Commit 54677fe9 authored by Vladimir Reinharz's avatar Vladimir Reinharz
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%% http://bibdesk.sourceforge.net/
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@article{Stich2010,
Author = {Stich, Michael and Manrubia, Susanna C and La, Ester},
Date-Added = {2017-08-15 05:40:41 +0000},
Date-Modified = {2017-08-15 05:40:41 +0000},
Doi = {10.1371/Citation},
File = {:Users/carlosgonzalez/Escuela/Papers/journal.pone.0011186.pdf:pdf},
Journal = {PLoS ONE},
Number = {6},
Title = {{Variable Mutation Rates as an Adaptive Strategy in Replicator Populations}},
Volume = {5},
Year = {2010},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/Citation}}
@article{Higgs:2015aa,
Abstract = {The RNA World concept posits that there was a period of time in primitive Earth's history - about 4 billion years ago - when the primary living substance was RNA or something chemically similar. In the past 50 years, this idea has gone from speculation to a prevailing idea. In this Review, we summarize the key logic behind the RNA World and describe some of the most important recent advances that have been made to support and expand this logic. We also discuss the ways in which molecular cooperation involving RNAs would facilitate the emergence and early evolution of life. The immediate future of RNA World research should be a very dynamic one.},
Author = {Higgs, Paul G and Lehman, Niles},
Date-Added = {2017-08-15 05:04:50 +0000},
Date-Modified = {2017-08-15 05:04:50 +0000},
Doi = {10.1038/nrg3841},
Journal = {Nat Rev Genet},
Journal-Full = {Nature reviews. Genetics},
Mesh = {Base Pairing; Evolution, Molecular; Models, Biological; Origin of Life; RNA; RNA, Catalytic},
Month = {Jan},
Number = {1},
Pages = {7-17},
Pmid = {25385129},
Pst = {ppublish},
Title = {The {RNA World:} molecular cooperation at the origins of life},
Volume = {16},
Year = {2015},
Bdsk-Url-1 = {http://dx.doi.org/10.1038/nrg3841}}
@article{Waldispuhl:2002aa,
Abstract = {MOTIVATION: S-attributed grammars (a generalization of classical Context-Free grammars) provide a versatile formalism for sequence analysis which allows to express long range constraints: the RNA folding problem is a typical example of application. Efficient algorithms have been developed to solve problems expressed with these tools, which generally compute the optimal attribute of the sequence w.r.t. the grammar. However, it is often more meaningful and/or interesting from the biological point of view to consider almost optimal attributes as well as approximate sequences; we thus need more flexible and powerful algorithms able to perform these generalized analyses.
RESULTS: In this paper we present a basic algorithm which, given a grammar G and a sequence omega, computes the optimal attribute for all (approximate) strings omega(') in L(G) such that d(omega, omega(')) < or = M, and whose complexity is O(n(r + 1)) in time and O(n(2)) in space (r is the maximal length of the right-hand side of any production of G). We will also give some extensions and possible improvements of this algorithm.},
Author = {Waldisp{\"u}hl, J and Behzadi, B and Steyaert, J-M},
Date-Added = {2017-08-15 04:54:49 +0000},
Date-Modified = {2017-08-15 04:54:49 +0000},
Journal = {Bioinformatics},
Journal-Full = {Bioinformatics (Oxford, England)},
Mesh = {Algorithms; Natural Language Processing; Pattern Recognition, Automated; Sequence Alignment; Sequence Analysis, RNA; Sequence Homology, Nucleic Acid},
Pages = {S250-9},
Pmid = {12386010},
Pst = {ppublish},
Title = {An approximate matching algorithm for finding (sub-)optimal sequences in {S}-attributed grammars},
Volume = {18 Suppl 2},
Year = {2002}}
@article{Fontana:1998aa,
Abstract = {Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness among phenotypes, independently of their similarity. Because of neutrality, phenotypes denote equivalence classes of genotypes. The definition of neighborhood relations among phenotypes relies, therefore, on the statistics of neighborhood relations among equivalence classes of genotypes in genotype space. The folding of RNA sequence (genotypes) into secondary structures (phenotypes) is an ideal case to implement these concepts. We study the extent to which the folding of RNA sequence induces a "statistical topology" on the set of minimum free energy secondary structures. The resulting nearness relation suggests a notion of "continuous" structure transformation. We can, then rationalize major transitions in evolutionary trajectories at the level of RNA structures by identifying those transformations which are irreducibly discontinuous. This is shown by means of computer simulations. The statistical topology organizing the set of RNA shapes explains why neutral drift in sequence space plays a key role in evolutionary optimization.},
Author = {Fontana, W and Schuster, P},
......@@ -318,4 +366,15 @@
Title = {Topological structure of the space of phenotypes: the case of {RNA} neutral networks},
Volume = {6},
Year = {2011},
Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0026324}}
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Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.pone.0026324}}
@article{turner2009nndb,
title={NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure},
author={Turner, Douglas H and Mathews, David H},
journal={Nucleic acids research},
volume={38},
number={suppl\_1},
pages={D280--D282},
year={2009},
publisher={Oxford University Press}
}
\ No newline at end of file
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