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On the Difficulty of Inferring Gene Regulatory Networks: A Study of the Fitness Landscape Generated by Relative Squared Error [chapter]

Francesco Sambo, Marco A. Montes de Oca, Barbara Di Camillo, Thomas Stützle
<span title="">2010</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;
In this paper, we use recurrent neural networks to model regulatory interactions and study systematically the "fitness landscape" that results from measuring the relative squared error.  ...  Although the results of the study indicate that the generated landscapes have a positive fitness-distance correlation, the error values span several orders of magnitude over very short distance variations  ...  gene regulation and relative squared error is chosen as a fitness function.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-14156-0_7">doi:10.1007/978-3-642-14156-0_7</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u4lb64urinao7j6y43v5axjnu4">fatcat:u4lb64urinao7j6y43v5axjnu4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226055929/http://pdfs.semanticscholar.org/6d50/2e92646826a6698c9104dce70341aca77501.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/6d/50/6d502e92646826a6698c9104dce70341aca77501.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-14156-0_7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Advances to Bayesian network inference for generating causal networks from observational biological data

J. Yu, V. A. Smith, P. P. Wang, A. J. Hartemink, E. D. Jarvis
<span title="2004-07-29">2004</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Here, we use a simulation approach to make advances in our dynamic Bayesian network (DBN) inference algorithm, especially in the context of limited quantities of biological data.  ...  We develop a novel influence score for DBNs that attempts to estimate both the sign (activation or repression) and relative magnitude of interactions among variables.  ...  ACKNOWLEDGEMENTS We thank Kurt Grandis and Derek Scott for assistance in the beginning stages of this project, and Kazuhiro Wada, Tom Smulders and other members of the Jarvis laboratory for critical comments  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth448">doi:10.1093/bioinformatics/bth448</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15284094">pmid:15284094</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5h5oqggowrhsjgxfdkrxthepua">fatcat:5h5oqggowrhsjgxfdkrxthepua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100602172503/http://www.cs.ucf.edu/%7ehaihu/cap6545/Readings/BN/AdvancesToBayesianNetworkInferenceGenerateCausalNetworkBioData_04bioinfo.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/e8/cce8b3cc78b97b3a7d60c20c17f03036c78095b9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth448"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Comparative Analysis of Gene Regulatory Networks: From Network Reconstruction to Evolution

Dawn Thompson, Aviv Regev, Sushmita Roy
<span title="2015-11-13">2015</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/swacjs3h6zcszjhmxj4u7xttia" style="color: black;">Annual Review of Cell and Developmental Biology</a> </i> &nbsp;
of gene regulatory processes and their adaptive contribution.  ...  In recent years, advances in genomic and computational tools have led to a wealth of methods for such analysis at the sequence, expression, pathway, module, and entire network level.  ...  ACKNOWLEDGMENTS We thank Leslie Gaffney for help with preparation of figures. D.T. is supported by the NIH (R01CA119176-01).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-cellbio-100913-012908">doi:10.1146/annurev-cellbio-100913-012908</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26355593">pmid:26355593</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sryxj3e2gvapnnnkmnzdhnyzr4">fatcat:sryxj3e2gvapnnnkmnzdhnyzr4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303015309/http://pdfs.semanticscholar.org/c083/85add1d7d475c0265843af8ace2d18069dfd.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/c0/83/c08385add1d7d475c0265843af8ace2d18069dfd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-cellbio-100913-012908"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Stress-response balance drives the evolution of a network module and its host genome

