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Investigating the dynamic behavior of biochemical networks using model families

M. D. Haunschild, B. Freisleben, R. Takors, W. Wiechert
<span title="2004-12-16">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: Supporting the evolutionary modeling process of dynamic biochemical networks based on sampled in vivo data requires more than just simulation.  ...  Powerful automatic methods are then required to assist the modeler in the organization and the evaluation of alternative models.  ...  However, in practice the regulatory structure of biochemical networks and in particular the reaction kinetic details are still only partially known.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti225">doi:10.1093/bioinformatics/bti225</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15604106">pmid:15604106</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3l4y5odjfrfs5cyklopcoijozi">fatcat:3l4y5odjfrfs5cyklopcoijozi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070128121432/http://bioinformatics.oxfordjournals.org:80/cgi/reprint/21/8/1617.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/06/49/064976c1a6639b4f038d87986a3efffc8027ed9a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti225"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Unravelling the regulatory structure of biochemical networks using stimulus response experiments and large-scale model selection

S.A. Wahl, M.D. Haunschild, M. Oldiges, W. Wiechert
<span title="">2006</span> <i title="Institution of Engineering and Technology (IET)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jcqfck5vhvabba7fe7yr56cuie" style="color: black;">IEE Proceedings - Systems Biology</a> </i> &nbsp;
To unravel the complex in vivo regulatory interdependences of biochemical networks, experiments with the living organism are absolutely necessary.  ...  SREs are applied to determine enzyme kinetic parameters and to find unknown enzyme regulatory mechanisms.  ...  There are strong structural similarities between biochemical networks and technical networks [2] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1049/ip-syb:20050089">doi:10.1049/ip-syb:20050089</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16986629">pmid:16986629</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f4gyfivgdncd3b7xkhedmz3cla">fatcat:f4gyfivgdncd3b7xkhedmz3cla</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060903020507/http://www.informatics.indiana.edu/schnell/papers/ieepsb153-275.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/53/65/536516f23d49ef3aa7d5f10a488cd5789d96a835.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1049/ip-syb:20050089"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Chemical Kinetics Based Modelling Approaches and Tools for Investigating Complex Biological Systems

<span title="">2014</span> <i title="Asian Journal of Chemistry"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/64p6ou7nvfevbdpianqf6sywei" style="color: black;">Asian Journal of Chemistry</a> </i> &nbsp;
This review presents a detailed account on how basic biochemical kinetics principles and computational tools are utilized to mathematically model and analyze such complex regulations.  ...  Biological systems are governed by their inherent complex molecular regulatory networks at multiple levels.  ...  Bhartiya and Prof. K.V. Venkatesh, IIT Bombay for useful discussions. This work was supported by the Prof. TRR Research grant provided by SASTRA University.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14233/ajchem.2014.15756">doi:10.14233/ajchem.2014.15756</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ueyzvfcxtbbyxfsebalju4mtgm">fatcat:ueyzvfcxtbbyxfsebalju4mtgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220309073051/https://asianjournalofchemistry.co.in/User/ViewFreeArticle.aspx?ArticleID=26_10_3" 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/e2/24/e2246cec55bb573c205d9be9a23a9e0c4ded3c76.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.14233/ajchem.2014.15756"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Odefy -- From discrete to continuous models

Jan Krumsiek, Sebastian Pölsterl, Dominik M Wittmann, Fabian J Theis
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
and a regulatory network giving rise to a specific spatial expression pattern at the mid-hindbrain boundary.  ...  As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable.  ...  This research was partially supported by the Initiative and Networking Fund of the Helmholtz Association within the Helmholtz Alliance on Systems Biology (project CoReNe).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-233">doi:10.1186/1471-2105-11-233</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20459647">pmid:20459647</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2873544/">pmcid:PMC2873544</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ypeph3oyfvgc5mrxlrbw5l3wmq">fatcat:ypeph3oyfvgc5mrxlrbw5l3wmq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830102615/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-11-233?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/86/57/8657cc5bbdd3a9db74ec5455e7b8980681b63b75.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-233"> <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/PMC2873544" 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 sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins

Brandon M. Invergo, Ludovica Montanucci, Jaume Bertranpetit
<span title="2015-12-02">2015</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;
We employed a comprehensive mathematical model of mammalian phototransduction to predict the degree of influence that each protein in the system exerts on the high-level dynamic behaviour.  ...  We have employed a combination of systems biology and molecular evolution analyses in a first attempt to unravel this relationship.  ...  We also thank Ben Lehner and Luis Serrano for helpful discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspb.2015.2215">doi:10.1098/rspb.2015.2215</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26631565">pmid:26631565</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4685781/">pmcid:PMC4685781</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fhzm2bmwzzfhzlxlo426dxywru">fatcat:fhzm2bmwzzfhzlxlo426dxywru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225180435/http://pdfs.semanticscholar.org/6625/daec2534703fe50e8b1f6bf267c7de6d25c1.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/66/25/6625daec2534703fe50e8b1f6bf267c7de6d25c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rspb.2015.2215"> <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/PMC4685781" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detailed map of a cis-regulatory input function

