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Parameter identification for stochastic hybrid models of biological interaction networks

Eugenio Cinquemani, Riccardo Porreca, Giancarlo Ferrari-Trecate, John Lygeros
<span title="">2007</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wjd7b2sxyfahnaei4xvi46vwsu" style="color: black;">2007 46th IEEE Conference on Decision and Control</a> </i> &nbsp;
Based on a model of subtilin production by Bacillus subtilis, in this paper we discuss the parameter identification of stochastic hybrid dynamics that are typically found in biological regulatory networks  ...  In accordance with the structure of the model, identification is split in two subproblems: estimation of the genetic network regulating subtilin production from gene expression data, and estimation of  ...  Finally, switches S 4 and S 5 are modeled as binary random processes, which makes the system a stochastic hybrid one.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/cdc.2007.4434647">doi:10.1109/cdc.2007.4434647</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/cdc/CinquemaniPFL07.html">dblp:conf/cdc/CinquemaniPFL07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/znbqu7jhyzhthp3vsinorii4da">fatcat:znbqu7jhyzhthp3vsinorii4da</a> </span>
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Review of stochastic hybrid systems with applications in biological systems modeling and analysis

Xiangfang Li, Oluwaseyi Omotere, Lijun Qian, Edward R. Dougherty
<span title="2017-06-30">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gm2h5mhstjf3tmwayeiyvkxxve" style="color: black;">EURASIP Journal on Bioinformatics and Systems Biology</a> </i> &nbsp;
Stochastic hybrid systems (SHS) have attracted a lot of research interests in recent years.  ...  Due to the nature of molecular interactions, many biological processes can be conveniently described as a mixture of continuous and discrete phenomena employing SHS models.  ...  An algorithm for estimating the parameters of a given biochemical reaction network based on a stochastic hybrid model is proposed by Mikeev et al. [70] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13637-017-0061-5">doi:10.1186/s13637-017-0061-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28667450">pmid:28667450</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5493609/">pmcid:PMC5493609</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oaxkf5lv7jhmbkxg4c5rvupyba">fatcat:oaxkf5lv7jhmbkxg4c5rvupyba</a> </span>
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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;
Integration of different kinds of biological processes is an ultimate goal for whole-cell modelling.  ...  different biological networks.  ...  Extensions such as stochastic, continuous and hybrid nets provide a great flexibility for modelling metabolic, regulatory and signalling networks.  ... 
<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>

Chemical Master Equation Closure for Computer-Aided Synthetic Biology [chapter]

Patrick Smadbeck, Yiannis N. Kaznessis
<span title="2014-11-13">2014</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
These models take the form of chemical reaction networks. The importance of stochasticity is discussed and methods to simulate stochastic reaction networks are reviewed.  ...  Because of its ambitious character, the master equation remained unsolved for all but the simplest of molecular interaction networks for over seventy years.  ...  Support from the University of Minnesota Digital Technology Center and the University of Minnesota Biotechnology Institute is also acknowledged.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-1878-2_9">doi:10.1007/978-1-4939-1878-2_9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25487098">pmid:25487098</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4820257/">pmcid:PMC4820257</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gnvveo3onzhtfefhgb5icihb3e">fatcat:gnvveo3onzhtfefhgb5icihb3e</a> </span>
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Perspectives on systems biology

Hiroaki Kitano
<span title="">2000</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tg7qlmhqujdc7af72ot22mh7y4" style="color: black;">New generation computing</a> </i> &nbsp;
System Structure Identification• Approaches for Structure Identification:3) Hybrid Approach -It is likely that some knowledge should be assumed in the process of gene network inference.  ...  -Aim: to build a precise simulation model so that dynamical properties of system can be analyzed by changing parameters. 4.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bf03037529">doi:10.1007/bf03037529</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/o7urcr7msvbh3fg6in42uxvdjm">fatcat:o7urcr7msvbh3fg6in42uxvdjm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809011713/http://www.bii.a-star.edu.sg/docs/sbg/jc/Feb_18_2003_Eric.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/0c/b9/0cb9661f5a524be6283b847efafd0209fa55ac28.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/bf03037529"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </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.  ...  However, the delineation of the possible associations and causalities of genes, proteins, metabolites, cells and other biological entities from high throughput time course omics data is challenging for  ...  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>

