Filters








7,920 Hits in 8.5 sec

Parameter identifiability analysis and visualization in large-scale kinetic models of biosystems

Attila Gábor, Alejandro F. Villaverde, Julio R. Banga
<span title="2017-05-05">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
It enables the practical identifiability analysis of dynamic models of large size, and accelerates their calibration.  ...  The results files can be visualized using Cytoscape, showing the identifiable and non-identifiable groups of parameters together with the model structure in the same graph.  ...  number 289384), and from the Spanish MINECO project "SYNBIOFACTORY" (grant number DPI2014-55276-C5-2-R).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-017-0428-y">doi:10.1186/s12918-017-0428-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28476119">pmid:28476119</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5420165/">pmcid:PMC5420165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3hz7p7sjirfndiktduz77m3bra">fatcat:3hz7p7sjirfndiktduz77m3bra</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725234309/http://digital.csic.es/bitstream/10261/149158/1/12918_2017_Article_428.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/7b/8c/7b8c2ba6db521f063231b97f4aca1a8a8669b2cc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12918-017-0428-y"> <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/PMC5420165" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Methods for checking structural identifiability of nonlinear biosystems: A critical comparison

Oana Chis, Julio R. Banga, Eva Balsa-Canto
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p3wtlm3j2fedxitkuu4bs3scau" style="color: black;">IFAC Proceedings Volumes</a> </i> &nbsp;
However, in many cases, a subset of model parameters may not be uniquely estimated, independently of the quantity and quality of data available or the numerical techniques used for estimation.  ...  Results reveal that the generating series approach combined with the identifiability tableau is the most promising to analyze large scale highly nonlinear models.  ...  INTRODUCTION The analysis of the structure and dynamics of biosystems through data-based mathematical models has received major attention in recent years.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3182/20110828-6-it-1002.00800">doi:10.3182/20110828-6-it-1002.00800</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zpvycvimbzgsrbcjmcsiaa3t64">fatcat:zpvycvimbzgsrbcjmcsiaa3t64</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200710104746/https://folk.ntnu.no/skoge/prost/proceedings/ifac11-proceedings/data/html/papers/0800.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/16/73/1673b1a47db39a00d152487086478c3affb18f56.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3182/20110828-6-it-1002.00800"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Modelling Cell Metabolism: A Review on Constraint-Based Steady-State and Kinetic Approaches

Mohammadreza Yasemi, Mario Jolicoeur
<span title="2021-02-09">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vt2hc3xcijfofb7cwnxv4hhszi" style="color: black;">Processes</a> </i> &nbsp;
We have also assessed the significance of metabolic model parameterization in kinetic models, summarizing a standard parameter estimation procedure frequently employed in kinetic metabolic modelling literature  ...  Studying cell metabolism serves a plethora of objectives such as the enhancement of bioprocess performance, and advancement in the understanding of cell biology, of drug target discovery, and in metabolic  ...  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/pr9020322">doi:10.3390/pr9020322</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vg2yj4qpxnbidoqihl7gkrtzie">fatcat:vg2yj4qpxnbidoqihl7gkrtzie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210717134826/https://res.mdpi.com/d_attachment/processes/processes-09-00322/article_deploy/processes-09-00322-v2.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/4c/89/4c8909af030ede2d33a1bbe8d148000ad7ee55db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pr9020322"> <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>

Engineering biological systems using automated biofoundries

Ran Chao, Shekhar Mishra, Tong Si, Huimin Zhao
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p47wd2skxvdwbanewzmokbss3a" style="color: black;">Metabolic Engineering</a> </i> &nbsp;
However, the artisanal processes of research and development are slow, expensive, and inconsistent, representing a major obstacle in biotechnology and bioengineering.  ...  Engineered biological systems such as genetic circuits and microbial cell factories have promised to solve many challenges in the modern society.  ...  Woese Institute for Genomic Biology at the University of Illinois at Urbana-Champaign (UIUC), Defense Advanced Research Program Agency, and National Institutes of Health (1U54DK107965).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2017.06.003">doi:10.1016/j.ymben.2017.06.003</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28602523">pmid:28602523</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5544601/">pmcid:PMC5544601</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5gx2ngwk2jeqhcmykjxtvdz7au">fatcat:5gx2ngwk2jeqhcmykjxtvdz7au</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191112170912/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5544601&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/57/8e/578e07f6f4f6daa37a15972286955782595d0a47.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymben.2017.06.003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5544601" 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 Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems [chapter]