Y. Setty, A. E. Mayo, M. G. Surette, U. Alon
<span title="2003-06-12">2003</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;
Some biochemical parameters appear only in combinations (␣a, ␤bd).  ...  The model has nine biochemical parameters, including affinities of CRP and LacI to their DNA sites and their inducers, affinity of RNAP to the promoter in the presence and absence of bound CRP-cAMP, and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1230759100">doi:10.1073/pnas.1230759100</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12805558">pmid:12805558</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC164651/">pmcid:PMC164651</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xgosgl3q5na4nhn6dgmu3jmlg4">fatcat:xgosgl3q5na4nhn6dgmu3jmlg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170813105536/http://www.sfu.ca/~eemberly/phys847/papers/lac_logic.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/a5/fe/a5fe1bd3eb8544bbd51b1a0596d3f1531e5c4b00.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1230759100"> <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/PMC164651" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational dynamic approaches for temporal omics data with applications to systems medicine

Yulan Liang, Arpad Kelemen
<span title="2017-06-17">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ormhpxv5gvemfj2eljfl5fxnzm" style="color: black;">BioData Mining</a> </i> &nbsp;
Modeling and predicting biological dynamic systems and simultaneously estimating the kinetic structural and functional parameters are extremely important in systems and computational biology.  ...  In this paper, we present various recently developed dynamic trajectory and causal network approaches for temporal omics data, which are extremely useful for those researchers who want to start working  ...  Availability of data and materials Data sharing not applicable to this article as no datasets were generated or analysed during the current study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13040-017-0140-x">doi:10.1186/s13040-017-0140-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28638442">pmid:28638442</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5473988/">pmcid:PMC5473988</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rscvtjlpgrf53fbwlt6t4i22em">fatcat:rscvtjlpgrf53fbwlt6t4i22em</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721164800/https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-017-0140-x?site=biodatamining.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/70/1e/701ec22d329a2a0284f3738e979836b61a367ed9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13040-017-0140-x"> <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/PMC5473988" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Robustness and lethality in multilayer biological molecular networks

Xueming Liu, Enrico Maiorino, Arda Halu, Kimberly Glass, Rashmi B. Prasad, Joseph Loscalzo, Jianxi Gao, Amitabh Sharma
<span title="2020-11-27">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
of interaction in models of complex biological systems.  ...  We integrate heterogeneous sources of data to construct a multilayer interaction network composed of a gene regulatory layer, a protein–protein interaction layer, and a metabolic layer.  ...  (grants D700382 and CV-19).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-19841-3">doi:10.1038/s41467-020-19841-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33247151">pmid:33247151</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bekp3trx3zcfhffmj3xz5shn7e">fatcat:bekp3trx3zcfhffmj3xz5shn7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429013324/https://www.nature.com/articles/s41467-020-19841-3.pdf?error=cookies_not_supported&amp;code=489592fa-a113-4a04-9d57-81d2e50ea60b" 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/aa/06/aa06fb724f27cc3edd133a285f493c3e87b9a32a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-020-19841-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a>

Computer-aided whole-cell design: taking a holistic approach by integrating synthetic with systems biology [article]

Lucia Marucci, Matteo Barberis, Jonathan Karr, Oliver Ray, Paul R. Race, Miguel de Souza Andrade, Claire Grierson, Stefan Andreas Hoffmann, Sophie Landon, Elibio Rech, Joshua Rees-Garbutt, Richard Seabrook (+2 others)
<span title="2020-06-04">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We show how these models could significantly aid in the design and learn phases while reducing experimental testing by presenting case studies spanning from genome minimization to cell-free systems, and  ...  Here, we present a perspective on how whole-cell, multiscale models could transform design-build-test-learn cycles in synthetic biology.  ...  We sincerely thank Dr Kathleen Sedgley for her support with the workshop organization, and Dr Thomas Gorochowski for participating in discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2006.02720v1">arXiv:2006.02720v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zyv26a5mhvfxnfm2wsmcyjn5km">fatcat:zyv26a5mhvfxnfm2wsmcyjn5km</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200914045804/https://arxiv.org/ftp/arxiv/papers/2006/2006.02720.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/f5/d8/f5d8ecb5ec922809262a37d8aecdabfc0ade99d0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2006.02720v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Hypoxic Adaptation of Mitochondrial Metabolism in Rat Cerebellum Decreases in Pregnancy