C. Gonzalez, J. C. J. Ray, M. Manhart, R. M. Adams, D. Nevozhay, A. V. Morozov, G. Balazsi
<span title="2015-08-31">2015</span> <i title="EMBO"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oayrvwhnr5a2jm4pbva2dvz3ui" style="color: black;">Molecular Systems Biology</a> </i> &nbsp;
Overall, these findings reveal how the timing and mechanisms of stress response network evolution depend on the environment.  ...  Here, we use a two-component synthetic gene circuit integrated into the budding yeast genome to model experimentally the adaptation of a stress response module and its host genome in three different scenarios  ...  Conflict of interest The authors declare that they have no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15252/msb.20156185">doi:10.15252/msb.20156185</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26324468">pmid:26324468</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4562500/">pmcid:PMC4562500</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rviiqxsh4vgrzpd5u2cfl6s3bu">fatcat:rviiqxsh4vgrzpd5u2cfl6s3bu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502191618/https://dash.harvard.edu/bitstream/handle/1/22856907/4562500.pdf;jsessionid=5F7F549856A6E3CB12DA3F06AE75A0CC?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/0a/c7/0ac77a6d242dd92dabfaa7e3134ebc3e6c749ebc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15252/msb.20156185"> <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/PMC4562500" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Reconstructing the Hopfield network as an inverse Ising problem

Haiping Huang
<span title="2010-03-10">2010</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;
Although performances of these network reconstruction algorithms on the simulated network of spiking neurons are extensively studied recently, the analysis of Hopfield networks is lacking so far.  ...  For the Hopfield network, we found that, in the retrieval phase favored when the network wants to memory one of stored patterns, all the reconstruction algorithms fail to extract interactions within a  ...  Acknowledgments The author is grateful to Pan Zhang and Haijun Zhou for valuable discussions. The present work was supported by the National Science  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physreve.81.036104">doi:10.1103/physreve.81.036104</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20365812">pmid:20365812</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i5kkd2ovnjgjjid7njro2udzhi">fatcat:i5kkd2ovnjgjjid7njro2udzhi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220135218/http://pdfs.semanticscholar.org/248f/aaaa6902bba4a621bbd4b484789fd7bfb924.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/24/8f/248faaaa6902bba4a621bbd4b484789fd7bfb924.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1103/physreve.81.036104"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> aps.org </button> </a>

Stages of Gene Regulatory Network Inference: the Evolutionary Algorithm Role [chapter]

Alina Sirbu, Heather J., Martin Crane
<span title="2011-04-26">2011</span> <i title="InTech"> Evolutionary Algorithms </i> &nbsp;
Acknowledgements We wish to acknowledge the SFI/HEA Irish Centre for High-End Computing (ICHEC) for the provision of computational facilities and assistance.  ...  This work has been conducted with support from the Irish Research Council for Science Engineering and Technology EMBARK Initiative.  ...  The fitness values for all points in the solution space generate the so called fitness landscape.535Stages of Gene Regulatory Network Inference: the Evolutionary Algorithm Role www.intechopen.com  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/15182">doi:10.5772/15182</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5kwdvbdzrnfythieaii3arhgxq">fatcat:5kwdvbdzrnfythieaii3arhgxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180726195248/https://api.intechopen.com/chapter/pdf-download/15639" 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/dc/0b/dc0bbc28dfaff28085c8d0c5c3528a807b187c0a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/15182"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Semi-supervised network inference using simulated gene expression dynamics

Phan Nguyen, Rosemary Braun, Inanc Birol
<span title="2017-11-27">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: Inferring the structure of gene regulatory networks from high--throughput datasets remains an important and unsolved problem.  ...  By using simulated dynamics to generate reference distributions, this approach incorporates previously known regulatory relationships and links the network to the dynamics to form a semi-supervised approach  ...  First, by using time-course gene expression data, we are able to make causal inferences about gene regulation, permitting the reconstruction of directed networks that reflect regulatory dependencies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx748">doi:10.1093/bioinformatics/btx748</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29186340">pmid:29186340</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/k4t3bqg7irbevjdanctui5dfpu">fatcat:k4t3bqg7irbevjdanctui5dfpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200929072019/https://arxiv.org/pdf/1706.00877v2.pdf" title="fulltext PDF download [not primary version]" 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] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8c/54/8c5455792addd71980850e9f312e6fa516bd9a43.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btx748"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