Daniel Machado, Rafael S. Costa, Miguel Rocha, Isabel Rocha, Bruce Tidor, Eugénio C. Ferreira
<span title="">2009</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;
We briefly review modelling formalisms that have been used in Systems Biology and identify the criteria that must be addressed by an integrating framework capable of modelling, analysing and simulating  ...  Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling.  ...  Nevertheless, they still require the estimation of a large number of parameters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-02481-8_161">doi:10.1007/978-3-642-02481-8_161</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a4jah5qo5vekpcol3c6fqyn2ua">fatcat:a4jah5qo5vekpcol3c6fqyn2ua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170818023303/http://dspace.mit.edu/bitstream/handle/1721.1/73902/Tidor_A%20critical%20review.pdf?sequence=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/6c/9a/6c9ac0cef3b3dfb29502a5c9a4ee15614279d278.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-02481-8_161"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Development of Hybrid Models for a Vapor-Phase Fungi Bioreactor

Giorgia Spigno, Stefania Tronci
<span title="">2015</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wpareqynwbgqdfodcyhh36aqaq" style="color: black;">Mathematical Problems in Engineering</a> </i> &nbsp;
the development of ad hoc experiments for the evaluation of fungi kinetics and the estimation of parameters related to biofilm characteristics.  ...  modelling), and the proper use of statistical tools for the model assessment and system understanding.  ...  Different experiments were conducted both on the lab-scale reactor and in batch conditions for assessing, respectively, fluid dynamic properties and kinetic parameters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2015/801213">doi:10.1155/2015/801213</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pjqqxvcpyzfk7gg6epexcfoghq">fatcat:pjqqxvcpyzfk7gg6epexcfoghq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181103051449/https://iris.unica.it/retrieve/handle/11584/105470/54997/MPE2015ID801213.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/c0/63/c063d1c8ad3aaac6c603e7906349f2e73c9d6b07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2015/801213"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a>

Systems level modeling of the cell cycle using budding yeast

B P Ingalls, B P Duncker, D R Kim, B J McConkey
<span title="2007-12-11">2007</span> <i title="Libertas Academica, Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/arhjbkogknfc5m4fvcz76b7r6m" style="color: black;">Cancer Informatics</a> </i> &nbsp;
To date, the budding yeast Saccharomyces cerevisiae has provided the largest amount of experimental and modeling data on the progression of the cell cycle, making it a logical choice for in-depth studies  ...  and protein levels, permitting modeling of the cell cycle on the systems level.  ...  Acknowledgements We would like to thank the anonymous reviewers for their helpful comments on the manuscript, and the Canadian Institutes of Health Research for providing fi nancial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19455254">pmid:19455254</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2675848/">pmcid:PMC2675848</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/csfojcwbobhbxd7cfyner4ahv4">fatcat:csfojcwbobhbxd7cfyner4ahv4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200513151351/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2675848&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/63/a7/63a7369b9287009e9cf238801afae0ba8fabf67e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675848" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Experimental design, validation and computational modeling uncover DNA damage sensing by DNA-PK and ATM

R. J. Flassig, G. Maubach, C. Täger, K. Sundmacher, M. Naumann
<span title="">2014</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zcnlz4nminfhjcp5esifetrr4u" style="color: black;">Molecular Biosystems</a> </i> &nbsp;
A computational model predicts biphasic activation of γH2AX by DNA-PKcs and ATM-P upon DNA damage, which is induced by ionizing irradiation (IR).  ...  Acknowledgements This work was supported by the German Federal Ministry of Education and Research (SysTec, 101-31P5900) and the Ministry of Education of Saxony-Anhalt (XD3639HP/0306).  ...  This analysis revealed that 8 kinetic parameters were not fully identifiable for the given optimization constraints, i.e. upper and lower bounds restricting the parameters to fall within 4 orders of magnitude  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4mb00093e">doi:10.1039/c4mb00093e</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24833308">pmid:24833308</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jnf4pgxnpjcdfpzpi2jdb5oj2u">fatcat:jnf4pgxnpjcdfpzpi2jdb5oj2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190306220146/http://pdfs.semanticscholar.org/ccb3/b172ea9b61f69a90dc927ff537a2847a466c.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/cc/b3/ccb3b172ea9b61f69a90dc927ff537a2847a466c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c4mb00093e"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Population Pharmacokinetic Modeling To Estimate the Contributions of Genetic and Nongenetic Factors to Efavirenz Disposition

