to assign each gene in the final network a ranking score, whilst considering its orthologous property and its global and local topological properties in  ...  Firstly, the active PPI networks of each time point were constructed and then they were fused into a final network according to the networks' similarities.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/genes10010031">doi:10.3390/genes10010031</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30626157">pmid:30626157</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6356314/">pmcid:PMC6356314</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2o3oa3n2ybhxdftzuxwfof72i4">fatcat:2o3oa3n2ybhxdftzuxwfof72i4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505141038/https://res.mdpi.com/genes/genes-10-00031/article_deploy/genes-10-00031-v2.pdf?filename=&amp;attachment=1" 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/a8/b7/a8b7ce87b3b7414e97f7c9f7c6fcacbb36f43d8a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/genes10010031"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6356314" 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 Publish-Subscribe Model of Genetic Networks

Brett Calcott, Duygu Balcan, Paul A. Hohenlohe, Andrea Califano
<span title="2008-09-19">2008</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Degree distributions of randomly constructed networks, particularly multimodal indegree distributions, which depend on the length of the regulatory sequences and the number of possible gene products, differed  ...  We explore the consequences of this publish-subscribe model of regulation for the properties of single networks and for the evolution of populations of networks.  ...  Erzan, faculty at the Santa Fe Institute and Istanbul Technical University, and one anonymous reviewer for useful discussion and comments. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0003245">doi:10.1371/journal.pone.0003245</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18802467">pmid:18802467</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2531231/">pmcid:PMC2531231</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zerxgqxjknbvdbkvgbkwsmuqj4">fatcat:zerxgqxjknbvdbkvgbkwsmuqj4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922225718/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0003245&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/bb/0d/bb0dde2da7d2e823b9a38a9aa56682dfd3bb13c9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0003245"> <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/PMC2531231" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dynamic network rewiring determines temporal regulatory functions in Drosophilamelanogaster development processes

Man-Sun Kim, Jeong-Rae Kim, Kwang-Hyun Cho
<span title="2010-05-18">2010</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4b3nxjjiivaspl2bdv5q6xppru" style="color: black;">Bioessays</a> </i> &nbsp;
of gene expression is an indispensable characteristic.  ...  We propose a concept of a "temporal sequence of network motifs", a sequence of network motifs in active sub-networks constructed over time, and investigate significant network motifs in the active temporal  ...  Acknowledgments Andrew Moore and anonymous reviewers contributed significantly to the improvement of a first draft of this article.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/bies.200900169">doi:10.1002/bies.200900169</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20486137">pmid:20486137</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e4nfc2a4tjga3fwnbt3m2mbwg4">fatcat:e4nfc2a4tjga3fwnbt3m2mbwg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808125341/http://sbie.kaist.ac.kr/ftp/Dynamic%20network%20rewiring%20determines%20temporal%20regulatory%20functions%20in%20the%20Drosophila%20melanogaster%20development%20processes.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/68/aa/68aa444cfb9c3a61ac98e5585765dd059291fd01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/bies.200900169"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Constructing Probabilistic Genetic Networks of Plasmodium falciparum from Dynamical Expression Signals of the Intraerythrocytic Development Cycle [chapter]

Junior Barrera, Roberto M. Cesar, David C. Martins, Ricardo Z. N. Vêncio, Emilio F. Merino, Márcio M. Yamamoto, Florencia G. Leonardi, Carlos A. de B. Pereira, Hernando A. del Portillo
<span title="">2007</span> <i title="Springer US"> Methods of Microarray Data Analysis V </i> &nbsp;
In the present paper, genes are annotated under a different perspective: a list of functional properties is attributed to networks of genes representing subsystems of the P. falciparum regulatory expression  ...  This model mimics the properties of a gene as a non-linear stochastic gate and the systems are built by coupling of these gates.  ...  In such networks, the expression of each gene depends both on its own expression and on the expression levels of other genes at previous time instants.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-0-387-34569-7_2">doi:10.1007/978-0-387-34569-7_2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h2uur4bdbvafdein5e2hueyhpy">fatcat:h2uur4bdbvafdein5e2hueyhpy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070613084110/http://www.vision.ime.usp.br/creativision/publications/pdf/barreracamda06.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/36/2e/362e4b39074c489496b37948d91ce01e59887b77.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-0-387-34569-7_2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Toward the dynamic interactome: it's about time