Graf, Trofimova, Ksenofontov, Baratova, Bunik
<span title="2020-01-07">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3iichab3fbz7jq46o55l6trkq" style="color: black;">Cells</a> </i> &nbsp;
Thus, the cerebellar amino acid levels and OGDHC activity provide sensitive markers of the physiology-dependent organization of metabolic network and its stress adaptations.  ...  Modelling such challenges by pregnancy and/or hypoxia, we characterize the amino acid pool in the rat cerebellum, quantifying the levels and correlations of 15 amino acids and activity of 2-oxoglutarate  ...  Kulakovskaya (Faculty of Biology, Moscow Lomonosov State University) and G.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cells9010139">doi:10.3390/cells9010139</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31936131">pmid:31936131</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7016955/">pmcid:PMC7016955</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tvwnpfgtuzdrrcyefn2dueoelq">fatcat:tvwnpfgtuzdrrcyefn2dueoelq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200109025954/https://res.mdpi.com/d_attachment/cells/cells-09-00139/article_deploy/cells-09-00139.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/3a/73/3a735bb9b8be8ec6f260559020580ccee619057b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cells9010139"> <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/PMC7016955" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multiscale statistical physics of the Human-SARS-CoV-2 interactome [article]

Arsham Ghavasieh, Sebastiano Bontorin, Oriol Artime, Manlio De Domenico
<span title="2020-08-21">2020</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our results show that classic analysis such as percolation is not sensitive to the distinguishing features of viruses, whereas the analysis of biochemical spreading patterns allows us to meaningfully categorize  ...  Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing  ...  In the context of Regulatory and Biochemical dynamics we model the effect of viral interaction as an inhibition in the activity of the affected nodes or decrease in the concentration.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2008.09649v1">arXiv:2008.09649v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ae3lnmyvvbblnmq4lflq4qg52e">fatcat:ae3lnmyvvbblnmq4lflq4qg52e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201016230429/https://arxiv.org/pdf/2008.09649v1.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] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2008.09649v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Parametric sensitivity analysis for biochemical reaction networks based on pathwise information theory

Yannis Pantazis, Markos A Katsoulakis, Dionisios G Vlachos
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks.  ...  The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks.  ...  complex models for gene regulatory networks, [55] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-311">doi:10.1186/1471-2105-14-311</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24148216">pmid:24148216</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4015035/">pmcid:PMC4015035</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pzcqd3parze7djy73ir6h3gra4">fatcat:pzcqd3parze7djy73ir6h3gra4</a> </span>
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Parametric Sensitivity Analysis for Biochemical Reaction Networks based on Pathwise Information Theory [article]

Yannis Pantazis and Markos A. Katsoulakis and Dionisios G. Vlachos
<span title="2013-08-01">2013</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Stochastic modeling and simulation provide powerful predictive methods for the intrinsic understanding of fundamental mechanisms in complex biochemical networks.  ...  The structure of the FIM turns out to be block-diagonal, revealing hidden parameter dependencies and sensitivities in reaction networks.  ...  gene regulatory networks, [54] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1304.3962v2">arXiv:1304.3962v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vq2phwokovgexfoxl4477pstsm">fatcat:vq2phwokovgexfoxl4477pstsm</a> </span>
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Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis

Clemens Kühn, Sara Checa
<span title="2019-03-27">2019</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;
Our analysis unravels the relevance of the stability of the active notch intracellular domain as a dominating hub in this regulatory network.  ...  We provide our computational model and simulation engine for integration in complementary modeling approaches.  ...  ACKNOWLEDGMENTS We thank Edda Klipp for providing computers at the Theoretical Biophysics Department of the Humboldt-Universität zu Berlin, and Ivo Maintz for helping with them.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fphys.2019.00288">doi:10.3389/fphys.2019.00288</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30971939">pmid:30971939</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6445957/">pmcid:PMC6445957</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/of6q4xcjvzhvrk7p5w5vnamemm">fatcat:of6q4xcjvzhvrk7p5w5vnamemm</a> </span>
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Autotrophic Stoichiometry Emerging from Optimality and Variable Co-limitation

Kai W. Wirtz, Onur Kerimoglu
<span title="2016-11-23">2016</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sdhva7kh2febjl6ejo6uomjrhq" style="color: black;">Frontiers in Ecology and Evolution</a> </i> &nbsp;
Our approach constitutes a basis for improved mechanistic understanding and modeling of acclimative processes in autotrophic organisms.  ...  The combination of network independence and optimal regulation displays unprecedented skill in reproducing rich stoichiometric patterns collected from a large number of published chemostat experiments.  ...  At large washout rate D approaching maximal growth rate, the model reacts sensitively to small variations of growth parameters that determine V C at replete conditions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fevo.2016.00131">doi:10.3389/fevo.2016.00131</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hy6yxblmkjeg7jh2lsasup6ux4">fatcat:hy6yxblmkjeg7jh2lsasup6ux4</a> </span>
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