Jason D. Robarge, Ingrid F. Metzger, Jessica Lu, Nancy Thong, Todd C. Skaar, Zeruesenay Desta, Robert R. Bies
<span title="2016-10-31">2016</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5yry76lrezcodh4zk6hgwgfwfi" style="color: black;">Antimicrobial Agents and Chemotherapy</a> </i> &nbsp;
Inclusion of fat-free mass and fat mass in the model mechanistically accounted for correlation between these disposition parameters and sex, weight, and body mass index.  ...  The aim of this analysis was to develop a pharmacometric model to quantify the contribution of genetic and nongenetic factors to efavirenz pharmacokinetics.  ...  This project was supported by award number R01GM078501, 3R01GM078501-04S1, R56 grant 2R56GM067308-09A1, and 5T32-GM008425 from the National Institute of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/aac.01813-16">doi:10.1128/aac.01813-16</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27799204">pmid:27799204</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5192152/">pmcid:PMC5192152</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hgyfu73rmbagxjtxyppom4umnq">fatcat:hgyfu73rmbagxjtxyppom4umnq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724031029/http://aac.asm.org/content/61/1/e01813-16.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/b0/e3/b0e331a218d6d2a809264c421233aa08d2c4e906.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/aac.01813-16"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5192152" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structural elucidation of SrtA enzyme in Enterococcus faecalis: an emphasis on screening of potential inhibitors against the biofilm formation

Chandrabose Selvaraj, Jeyachandran Sivakamavalli, Baskaralingam Vaseeharan, Poonam Singh, Sanjeev Kumar Singh
<span title="">2014</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zcnlz4nminfhjcp5esifetrr4u" style="color: black;">Molecular Biosystems</a> </i> &nbsp;
Present work is an inclusive report of structural elucidation in SrtA and screening of potent inhibitors targeting E. faecalis through computational and experimental methodologies.  ...  The overall simulation process is a large scale 100ns timescale and represent up and down deviations in RMSD plot.  ...  ΔG SA = G SA (complex) -G SA (protein) -G SA (ligand) (4) Growth curve Kinetics Bacterial growth kinetics in the presence of screened compounds and control are monitored by inoculating in the microtiter  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c3mb70613c">doi:10.1039/c3mb70613c</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24718729">pmid:24718729</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r3h25o63z5cpbi47teq55yc6wm">fatcat:r3h25o63z5cpbi47teq55yc6wm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305134549/http://pdfs.semanticscholar.org/ca5e/45fac294b0e17fb46d5900ecc778a505fd35.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/ca/5e/ca5e45fac294b0e17fb46d5900ecc778a505fd35.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/c3mb70613c"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Multi-Scale Spatio-Temporal Modeling: Lifelines of Microorganisms in Bioreactors and Tracking Molecules in Cells [chapter]

Alexei Lapin, Michael Klann, Matthias Reuss
<span title="">2010</span> <i title="Springer Berlin Heidelberg"> Biosystems Engineering II </i> &nbsp;
The approach permits analysis of the lifelines of individual cells in space and time.  ...  In context with bioprocess and biosystems engineering there are several interesting and important applications.  ...  Acknowledgements The authors acknowledge support of the Deutsche Forschungsgemeinschaft (DFG) within the collaborative research center "Sonderforschungsbereich 412" and the Ministry of Science, Research  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/10_2009_53">doi:10.1007/10_2009_53</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20140659">pmid:20140659</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ywqd4jknerhajodlo6fukdtiw4">fatcat:ywqd4jknerhajodlo6fukdtiw4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303134545/http://pdfs.semanticscholar.org/ca70/ee21288d71b368fd5d6bc3004f99759ef8ee.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/ca/70/ca70ee21288d71b368fd5d6bc3004f99759ef8ee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/10_2009_53"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Bioinformatics—from genes to pathways

