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A Non-deterministic Grammar Inference Algorithm Applied to the Cleavage Site Prediction Problem in Bioinformatics [chapter]

Gloria Inés Alvarez, Jorge Hernán Victoria, Enrique Bravo, Pedro García
<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;
We report results on applying the OIL (Order Independent Language) grammar inference algorithm to predict cleavage sites in polyproteins from translation of Potivirus genome.  ...  This non-deterministic algorithm is used to generate a group of models which vote to predict the occurrence of the pattern.  ...  Algorithm OIL This algorithm was first published in [3] , the Order Independent Language (OIL) inference algorithm is a non deterministic approach to grammar inference for regular languages.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-15488-1_23">doi:10.1007/978-3-642-15488-1_23</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5elya7l2p5htbjheyyia5ivnyi">fatcat:5elya7l2p5htbjheyyia5ivnyi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120626104209/http://users.dsic.upv.es/grupos/tlcc/papers/fullpapers/AHBG10.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/d2/5a/d25a82b18fd3653baeb7d05dfeb0f5f28c3ac71d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-15488-1_23"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Learning the Language of Biological Sequences [chapter]

François Coste
<span title="">2016</span> <i title="Springer Berlin Heidelberg"> Topics in Grammatical Inference </i> &nbsp;
, it is still a source of open and nice inspirational problems for grammatical inference, enabling us to confront our ideas to real fundamental applications.  ...  While some first successes have already been recorded, such as the inference of profile hidden Markov models or stochastic context-free grammars which are now part of the classical bioinformatics toolbox  ...  Shifting from a deterministic to a non-deterministic setting in the state merging approach requires simply starting from the Minimal Canonical Automaton (MCA) of the sample set (the non-deterministic automaton  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-662-48395-4_8">doi:10.1007/978-3-662-48395-4_8</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eojckskf65f5phcbmjsfbq7era">fatcat:eojckskf65f5phcbmjsfbq7era</a> </span>
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Predicting the Impact of cis-Regulatory Variation on Alternative Polyadenylation [article]

Nicholas Bogard, Johannes Linder, Alexander B Rosenberg, Georg Seelig
<span title="2018-04-12">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone.  ...  Visualizing features learned across all network layers reveals that APARENT recognizes sequence motifs known to recruit APA regulators, discovers previously unknown sequence determinants of cleavage site  ...  Remarkably, APARENT is able to predict these sites with high 321 precision, suggesting the choice of cleavage site itself is governed by a deterministic regulatory 322 code. 323 324 The Determinants of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/300061">doi:10.1101/300061</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/f6eswccswnal7hhqxtmdshr3lm">fatcat:f6eswccswnal7hhqxtmdshr3lm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502152839/https://www.biorxiv.org/content/biorxiv/early/2018/04/12/300061.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/a6/c9/a6c93299807c19fb9becf78ce93519320c1433bf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/300061"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Mathematical modeling of gene expression: a guide for the perplexed biologist

Ahmet Ay, David N. Arnosti
<span title="2011-03-21">2011</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jf6xzofahfdgdpjb2zn6cikmli" style="color: black;">Critical reviews in biochemistry and molecular biology</a> </i> &nbsp;
The detailed analysis of transcriptional networks holds a key for understanding central biological processes, and interest in this field has exploded due to new large-scale data acquisition techniques.  ...  Mathematical modeling can provide essential insights, but the diversity of modeling approaches can be a daunting prospect to investigators new to this area.  ...  This project was supported by a Special Projects Grant from the MSU Foundation and NIH GM 56976 to D.N.A., and fellowships from the MSU Quantitative Biology Initiative and Gene Expression in Development  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3109/10409238.2011.556597">doi:10.3109/10409238.2011.556597</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21417596">pmid:21417596</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3086598/">pmcid:PMC3086598</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uei7p4jtbnfoxfpm67va4ucwrq">fatcat:uei7p4jtbnfoxfpm67va4ucwrq</a> </span>
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OUP accepted manuscript

<span title="">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
This work shows that combining human-curated "big mechanisms" with extracted "big data" can lead to a causal, predictive understanding of cellular processes and unlock important downstream applications  ...  We demonstrate that combining the extracted pathway fragments with existing biological data analysis algorithms that rely on curated models helps identify and explain a large number of previously unidentified  ...  Acknowledgments We thank MITRE for defining and implementing the evaluation described in Section 4.1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bay098">doi:10.1093/database/bay098</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xpnrphqq6jgsbeuafu5pogr2uq">fatcat:xpnrphqq6jgsbeuafu5pogr2uq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190227093407/http://pdfs.semanticscholar.org/7dfe/e3339d999081e8a0f94b970cff646aaa50d7.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/7d/fe/7dfee3339d999081e8a0f94b970cff646aaa50d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/bay098"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

