Filters








149,819 Hits in 4.1 sec

Towards dynamic genome-scale models

David Gilbert, Monika Heiner, Yasoda Jayaweera, Christian Rohr
<span title="2017-10-13">2017</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;
The analysis of the dynamic behaviour of genome-scale models of metabolism (GEMs) currently presents considerable challenges because of the difficulties of simulating such large and complex networks.  ...  We describe a methodology and related workflow based on publicly available tools to profile and analyse whole-genome-scale biochemical models.  ...  metabolite concentrations 2, 3 Adding kinetic rates following the mass action law 2 Towards dynamic genome-scale models | 5 observe.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbx096">doi:10.1093/bib/bbx096</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29040409">pmid:29040409</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pfouxmijrzcobbsqwpsp3zaomy">fatcat:pfouxmijrzcobbsqwpsp3zaomy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501223924/https://bura.brunel.ac.uk/bitstream/2438/14963/3/Fulltext.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/37/53/3753bbe4bb35fa107020c769fe005156d2a8bad6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbx096"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Toward a Genome Scale Sequence Specific Dynamic Model of Cell-Free Protein Synthesis in Escherichia coli [article]

Nicholas Horvath, Michael Vilkhovoy, Joseph A. Wayman, Kara Calhoun, James Swartz, Jeffrey Varner
<span title="2017-11-06">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This study is the first to use kinetic modeling to predict dynamic protein production in a cell-free E. coli system, and should provide a foundation for genome scale, dynamic modeling of cell-free E. coli  ...  In this study, we developed an ensemble of dynamic E. coli cell-free protein synthesis (CFPS) models.  ...  Taken303 together, these findings represent the first dynamic model of E. coli cell-304 free protein synthesis, an important step toward a functional genome scale 305 description of cell free systems.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/215012">doi:10.1101/215012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhktxwictffuhloyeod4wkshqm">fatcat:zhktxwictffuhloyeod4wkshqm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429160729/https://www.biorxiv.org/content/biorxiv/early/2017/11/06/215012.full.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/b6/4c/b64c7a046100b916df1dd9f57bf433785706ddb4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/215012"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Towards a Holistic Understanding of the Human Genome by Determination and Integration of Its Sequential and Three-Dimensional Organization [chapter]

Tobias A. Knoch
<span title="">2003</span> <i title="Springer Berlin Heidelberg"> High Performance Computing in Science and Engineering &#39;03 </i> &nbsp;
Monte Carlo and Brownian Dynamic methods lead to thermodynamical equilibrium configurations. All models form chromosome territories with big voids and different chromatin morphologies.  ...  MLS model, loop size 126kbp, linker size 126 kbp, after ~50.000 MC and 1000 relaxing BD steps. Here rosettes form subcompartments as separated organizational and dynamic entities.  ...  Dynamic and Hierarchical Genome Organization 10 and 13 orders of magnitude concerning length and time scales are bridged.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-55876-4_31">doi:10.1007/978-3-642-55876-4_31</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gwmdtjvwuzbtphmfnla572wdfy">fatcat:gwmdtjvwuzbtphmfnla572wdfy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817010608/https://repub.eur.nl/pub/78165/045-Diss-Lecture-2002-Holistic-Print-Repaired-Nanoscopy-UMannheim-AbsKeyLitRef-150302opt.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/e5/96e5267930eb62c894cc6e0201943b7f00aedbcb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-55876-4_31"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Topological Evolution of Dynamical Networks: Global Criticality from Local Dynamics

Stefan Bornholdt, Thimo Rohlf
<span title="2000-06-26">2000</span> <i title="American Physical Society (APS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/pkmpevvs3bgkhal5dvrmsu5mvq" style="color: black;">Physical Review Letters</a> </i> &nbsp;
This leads to convergence of the average connectivity of the network towards the critical value K_c =2 in the limit of large system size N.  ...  How this principle could generate self-organization in natural complex systems is discussed for two examples: neural networks and regulatory networks in the genome.  ...  . + i, 87.16.Yc, 87.23.Kg FIG. 2 . 2 The average connectivity of the evolved networks converges towards K c with a scaling law ϳN 2d , d 0.47 6 0.01.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physrevlett.84.6114">doi:10.1103/physrevlett.84.6114</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10991137">pmid:10991137</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7ng67xhd2rehjd7leimzidnu34">fatcat:7ng67xhd2rehjd7leimzidnu34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809013621/http://www.ffn.ub.es/albert/complex_networks/bornholdt-rohlf.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/35/b7/35b75be423fc56cf8f86c3d40b3fdb54b238c707.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physrevlett.84.6114"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> aps.org </button> </a>

