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33
A statistical sampling algorithm for RNA secondary structure prediction
 Nucleic Acids Res
, 2003
"... An RNA molecule, particularly a longchain mRNA, may exist as a population of structures. Furthermore, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sa ..."
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Cited by 175 (11 self)
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An RNA molecule, particularly a longchain mRNA, may exist as a population of structures. Furthermore, multiple structures have been demonstrated to play important functional roles. Thus, a representation of the ensemble of probable structures is of interest. We present a statistical algorithm to sample rigorously and exactly from the Boltzmann ensemble of secondary structures. The forward step of the algorithm computes the equilibrium partition functions of RNA secondary structures with recent thermodynamic parameters. Using conditional probabilities computed with the partition functions in a recursive sampling process, the backward step of the algorithm quickly generates a statistically representative
Landscapes and Their Correlation Functions
, 1996
"... Fitness landscapes are an important concept in molecular evolution. Many important examples of landscapes in physics and combinatorial optimation, which are widely used as model landscapes in simulations of molecular evolution and adaptation, are "elementary", i.e., they are (up to an addi ..."
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Cited by 107 (16 self)
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Fitness landscapes are an important concept in molecular evolution. Many important examples of landscapes in physics and combinatorial optimation, which are widely used as model landscapes in simulations of molecular evolution and adaptation, are "elementary", i.e., they are (up to an additive constant) eigenfuctions of a graph Laplacian. It is shown that elementary landscapes are characterized by their correlation functions. The correlation functions are in turn uniquely determined by the geometry of the underlying configuration space and the nearest neighbor correlation of the elementary landscape. Two types of correlation functions are investigated here: the correlation of a time series sampled along a random walk on the landscape and the correlation function with respect to a partition of the set of all vertex pairs.
Analysis of RNA Sequence Structure Maps by Exhaustive Enumeration
, 1996
"... Global relations between RNA sequences and secondary structues are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique od tries is used for economic data storage and f ..."
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Cited by 83 (36 self)
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Global relations between RNA sequences and secondary structues are understood as mappings from sequence space into shape space. These mappings are investigated by exhaustive folding of all GC and AU sequences with chain lengths up to 30. The technique od tries is used for economic data storage and fast retrieval of information. The computed structural data are evaluated through exhaustive enumeration and used as an exact reference for testing analytical results derived from mathematical models and sampling based of statistical methods. Several new concepts of RNA sequence to secondary structure mappings are investigated, among them the structure of neutral networks (being sets of sequences folding into the same structure), percolation of sequence space by neutral networks, and the principle of shape space covering . The data of exhaustive enumeration are compared to the analytical results of a random graph model that reveals the generic properties of sequence to structure mappings based on some base pairing logic. The differences between the numerical and the analytical results are interpreted in terms of specific biophysical properties of RNA molecules.
Landscapes And Molecular Evolution
, 1996
"... that allows to choose the direction for the next step at random from all directions along which fitness does not decrease. Stationary states of populations correspond to local optima of the fitness landscape. Evolution is seen as a series of transitions between optima with increasing fitness values. ..."
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Cited by 46 (6 self)
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that allows to choose the direction for the next step at random from all directions along which fitness does not decrease. Stationary states of populations correspond to local optima of the fitness landscape. Evolution is seen as a series of transitions between optima with increasing fitness values. Wright's metaphor saw a recent revival when sufficiently simple models of fitness landscapes became available [1, 41]. These models are based on spin glass theory [63, 66] or closely related to it like Kauffman's Nk model [42]. Evolution of RNA molecules has been studied by more realistic models that deal explicitly with molecular structures obtained from folding RNA sequences [23, 24]. Fitness values serving as input parameters for evolutionary dynamics were derived through evaluation of the structures. The complexity of RNA fitness landscapes originates from conflicting consequences of structural changes that are reminiscent of "frustration" in the theory of spin glasses [2]. Fitness in t
Combinatorial Landscapes
 SIAM REVIEW
, 2002
"... Fitness landscapes have proven to be a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. A fitness landscape is a mapping from a configuration space into the real numbers. The configuration space is equipped with some notion of adjacency, ne ..."