Multiple pattern matching: A Markov chain approach [article]

Manuel Lladser, M. D. Betterton, Rob Knight
<span title="2007-04-24">2007</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
This conceptualization, together with the capability of automata to recognize complicated patterns, allows a systematic analysis of problems related to the occurrence and frequency of patterns in random  ...  We formalize, in a general framework, the concept of Markov chain embedding to analyze patterns in random strings produced by a memoryless source.  ...  This view of the pattern matching problem allows many different problems to be addressed in a general framework, and unifies different ideas addressed in the computer science, mathematics, and bioinformatics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/0704.3221v1">arXiv:0704.3221v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6262oecu2jazjpvlolyhayikmy">fatcat:6262oecu2jazjpvlolyhayikmy</a> </span>
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Multiple pattern matching: a Markov chain approach

Manuel E. Lladser, M. D. Betterton, Rob Knight
<span title="2007-08-01">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kngnkwdthrbili3232uvzfjyyi" style="color: black;">Journal of Mathematical Biology</a> </i> &nbsp;
This conceptualization, together with the capability of automata to recognize complicated patterns, allows a systematic analysis of problems related to the occurrence and frequency of patterns in random  ...  We formalize, in a general framework, the concept of Markov chain embedding to analyze patterns in random strings produced by a memoryless source.  ...  This view of the pattern matching problem allows many different problems to be addressed in a general framework, and unifies different ideas addressed in the computer science, mathematics, and bioinformatics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-007-0109-3">doi:10.1007/s00285-007-0109-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17668213">pmid:17668213</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t2bxugnwsjcrhpqx6kyv4jtnua">fatcat:t2bxugnwsjcrhpqx6kyv4jtnua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810034000/http://spot.colorado.edu/~mdb/Lladser2008.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/76/9c/769c2b16d1fe2763ed8fe12bf65d27e01dcce01d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00285-007-0109-3"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Physical Principles and Visual-OMP Software for Optimal PCR Design [chapter]

John SantaLucia
<span title="">2007</span> <i title="Humana Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
Importantly, all the T m equations above apply only to "two-state transitions" (i.e., the molecules that form only random coil and duplex states), and they do not apply to transitions that involve intermediate  ...  BLAST also uses a minimum 8 nt "word length," which must be a perfect match; this is used to make the BLAST algorithm fast, but it also means that BLAST will miss structures that have fewer than eight  ...  The authors thank Katre Palm for a valuable help with English grammar.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-59745-528-2_1">doi:10.1007/978-1-59745-528-2_1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17951788">pmid:17951788</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tghqvlsslzcspmi673q4m4q32m">fatcat:tghqvlsslzcspmi673q4m4q32m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809084852/http://theaasm.org/my_doc/pezeshki/E-Learning/E-Learning/E-BOOK/PCR%20Primer%20Design.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/6a/1b/6a1b0cfcd543491b2f405b66e43055205568829d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-59745-528-2_1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

OASIcs, Volume 34, GCB'13, Complete Volume [article]

Tim Beißbarth, Martin Kollmar, Andreas Leha, Burkhard Morgenstern, Anne-Kathrin Schultz, Stephan Waack, Edgar Wingender
<span title="2013-09-09">2013</span>
Acknowledgements We wish to thank Nataša Pržulj from Imperial College London for interesting discussions and her help with the data sets used in her C-GRAAL and MI-GRAAL papers.  ...  All authors with to thank the DFG Cluster of Excellence for Multimodal Computing and Interaction (MMCI) for support. JB is also grateful for funding from the Villum Foundation.  ...  at specific cleavage sites 1 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/oasics.gcb.2013">doi:10.4230/oasics.gcb.2013</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fdkilknhcbgaxezovczcw5syby">fatcat:fdkilknhcbgaxezovczcw5syby</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180520192206/http://drops.dagstuhl.de/opus/volltexte/2013/4256/pdf/oasics-vol034-gcb2013-complete.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/83/54/8354b7f1696ca6168b6d6c618f6e33e1b717c21c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4230/oasics.gcb.2013"> <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>

Preface Modeling and Simulation of Gene Regulation and Metabolic Pathways

Julio Collado-Vides, Ralf Hofestädt, Michael Mavrovouniotis, Gerhard Michal, Julio Collado-Vides
<span title="">1998</span> <span class="release-stage">unpublished</span>
The detection of promoter structures is one actual example, which shows also the algorithmic problems of this research field.  ...  The prediction of promoter sequences is of importance, because the promoter is the starting signal for a structure gene which represents the genetic information.  ...  Acknowledgement The organisers thank the Volkswagen Stiftung and the European Community (TMR Grant) for its generous financial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tw324dirsrhi7dcisfx5occ3iy">fatcat:tw324dirsrhi7dcisfx5occ3iy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180510235655/https://www.dagstuhl.de/Reports/98/98251.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/33/49/334997bb0dc454488657db5206c473797bdfaca6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>