Pablo Meyer, Thomas Cokelaer, Deepak Chandran, Kyung Kim, Po-Ru Loh, George Tucker, Mark Lipson, Bonnie Berger, Clemens Kreutz, Andreas Raue, Bernhard Steiert, Jens Timmer (+5 others)
<span title="">2014</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;
Results: We proposed two challenges; in the first, participants were given the topology and underlying biochemical structure of a 9-gene regulatory network and were asked to determine its parameter values  ...  We created an in silico test framework under which participants could probe a network with hidden parameters by requesting a range of experimental assays; results of these experiments were simulated according  ...  Acknowledgments We acknowledge the financial aid received from the EU through project  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-8-13">doi:10.1186/1752-0509-8-13</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24507381">pmid:24507381</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3927870/">pmcid:PMC3927870</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/z5swagyqqbbatjp3iysrjhzeda">fatcat:z5swagyqqbbatjp3iysrjhzeda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190217132025/https://pure.tue.nl/ws/files/3940717/362362116805649.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/a7/eb/a7eb8f6d25ae780f0da3d506110d46372c5a450e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-8-13"> <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/PMC3927870" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Reverse engineering a gene network using an asynchronous parallel evolution strategy

Luke Jostins, Johannes Jaeger
<span title="">2010</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;
The use of reverse engineering methods to infer gene regulatory networks by fitting mathematical models to gene expression data is becoming increasingly popular and successful.  ...  Results: Here, we present synchronous and asynchronous versions of the piES algorithm, and apply them to a real reverse engineering problem: inferring parameters in the gap gene network.  ...  This reverse-engineering approach is generally applicable to the quantitative study of pattern-forming and other complex gene regulatory networks, if powerful optimisation methods are available to fit  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-17">doi:10.1186/1752-0509-4-17</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20196855">pmid:20196855</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2850326/">pmcid:PMC2850326</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/td3fj6tzovewla4per5f7qc35m">fatcat:td3fj6tzovewla4per5f7qc35m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829192522/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-4-17?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/24/f3/24f302739c91b4f212d77010a7510397006bef54.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-17"> <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/PMC2850326" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Time-lagged Ordered Lasso for network inference [article]

Phan Nguyen, Rosemary Braun
<span title="2018-12-10">2018</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Many methods have been proposed to infer networks from gene expression data but have been hampered by problems such as low sample size, inaccurate constraints, and incomplete characterizations of regulatory  ...  In addition, temporal methods typically assume that the expression of a gene at a time point depends on the expression of other genes at only the immediately preceding time point, while other methods include  ...  Due to the large number of genes relative to the number of samples, fitting even simple one-lag models in which the expression of a gene depends on the expression of other genes at a previous time point  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1807.00226v2">arXiv:1807.00226v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bh22d42ta5bpxicswgvs3wcnta">fatcat:bh22d42ta5bpxicswgvs3wcnta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200826214459/https://arxiv.org/pdf/1807.00226v2.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/b9/a0/b9a0ba6a0ab473e7d3dcee98a46c3585e09c5bff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1807.00226v2" 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>

Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape

Yangyun Zou, Zhixi Su, Jian Yang, Yanwu Zeng, Xun Gu
<span title="2009-11-15">2009</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/refoudi6rnfezhtj7cscsjetby" style="color: black;">Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</a> </i> &nbsp;
We conclude that eQTL analysis provides a novel approach to explore the effect of gene duplications on the genetic regulatory network. X. 2009.  ...  Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape.  ...  We also give great thanks to two anonymous reviewers' constructive comments, conducing to refine our study.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jez.b.21290">doi:10.1002/jez.b.21290</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19373876">pmid:19373876</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s5xmfd5yifdlbl3fe3oltjn544">fatcat:s5xmfd5yifdlbl3fe3oltjn544</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160416173540/http://xungulab.com/publications/Zou_eQTL_JEZB_2009.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/c7/a5/c7a5052dbae7930889b6a22f5aeb9c11e93884aa.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/jez.b.21290"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a>