Systems interface biology

Francis J. Doyle, Jörg Stelling
<span title="2006-08-08">2006</span> <i title="The Royal Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kdv34qlmv5gsfphm6vnme655ia" style="color: black;">Journal of the Royal Society Interface</a> </i> &nbsp;
networks.  ...  The field of systems biology has attracted the attention of biologists, engineers, mathematicians, physicists, chemists and others in an endeavour to create systems-level understanding of complex biological  ...  We acknowledge the financial support to F.J.D. from the Institute for Collaborative Biotechnologies through grant DAAD19-03-D-0004 from the US Army Research Office.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2006.0143">doi:10.1098/rsif.2006.0143</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16971329">pmid:16971329</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1664650/">pmcid:PMC1664650</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rqtnqq6ulvc5ldya75qha7di5u">fatcat:rqtnqq6ulvc5ldya75qha7di5u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100627162823/http://cepac.cheme.cmu.edu/pasi2008/slides/doyle/library/reading/Doyle_and_Stelling_Interface_2006.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/81/21/812140e0cfc17e0b37ad6d47b19b0579c669030e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1098/rsif.2006.0143"> <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/PMC1664650" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Foundations of formal reconstruction of biochemical networks

Monika Heiner, Adelinde Uhrmacher
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/elaf5sq7lfdxfdejhkqbtz6qoq" style="color: black;">Theoretical Computer Science</a> </i> &nbsp;
On the contrary, the second paper, ''Parameter estimation for Boolean models of biological networks'' by Dimitrova et al., follows an algebraic approach to structure identification within the modelling  ...  The next step consists of refining a qualitative model into a quantitative one; i.e. the outcome is a stochastic, continuous or hybrid model.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tcs.2011.02.001">doi:10.1016/j.tcs.2011.02.001</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n4sca5lyk5annbkdl36a2aa57i">fatcat:n4sca5lyk5annbkdl36a2aa57i</a> </span>
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Multi-level and hybrid modelling approaches for systems biology

R. Bardini, G. Politano, A. Benso, S. Di Carlo
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cmflnsn2l5gylcviv447te3mku" style="color: black;">Computational and Structural Biotechnology Journal</a> </i> &nbsp;
A B S T R A C T During the last decades, high-throughput techniques allowed for the extraction of a huge amount of data from biological systems, unveiling more of their underling complexity.  ...  Models which are both multi-level and hybrid satisfy both these requirements, making a very useful tool in computational systems biology.  ...  On average, models in systems biology aim at representing large networks of interacting entities, each interaction corresponding to one of such parameters.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.csbj.2017.07.005">doi:10.1016/j.csbj.2017.07.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28855977">pmid:28855977</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5565741/">pmcid:PMC5565741</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pgzmw6qv2vbi5gmqfympokm6hm">fatcat:pgzmw6qv2vbi5gmqfympokm6hm</a> </span>
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A Logical Paradigm for Systems Biology (Invited Talk)

François Fages, Marc Herbstritt
<span title="2010-06-25">2010</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lp3a6vqizfdbvlneh2os4i6swe" style="color: black;">International Conference on Logic Programming</a> </i> &nbsp;
Our approach relies on a logical paradigm for systems biology which consists in making the following identifications: biological model = quantitative state transition system biological properties = temporal  ...  Based on these structures, mathematical models can be developed by equipping such molecular interaction networks with kinetic expressions leading to quantitative models of mainly two kinds: ordinary differential  ...  BioCham has been used for querying large Boolean models of the cell cycle by symbolic model-checking [1] , formalizing phenotypes in temporal logic [3] , searching parameter values from temporal specification  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/lipics.iclp.2010.2">doi:10.4230/lipics.iclp.2010.2</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/iclp/Fages10.html">dblp:conf/iclp/Fages10</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j2p4jn3lfrczhnbrj6nmd72ogu">fatcat:j2p4jn3lfrczhnbrj6nmd72ogu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200322214004/http://contraintes.inria.fr/~fages/Papers/Fages10iclp.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/46/88/4688772f0cc023dbc31b6a96b48c74ccfabd33a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/lipics.iclp.2010.2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Importance of Input Perturbations and Stochastic Gene Expression in the Reverse Engineering of Genetic Regulatory Networks: Insights From an Identifiability Analysis of an In Silico Network

D. E. Zak
<span title="2003-11-01">2003</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
Also, with the exception of cases where the noise due to stochastic gene expression was high, complex perturbations were more favorable for identifying the network than simple ones.  ...  It was observed that, in addition to prior structural knowledge, prior knowledge of kinetic parameters, particularly mRNA degradation rate constants, was necessary for the network to be identifiable.  ...  for network identification.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1198103">doi:10.1101/gr.1198103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14597654">pmid:14597654</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC403758/">pmcid:PMC403758</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eisin6ifxbfyrdx5blum5wjwd4">fatcat:eisin6ifxbfyrdx5blum5wjwd4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720101756/https://genome.cshlp.org/content/13/11/2396.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/ff/82/ff82d904bf4fd72285991f94c519fc5b64e9f44a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.1198103"> <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/PMC403758" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Optimization in computational systems biology