Bioinformatics tools to assist drug candidate discovery in venom gland transcriptomes

Dominique Kadio Koua, Ron David Appel, Frédérique Lisacek, Reto Stocklin
<span title="">2012</span>
Bioinformatics tools to assist drug candidate discovery in venom gland transcriptomes.  ...  Bioinformatics tools to assist drug candidate discovery in venom gland transcriptomes. Thèse de doctorat : Univ. Genève, 2012, no. Sc.  ...  We are also grateful to Frédérique Lisacek from the Swiss Institute of Bioinformatics for ongoing help. We would like to thank Dr Ron Hogg of OmniScience SA for editorial support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.13097/archive-ouverte/unige:23951">doi:10.13097/archive-ouverte/unige:23951</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e4p2d7s3nve4dmutil7msltlpa">fatcat:e4p2d7s3nve4dmutil7msltlpa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200423114643/https://archive-ouverte.unige.ch/files/downloads/0/0/0/2/3/9/5/1/unige_23951_attachment01.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ea/83/ea83bf1ffebd859457448592e50461f4f8dea4ab.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.13097/archive-ouverte/unige:23951"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Novel Algorithms for Structural Alignment of Non-coding RNAs

Diana Kolbe
<span title="">2010</span>
New algorithms for dealing with structural RNAs are developed to address some of the practical deficiencies of covariance models.  ...  As a whole, these improvements provide a foundation for and point toward future improvements in noncoding RNA homology search. ii  ...  The trCYK algorithm rests on good theoretical ground by viewing the sequence truncation problem formally as a missing data inference problem, and it makes only two minor assumptions to simplify the missing  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7936/k7cr5rc5">doi:10.7936/k7cr5rc5</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mxvslvzfbnclhfobj2peodh47u">fatcat:mxvslvzfbnclhfobj2peodh47u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170222232439/http://openscholarship.wustl.edu/cgi/viewcontent.cgi?article=1185&amp;context=etd" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/45/2f/452f0fb2b09b4858a0bc2c2b9ce3f9fb9e9b0aaf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7936/k7cr5rc5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

RNA secondary structure thermodynamics and kinetics

Ronny Lorenz
<span title="">2014</span> <span class="release-stage">unpublished</span>
In my PhD thesis I present novel heuristic algorithms to predict optimal folding paths and folding behavior on top of an abstract view of the energy landscape using distance class partitioning.  ...  By exploration of variable and static energy landscapes with stochastic and deterministic techniques the new approaches can even be used to predict folding kinetics during transcription.  ...  We thank all major contributers to earlier versions of the ViennaRNA Package whose implementation of algorithms and programs helped to create this versatile and comprehensive software collection (in alphabetical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25365/thesis.34176">doi:10.25365/thesis.34176</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xs3v7buvcjhwfnq3hgfrvqfrje">fatcat:xs3v7buvcjhwfnq3hgfrvqfrje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200301234558/http://othes.univie.ac.at/34176/1/2014-08-20_0746134.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/a0/a8/a0a84098f2e47b8084b3f452a80c9f12efc79e47.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25365/thesis.34176"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

SPECIAL ISSUE: ABSTRACTS FROM THE 2008 ISSOL MEETING

<span title="2009-05-26">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/som6xng6qnh4riryarjzxutv4m" style="color: black;">Origins of life and evolution of the biosphere</a> </i> &nbsp;
To appear in the Journal of Physical Chemistry A E-mail: jaroslav.cihelka@jh-inst.cas.cz Acknowledgements Financial support from the Deutsche Forschungsgemeinschaft is gratefully acknowledged.  ...  Journal of Physical Chemistry A, 110:12113-12120. Babánková D., Civiš S., Juha L. (2006). Chemical consequencies of laser-induced breakdown in molecular gases.  ...  algorithm-generated were divided in 16 intervals to which A,C,G,T (U), letters were attributed.  ... 
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Modelling and measurement in synthetic biology [article]

William Waites, University Of Edinburgh, University Of Edinburgh, Vincent Danos, Gordon Plotkin
<span title="2020-02-26">2020</span>
Synthetic biology applies engineering principles to make progress in the study of complex biological phenomena. The aim is to develop understanding through the praxis of construction and design.  ...  We use a vertex model that consists of a potential energy minimisation process interwoven with topological changes in the graph structure of the tissue.  ...  binding) 46 ## Apply a predictable ordering on the sites so that 47 ## edges do not appear twice.  ... 
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