Cell-free gene-regulatory network engineering with synthetic transcription factors

Zoe Swank, Nadanai Laohakunakorn, Sebastian J. Maerkl
<span title="2019-03-08">2019</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
The well-characterized synthetic parts and insights gained should be useful for rationally engineering gene-regulatory networks and for studying the biophysics of transcriptional regulation.  ...  Gene-regulatory networks are ubiquitous in nature and critical for bottom-up engineering of synthetic networks.  ...  Gene-regulatory networks (GRNs) are one such critical subsystem, and here we demonstrate de novo bottom-up engineering and comprehensive characterization of synthetic GRNs in a cell-free system.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1816591116">doi:10.1073/pnas.1816591116</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t5brcnliwzhunfhcflejmo3qte">fatcat:t5brcnliwzhunfhcflejmo3qte</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428203219/https://www.pure.ed.ac.uk/ws/portalfiles/portal/173819806/5892.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/3b/04/3b04f9f11700761024aeddae8dacf5d9d1dbe270.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.1816591116"> <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>

Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks

Alexander Spirov, David Holloway
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3jmevtg2ajcdnpgyntimblv7iu" style="color: black;">Methods</a> </i> &nbsp;
This paper surveys modeling approaches for studying the evolution of gene regulatory networks (GRNs).  ...  Modeling of the design or 'wiring' of GRNs has become increasingly common in developmental and medical biology, as a means of quantifying gene-gene interactions, the response to perturbations, and the  ...  Acknowledgments We thank the U.S. NIH for financial support, grant R01-GM072022.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymeth.2013.05.013">doi:10.1016/j.ymeth.2013.05.013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23726941">pmid:23726941</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3743956/">pmcid:PMC3743956</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fec6itwwbnd6zpiude23du6i44">fatcat:fec6itwwbnd6zpiude23du6i44</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191122114019/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3743956&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/96/e2/96e2f5cd9c83efc2002a878eebdb9b982098c8b8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymeth.2013.05.013"> <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/PMC3743956" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cell biology: Networks, regulation, pathways [article]

Gasper Tkacik, William Bialek
<span title="2007-12-28">2007</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We begin with the building blocks of cellular networks, and proceed toward the different classes of models being explored, finally discussing the "design principles" which have been suggested for these  ...  Although largely a dispassionate review, we do draw attention to areas where there seems to be general consensus on ideas that have not been tested very thoroughly and, more optimistically, to areas where  ...  Our work was supported in part by NIH grants P50 GM071508 and R01 GM077599, by NSF Grants IIS-0613435 and PHY-0650617, by the Swartz Foundation, and by the Burroughs Wellcome Fund.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0712.4385v1">arXiv:0712.4385v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aeu72h57wnhsnb2ubrjdwbgb6a">fatcat:aeu72h57wnhsnb2ubrjdwbgb6a</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/arxiv-0712.4385/0712.4385.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/0712.4385v1" 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>

Toward deciphering developmental patterning with deep neural network [article]

Jingxiang Shen, Mariela D Petkova, Feng Liu, Chao Tang
<span title="2018-07-22">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Dynamics of complex biological systems is driven by intricate networks, the current knowledge of which are often incomplete.  ...  The model yields perfect fitting and impressively accurate predictions on mutant patterns.  ...  a presumed network inferred from a body of experimental work, and/or simplified by the author's opinion of what is important.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/374439">doi:10.1101/374439</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6szjv4ddsvbuflvthrbkti4wtu">fatcat:6szjv4ddsvbuflvthrbkti4wtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501120904/https://www.biorxiv.org/content/biorxiv/early/2018/08/09/374439.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/44/e6/44e64674236e99026c89a1a05d6b50c0abc70eac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/374439"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>
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