Information Dynamics of Whole Genome Adaptation

William Hercules, James Lindesay, Tshela E. Mason, Georgia M. Dunston
<span title="">2014</span> <i title="Scientific Research Publishing, Inc,"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h6mtc3fujvaonj7t5izdcljls4" style="color: black;">Natural Science</a> </i> &nbsp;
towards homeostasis.  ...  Characterizing genomic information through the lens of physics has allowed us to develop energy measures for modeling genome-environment interactions.  ...  Acknowledgements The authors wish to convey appreciation for the continuing support of the National Human Genome Center, and the Computational Physics Laboratory, at Howard University.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4236/ns.2014.615110">doi:10.4236/ns.2014.615110</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25705560">pmid:25705560</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4332707/">pmcid:PMC4332707</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pdbmspj2orhv3p74kfd3x62brq">fatcat:pdbmspj2orhv3p74kfd3x62brq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20151011121659/http://www.scirp.org/journal/PaperDownload.aspx?paperID=50325" 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/7c/d1/7cd17fbdc056726ed67af3cb3c7b3650cabbe863.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4236/ns.2014.615110"> <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/PMC4332707" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Two-dimensional annotation of genomes

Bernhard Palsson
<span title="">2004</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2bqrmk7orfmxpqzqwiiyjwide" style="color: black;">Nature Biotechnology</a> </i> &nbsp;
A growing number of genome-scale matrices are being formulated. I expect that work over the coming 5 to 10 years will determine how completely we can specify such matrices for model organisms.  ...  Genome-scale analysis in cell and molecular biology is now upon us.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt1004-1218">doi:10.1038/nbt1004-1218</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15470454">pmid:15470454</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/axmvb6adhjbldiq3i2toy6umzu">fatcat:axmvb6adhjbldiq3i2toy6umzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20050422002459/http://www.nature.com:80/cgi-taf/DynaPage.taf?file=/nbt/journal/v22/n10/full/nbt1004-1218.html&amp;filetype=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/b7/a3/b7a362793311e92f3abe2632111e9d6920e30bfc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt1004-1218"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Quantitative modeling of human metabolism: A call for a community effort

Maria Masid, Vassily Hatzimanikatis
<span title="">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2kiamltyofgjtedu6gpvliyzyy" style="color: black;">Current Opinion in Systems Biology</a> </i> &nbsp;
In this context, the human genome-scale metabolic models (GEMs) combined with mathematical methods and experimental data have been powerful tools to investigate cellular metabolism under different conditions  ...  Here, we review current methods and models to study human metabolism, and we discuss future perspectives, including a community call for an agreement on how to use GEMs in a context-specific manner for  ...  This study presents one of the most comprehensive genome-scale metabolic models for human cells.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.coisb.2021.04.008">doi:10.1016/j.coisb.2021.04.008</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vomds6sqlrasjockmi6zvjwk3y">fatcat:vomds6sqlrasjockmi6zvjwk3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716085118/https://os.zhdk.cloud.switch.ch/tind-tmp-epfl/e515a7ab-6ccc-4db3-8589-167f998390c6?response-content-disposition=attachment%3B%20filename%2A%3DUTF-8%27%271-s2.0-S2452310021000196-main.pdf&amp;response-content-type=application%2Fpdf&amp;AWSAccessKeyId=ded3589a13b4450889b2f728d54861a6&amp;Expires=1626448389&amp;Signature=dNOTQWBXoGPYn%2BClyI7k72J%2B9Yo%3D" 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/6b/4d/6b4de0ceb5bd23352411574fe3ac5d110569e87d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.coisb.2021.04.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