Julio R Banga
<span title="">2008</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;
Examples are given where optimization methods are used for topics ranging from model building and optimal experimental design to metabolic engineering and synthetic biology.  ...  This commentary is focused on applications of mathematical optimization in computational systems biology.  ...  Acknowledgements The author would like to thank Matt Hodgkinson for his valuable comments, and acknowledges financial support from EU project BaSysBio LSHG-CT-2006-037469  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-2-47">doi:10.1186/1752-0509-2-47</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18507829">pmid:18507829</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2435524/">pmcid:PMC2435524</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/st2yu6xte5d5hkg2ez3plk4daa">fatcat:st2yu6xte5d5hkg2ez3plk4daa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171129043027/https://core.ac.uk/download/pdf/36016853.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/7f/ed/7fed224dd7b5c4511ba5deba83ba055f52ba8d84.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-2-47"> <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/PMC2435524" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modelling cellular signalling systems

Padmini Rangamani, Ravi Iyengar
<span title="2008-09-30">2008</span> <i title="Portland Press Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y5hbc7qpnjd73b3umji6wrwbce" style="color: black;">Essays in Biochemistry</a> </i> &nbsp;
Computational modelling of cell signalling pathways is emerging as a tool that facilitates mechanistic understanding of complex biological systems.  ...  Depending on the nature of the process being modelled and the scale of the model, different mathematical formulations, ranging from stochastic representations to ordinary and partial differential equations  ...  It is anticipated that for large signalling networks, hybrid models will be built where part of the system follows deterministic behaviour and the rest of the system follows stochastic behaviour.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1042/bse0450083">doi:10.1042/bse0450083</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18793125">pmid:18793125</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3270941/">pmcid:PMC3270941</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xual5zki7jfn3oxlnxpygldlky">fatcat:xual5zki7jfn3oxlnxpygldlky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208230601/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3270941&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/d1/74/d174088799e59ec71e175c38a8dff0a043c8124e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1042/bse0450083"> <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/PMC3270941" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Construction of a cancer-perturbed protein-protein interaction network for discovery of apoptosis drug targets

Liang-Hui Chu, Bor-Sen Chen
<span title="">2008</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;
Next, we applied a nonlinear stochastic model, maximum likelihood parameter estimation, and Akaike Information Criteria (AIC) to eliminate false-positive protein-protein interactions in our initial protein  ...  Conclusion: Our method allows identification of cancer-perturbed protein-protein interactions involved in apoptosis and identification of potential molecular targets for development of anticancer drugs  ...  Acknowledgements The study is supported by the National Science Council of Taiwan under grant No. NSC 95-2627-B-007-011.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-2-56">doi:10.1186/1752-0509-2-56</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18590547">pmid:18590547</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2488323/">pmcid:PMC2488323</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xwyvu2uxyngp5m2yh76ewzdt6m">fatcat:xwyvu2uxyngp5m2yh76ewzdt6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830054154/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-2-56?site=http://bmcsystbiol.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/25/81/25817a169ac493c22ab3d611b4a012449965fc72.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-2-56"> <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/PMC2488323" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Modeling of gene regulatory networks: A review

Nedumparambathmarath Vijesh, Swarup Kumar Chakrabarti, Janardanan Sreekumar
<span title="">2013</span> <i title="Scientific Research Publishing, Inc,"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ok4mzlk3yfcl5gpvlswfyknepa" style="color: black;">Journal of Biomedical Science and Engineering</a> </i> &nbsp;
Gene regulatory networks play an important role the molecular mechanism underlying biological processes. Modeling of these networks is an important challenge to be addressed in the post genomic era.  ...  Computational methods for development of network models and analysis of their functionality have proved to be valuable tools in bioinformatics applications.  ...  ACKNOWLEDGEMENTS The authors wish to acknowledge the financial support provided by Department of Information Technology (DIT) Government of India for carrying out this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4236/jbise.2013.62a027">doi:10.4236/jbise.2013.62a027</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dxpzycz4cbd47oz6oa32prmpiy">fatcat:dxpzycz4cbd47oz6oa32prmpiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923022043/http://file.scirp.org/pdf/JBiSE_2013022716483315.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/c0/80/c0808885948f8fc0d3c31dd9594646e317017cd1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4236/jbise.2013.62a027"> <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>
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