T. M. Przytycka, M. Singh, D. K. Slonim
<span title="2010-01-01">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Here we review the beginnings of a new subfield within computational biology, one focused on the global inference and analysis of the dynamic interactome.  ...  Dynamic molecular interactions play a central role in regulating the functioning of cells and organisms.  ...  Acknowledgements This article was inspired by our involvement in the Pacific Symposium on Biocomputing session 'Dynamics of Biological Networks', which we are co-organizing with Tanya Berger-Wolf (University  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbp057">doi:10.1093/bib/bbp057</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20061351">pmid:20061351</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2810115/">pmcid:PMC2810115</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xbj7ugs6nbed7guys2ie5z3efa">fatcat:xbj7ugs6nbed7guys2ie5z3efa</a> </span>
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A novel procedure for statistical inference and verification of gene regulatory subnetwork

Haijun Gong, Jakob Klinger, Kevin Damazyn, Xiangrui Li, Shiyang Huang
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
But how to correctly and efficiently decifer the gene regulatory network from high-throughput gene expression data is a big challenge due to the relatively small amount of observations and curse of dimensionality  ...  The reconstruction of gene regulatory network from time course microarray data can help us comprehensively understand the biological system and discover the pathogenesis of cancer and other diseases.  ...  Declarations Publication of this article was funded by the Saint Louis University to HG. This article has been published as part of BMC Bioinformatics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-16-s7-s7">doi:10.1186/1471-2105-16-s7-s7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25952938">pmid:25952938</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4423581/">pmcid:PMC4423581</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bnigq6zcsbgnnixoqjb3qk7bpy">fatcat:bnigq6zcsbgnnixoqjb3qk7bpy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819061622/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-16-S7-S7?site=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/fb/42/fb42b3d0e4179056814051880eea4beb61fe24b6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-16-s7-s7"> <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/PMC4423581" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Data Sources and Computational Approaches for Generating Models of Gene Regulatory Networks [chapter]

Baltazar D. Aguda, Georghe Craciun, Rengul Cetin-Atalay
<span title="2005-01-27">2005</span> <i title="John Wiley &amp; Sons, Inc."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/snjas3fv45e6tazpxuzt6igysi" style="color: black;">Reviews in computational chemistry</a> </i> &nbsp;
High-throughput gene expression measurements using DNA microarrays provide global snapshots of the dynamics of gene networks at the RNA level.  ...  Although the operon structure is not a general property of all genomes, one can expect that genomic DNA sequence organization affects the dynamics of the GRN; this is primarily due to co-expression of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/0471720895.ch6">doi:10.1002/0471720895.ch6</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iaodscfur5e3pjy2z2oejtufyy">fatcat:iaodscfur5e3pjy2z2oejtufyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922013040/http://www.math.wisc.edu/~craciun/PAPERS/AgudaCraciunAtalay_FINAL.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/cb/95/cb951aec503cc249527b9a748723c5a7e9e53ac7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/0471720895.ch6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Modelling the evolution of genetic regulatory networks

A.P. Quayle, S. Bullock
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fydada535zbx7el5lxtbdrx6ga" style="color: black;">Journal of Theoretical Biology</a> </i> &nbsp;
The gene expression dynamics are determined by updating the gene network as if it were a simple Boolean network. The generic behaviour of the AG model is investigated in detail.  ...  These properties are demonstrated to agree with a probabilistic analysis of the model, and the typical network structures generated by the model are shown to lie between those of random networks and scale-free  ...  The dynamics of the resulting network can then be determined from the starting states of the genes in a network, given a set of rules to describe how the state of each gene depends on the states of the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jtbi.2005.06.020">doi:10.1016/j.jtbi.2005.06.020</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16095624">pmid:16095624</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eovzfwgiyrdx3g4exksrxeuvdu">fatcat:eovzfwgiyrdx3g4exksrxeuvdu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171112215328/https://core.ac.uk/download/pdf/1505052.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/7a/cd/7acd08daef1a0852a433cf159bc6c67970d20955.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jtbi.2005.06.020"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Modelling gene networks at different organisational levels