Laura Bonetta
<span title="">2004</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
Because few researchers have the resources to develop their own bioinformatics software, companies have stepped in to meet this need. Laura Bonetta reports.  ...  Data analysis and visualization A large number of companies offer software for analyzing microarray experiments.  ...  The promise of pathways Identifying hundreds of genes whose expression is markedly higher in one sample than in another provides a large amount of potentially valuable data; the trick is to home in on  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth1104-169">doi:10.1038/nmeth1104-169</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mc4zsnzxnfgi5abdsv3fzhhhgm">fatcat:mc4zsnzxnfgi5abdsv3fzhhhgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210718092737/https://www.nature.com/articles/nmeth1104-169.pdf?error=cookies_not_supported&amp;code=330f6974-5d88-479b-932f-77072016a0bf" 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/9d/25/9d25546f0bd574ba0e3c310e4b8e444ea568b7f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth1104-169"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

Maps for when the living gets tough: Maneuvering through a hostile energy landscape

Thierry D.G.A. Mondeel, Samrina Rehman, Yanfei Zhang, Malkhey Verma, Peter Dürre, Matteo Barberis, Hans V. Westerhoff
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4oklsgzkjvbihhegxblzc6b7re" style="color: black;">IFAC-PapersOnLine</a> </i> &nbsp;
We discuss the potential application of this computational framework to large-scale kinetic models of metabolism and signal transduction.  ...  We embedded enzyme kinetic model identification into a workflow consisting of derivation of kinetic equations, identifiability analysis, incremental parameter estimation, and optimal experimental design  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ifacol.2017.03.002">doi:10.1016/j.ifacol.2017.03.002</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tmddfevk7ngd3p4wdpbq7xisb4">fatcat:tmddfevk7ngd3p4wdpbq7xisb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722015650/http://www.fosbe2016.ovgu.de/fosbe2016_media/Conference+booklet.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/55/03/5503a3e787e3fdc70bc7ed886ac55a13e4e4c0ce.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.2017.03.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Towards the automated engineering of a synthetic genome

Javier Carrera, Guillermo Rodrigo, Alfonso Jaramillo
<span title="">2009</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zcnlz4nminfhjcp5esifetrr4u" style="color: black;">Molecular Biosystems</a> </i> &nbsp;
This fitness function, usually cell growth, relies on the ability to quantitatively model the biochemical networks of the cell at the genome scale using parameters inferred from high-throughput data.  ...  We restrict ourselves to global models of metabolism, transcription and DNA structure.  ...  Hence, formal methods and computational tools for the modeling and simulation of global regulatory networks have been developed. 3, 4 However, the lack of kinetic parameters for global models has promoted  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b904400k">doi:10.1039/b904400k</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19562112">pmid:19562112</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2us2zczupjcy3g6niyb4pweeje">fatcat:2us2zczupjcy3g6niyb4pweeje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120627002827/http://www.ibmcp.upv.es/JavierCarrera/papers/biosyst09.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/09/56/0956ddef794eef47cbae336a79aaac0d33a68950.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b904400k"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Data Mining, a Tool for Systems Biology or a Systems Biology Tool

Nicolas Turenne
<span title="">2009</span> <i title="OMICS Publishing Group"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cfj7yw2qavhc5f35je6wes764m" style="color: black;">Journal of computer science and systems biology</a> </i> &nbsp;
Some questions, however, remain hard to answer, for instance, which genes and interactions are required to be included in a model, how to estimate kinetic parameters and how to select a particular solution  ...  Large-scale graphical visualization (spectral, Boolean, and sparse representation) has been used recently to permit important clues in identification, in terms, for instance of dense graph components such  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jcsb.1000034e">doi:10.4172/jcsb.1000034e</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/it7fvvc5zjbsvaz5io7dp2fy74">fatcat:it7fvvc5zjbsvaz5io7dp2fy74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106152146/https://hal.inrae.fr/hal-02653741/file/2009_Turenne_Journal%20of%20Computer%20Science%20and%20Systems%20Biology_1.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/76/e8/76e8153a11f64c8872186f0284c0830c30d99470.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4172/jcsb.1000034e"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 7,920 results