Optimal Mutation Rates in Dynamic Environments

M Nilsson
<span title="">2002</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zasl75vjunffjdn7osabykmsua" style="color: black;">Bulletin of Mathematical Biology</a> </i> &nbsp;
In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments.  ...  Surprisingly it turns out that the optimal mutation rate per genome is approximately independent of genome length, something that also has been observed in nature.  ...  same types of time-dynamics and time-scales.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/bulm.2002.0314">doi:10.1006/bulm.2002.0314</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12508529">pmid:12508529</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2tkjrdqqhrgqbno2fwdcunewei">fatcat:2tkjrdqqhrgqbno2fwdcunewei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723151703/http://cds.cern.ch/record/435247/files/0004042.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/ea/47/ea4740f02ff9bf3c2e58e1e3e4e0e8648529bf7d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/bulm.2002.0314"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Optimal Mutation Rates in Dynamic Environments [article]

Martin Nilsson, Nigel Snoad
<span title="2000-04-19">2000</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
In this paper we study the evolution of the mutation rate for simple organisms in dynamic environments.  ...  Surprisingly it turns out that the optimal mutation rate per genome is approximately independent of genome length, something that also has been observed in nature.  ...  same types of time-dynamics and time-scales.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/physics/0004042v1">arXiv:physics/0004042v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dcyafufzpzgozehvsjfcooascy">fatcat:dcyafufzpzgozehvsjfcooascy</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/arxiv-physics0004042/physics0004042.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> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/physics/0004042v1" 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>

Navigating Multi-scale Cancer Systems Biology towards Model-driven Personalized Therapeutics [article]

Mahnoor Naseer Gondal, Safee Ullah Chaudhary
<span title="2021-05-17">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
of personalized in silico multi-scale models in clinical settings.  ...  Furthermore, the annotation of these single- or multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making  ...  Towards addressing this challenge, in 2008, Albert et al. reported BooleanNet (250), an open-source, freely available Boolean modeling software for large-scale simulations of dynamic .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.17.444410">doi:10.1101/2021.05.17.444410</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vbfvmtb5irdapglgkmh5na73je">fatcat:vbfvmtb5irdapglgkmh5na73je</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718093457/https://www.biorxiv.org/content/biorxiv/early/2021/05/17/2021.05.17.444410.full.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/64/ee/64eeb846895c5381e03d3df287b49bd2baaed373.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.05.17.444410"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Principles of chromatin organization in yeast: relevance of polymer models to describe nuclear organization and dynamics

Renjie Wang, Julien Mozziconacci, Aurélien Bancaud, Olivier Gadal
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ixz5kl2tebc7ncnuhe4feep6ly" style="color: black;">Current Opinion in Cell Biology</a> </i> &nbsp;
(a) Contact map of the 16 chromosomes as obtained by genome-wide 3C ([23] model of polymer dynamics.  ...  The second regime corresponds to Rouse model of polymer dynamics, in which the MSD increases with time with a power-law scaling of 0.54.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ceb.2015.04.004">doi:10.1016/j.ceb.2015.04.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25956973">pmid:25956973</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fyejbmgeafbutmxurx6e7lu6ja">fatcat:fyejbmgeafbutmxurx6e7lu6ja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922064607/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/008/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDk1NTA2NzQxNTAwMDQ0Nw%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/17/b3/17b345f711981c163c079269b800a3b34cc3fda9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ceb.2015.04.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

4D nucleome modeling

Marco Di Stefano, Jonas Paulsen, Daniel Jost, Marc A Marti-Renom
<span title="2020-11-27">2021</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qhtovwh4tnbidpwnclhjhvvr6u" style="color: black;">Current Opinion in Genetics and Development</a> </i> &nbsp;
The intrinsic dynamic nature of chromosomes is emerging as a fundamental component in regulating DNA transcription, replication, and damage-repair among other nuclear functions.  ...  With this increased awareness, reinforced over the last ten years, many new experimental techniques, mainly based on microscopy and chromosome conformation capture, have been introduced to study the genome  ...  Once defined, this null chromatin model should allow developing efficient multi-scale coarse-graining strategies to simulate both the local fast dynamics and the slow full genome motion over relevant time-scales  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gde.2020.10.004">doi:10.1016/j.gde.2020.10.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33253996">pmid:33253996</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8098745/">pmcid:PMC8098745</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ccowownenfdkdjcyg5fgxgdwpe">fatcat:ccowownenfdkdjcyg5fgxgdwpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220126024126/https://www.duo.uio.no/bitstream/handle/10852/83132/1-s2.0-S0959437X2030143X-main.pdf?sequence=2" 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/f6/d4/f6d4123d75da93f452580a3c8d156503f15675c5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.gde.2020.10.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8098745" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Parameter Estimation for Dynamic Resource Allocation in Microorganisms: A Bi-level Optimization Problem