Thomas Schlitt, Alvis Brazma
<span title="2005-02-12">2005</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kn6dhptylrb77b5atyiom5ysjm" style="color: black;">FEBS Letters</a> </i> &nbsp;
We discuss the current state of the art for each of these approaches. There is a gap between the parts list and topology models on one hand, and control logic and dynamic models on the other hand.  ...  Approaches to modelling gene regulation networks can be categorized, according to increasing detail, as network parts lists, network topology models, network control logic models, or dynamic models.  ...  We think that the answer largely depends on the robustness and modularity properties of the real world biological networks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.febslet.2005.01.073">doi:10.1016/j.febslet.2005.01.073</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15763564">pmid:15763564</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/74vllg3fmjbvriro6r6uuy76uy">fatcat:74vllg3fmjbvriro6r6uuy76uy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171002000820/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/ace/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAxNDU3OTMwNTAwMTg2OQ%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/96/61/9661b6ce75a9555fcf996ccae45181a8945c4263.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.febslet.2005.01.073"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Dynamical properties of model gene networks and implications for the inverse problem

Theodore J. Perkins, Mike Hallett, Leon Glass
<span title="">2006</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dbxvzia7tzcdzoff4xmqtr4qrq" style="color: black;">Biosystems (Amsterdam. Print)</a> </i> &nbsp;
We study the inverse problem, or the "reverse-engineering" problem, for two abstract models of gene expression dynamics, discrete-time Boolean networks and continuous-time switching networks.  ...  However, differences in the dynamical properties of these two types of networks affect the amount of data that is necessary for solving the inverse problem.  ...  Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.biosystems.2005.09.010">doi:10.1016/j.biosystems.2005.09.010</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16386356">pmid:16386356</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u7cynvlqgjahde2th2odmb6chi">fatcat:u7cynvlqgjahde2th2odmb6chi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812195321/http://www.medicine.mcgill.ca/physio/glasslab/pub_pdf/dynamical_2006.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/e4/e7/e4e7678eedb1561fe903a0ec33854b8ade98e9bd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.biosystems.2005.09.010"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Dynamics of Gene Expression in an Artificial Genome — Implications for Biological and Artificial Ontogeny [chapter]

Torsten Reil
<span title="">1999</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
An arti cial genome with biologically plausible properties was developed and the dynamics of gene expression were studied.  ...  The results of the experiments suggest that many features of real-life development, such as cyclic gene activity, di erentiation into multiple cell types, and robusteness may be inherent properties of  ...  Acknowledgements Many thanks to Greg Werner, Julian Worby, Stevan Anastaso and Josh Bongard for helpful suggestions. I am also grateful to the EPSRC for nancial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-48304-7_63">doi:10.1007/3-540-48304-7_63</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aahhnwkzindsfblflimzjavu5a">fatcat:aahhnwkzindsfblflimzjavu5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309100220/http://pdfs.semanticscholar.org/f77f/0d3643cf2a8b43e4f17ea0b780c899980c82.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/f7/7f/f77f0d3643cf2a8b43e4f17ea0b780c899980c82.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/3-540-48304-7_63"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Effects of alternative connectivity on behavior of randomly constructed Boolean networks

Chikoo Oosawa, Michael A Savageau
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jsigantcpjamteymlcjp25zyvq" style="color: black;">Physica D : Non-linear phenomena</a> </i> &nbsp;
The dynamical properties and mutual information of these networks depend not only on their size but also on their topology and Boolean functions.  ...  Random Boolean networks (RBNs) were first introduced and used to model regulatory gene networks by Kauffman in 1969 and since then have been frequently used to model networks at various levels of biological  ...  Networks with different numbers of nodes are often used to investigate the dependence of dynamical properties on network size, and many networks are generated and analyzed under fixed K and N to identify  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-2789(02)00530-4">doi:10.1016/s0167-2789(02)00530-4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/su7y2mc5wrcypak5u73mp7n65a">fatcat:su7y2mc5wrcypak5u73mp7n65a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813033737/https://nms.kcl.ac.uk/ton.coolen/cellreprogramming/papers_mathematical/2002OosawaSavageau.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/fb/25/fb257144c9ff469d2d9fe47dc2a80618f24bc93a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-2789(02)00530-4"> <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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