Francis Mairet, Térence Bayen
<span title="">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4oklsgzkjvbihhegxblzc6b7re" style="color: black;">IFAC-PapersOnLine</a> </i> &nbsp;
In compliance with evolutionary principles, coarse-grained or genome-scale models of microbial growth can be used to determine optimal resource allocation scheme under dynamic environmental conditions.  ...  In compliance with evolutionary principles, coarse-grained or genome-scale models of microbial growth can be used to determine optimal resource allocation scheme under dynamic environmental conditions.  ...  These approaches involve a number of (unknown) parameters, ranging from a few for coarse-grained models to hundreds, even thousands for genome-scale models.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ifacol.2020.12.1163">doi:10.1016/j.ifacol.2020.12.1163</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qx3symbcnjadnblgse2rqlu24e">fatcat:qx3symbcnjadnblgse2rqlu24e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715193414/https://archimer.ifremer.fr/doc/00690/80163/83228.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/98/46/98463b40a8091e439cbf9c9e77819b860517b556.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ifacol.2020.12.1163"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Scale-free duplication dynamics: A model for ultraduplication

M. V. Koroteev, J. Miller
<span title="2011-12-28">2011</span> <i title="American Physical Society (APS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nuk2stxzvvhf7ljciu325kj77m" style="color: black;">Physical Review E</a> </i> &nbsp;
We propose and study here scale-free duplication dynamics, a class of model for genome sequence evolution that generates the observed shapes of this distribution.  ...  dynamics; values of the exponents for this model have been derived analytically [5] .  ...  We thank Sydney Brenner for stressing the fundamental role of linkage in our earlier observations [15] ; Holger Jenke-Kodama for suggesting cyanobacterial genomes; Alexander Mikheyev, Sydney Brenner,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physreve.84.061919">doi:10.1103/physreve.84.061919</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22304128">pmid:22304128</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ywkc2yjqvncgrmczm4pz4pisru">fatcat:ywkc2yjqvncgrmczm4pz4pisru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808215916/http://mediasv.oist.jp/images/stories/annual_report/fy2010/phys-a-bio/Scale-free_duplication_dynamics_a_model_for_ultraduplication2.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/72/a7/72a737baeb0dddfb13637b1d56c18683587132b9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physreve.84.061919"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> aps.org </button> </a>

Review and perspective on mathematical modeling of microbial ecosystems

Antonella Succurro, Oliver Ebenhöh
<span title="2018-03-14">2018</span> <i title="Portland Press Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7mkbrnlivja5pa4r3nxerw3ubi" style="color: black;">Biochemical Society Transactions</a> </i> &nbsp;
Indeed, approaches that can capture multiple scales are needed in order to understand emergent patterns in ecosystems and their dynamics regulated by different spatio-temporal phenomena.  ...  Mathematical models with their abstraction capability are essential to capture the underlying phenomena and connect the different scales at which these systems act.  ...  However, genome-scale metabolic modeling alone ignores a fundamental aspect of ecosystems: the cellular response to dynamic environmental changes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1042/bst20170265">doi:10.1042/bst20170265</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29540507">pmid:29540507</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5906705/">pmcid:PMC5906705</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/elohppvrifcnxahhzl2jwuujaq">fatcat:elohppvrifcnxahhzl2jwuujaq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223092339/http://pdfs.semanticscholar.org/452f/4148d9b8c0899a0f06ea3063b5fc689389d6.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/45/2f/452f4148d9b8c0899a0f06ea3063b5fc689389d6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1042/bst20170265"> <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/PMC5906705" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 149,819 results