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Cited by 37 (2 self)
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Fitness landscapes have proven to be a valuable concept in evolutionary biology, combinatorial optimization, and the physics of disordered systems. A fitness landscape is a mapping from a configuration space into the real numbers. The configuration space is equipped with some notion of adjacency, nearness, distance or accessibility. Landscape theory has emerged as an attempt to devise suitable mathematical structures for describing the "static" properties of landscapes as well as their influence on the dynamics of adaptation. In this review we focus on the connections of landscape theory with algebraic combinatorics and random graph theory, where exact results are available.
The algebraic theory of recombination spaces
, 2000
"... A new mathematical representation is proposed for the configuration space structure induced by recombination which we called "Pstructure". It consists of a mapping of pairs of objects to the power set of all objects in the search space. The mapping assigns to each pair of parental "g ..."
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Cited by 35 (16 self)
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A new mathematical representation is proposed for the configuration space structure induced by recombination which we called "Pstructure". It consists of a mapping of pairs of objects to the power set of all objects in the search space. The mapping assigns to each pair of parental "genotypes" the set of all recombinant genotypes obtainable from the parental ones. It is shown that this construction allows a Fourierdecomposition of fitness landscapes into a superposition of "elementary landscapes". This decomposition is analogous to the Fourier decomposition of fitness landscapes on mutation spaces. The elementary landscapes are obtained as eigenfunctions of a Laplacian operator defined for Pstructures. For binary string recombination the elementary landscapes are exactly the pspin functions (Walsh functions), i.e. the same as the elementary landscapes of the string point mutation spaces (i.e. the hypercube). This supports the notion of a strong homomorphisms between string mutation ...
Evolutionary Dynamics and Optimization  Neutral Networks as ModelLandscapes for RNA SecondaryStructure FoldingLandscapes
, 1995
"... We view the folding of RNAsequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure s). By interpreting the secondary structure as biological i ..."
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Cited by 30 (6 self)
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We view the folding of RNAsequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure s). By interpreting the secondary structure as biological information we can formulate the so called Error Threshold of Shapes as an extension of Eigen's et al. concept of an error threshold in the single peak landscape [5]. Analogue to the approach of Derrida & Peliti [3] for a flat landscape we investigate the spatial distribution of the population on the neutral network. On the one hand this model of a single shape landscape allows the derivation of analytical results, on the other hand the concept gives rise to study various scenarios by means of simulations, e.g. the interaction of two different networks [29]. It turns out that the intersection of two sets of compatible sequences (with respect to the pair of secondary structures) plays a key role in the search for "fitter" secondary structures.
Evolution of Model Proteins on a Foldability Landscape
 Proteins
, 1997
"... We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dyn ..."
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Cited by 26 (1 self)
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We model the evolution of simple lattice proteins as a random walk in a fitness landscape, where the fitness represents the ability of the protein to fold. At higher selective pressure, the evolutionary trajectories are confined to neutral networks where the native structure is conserved and the dynamics are non selfaveraging and nonexponential. The optimizability of the corresponding native structure has a strong effect on the size of these neutral networks and thus on the nature of the evolutionary process. Proteins 29:461466, 1997. # 1997 WileyLiss, Inc. Key words: protein folding; molecular evolution; lattice models; fitness landscapes; neutral networks; spinglass theory INTRODUCTION Biological macromolecules are the result of eons of evolution. To understand these macromolecules, it is necessary to understand the evolutionary processes that determined their form and function. Similarly, biological evolution is constrained by the properties of the polymers that encode, repre...
Genotypes with phenotypes: Adventures in an RNA toy world
 Biophys. Chem
, 1997
"... Evolution has created the complexity of the animate world and deciphering the language of evolution is the key towards understanding nature. The dynamics of evolution is simplified by considering it as a superposition of three less sophisticated processes: population dynamics, population support dyn ..."
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Cited by 23 (6 self)
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Evolution has created the complexity of the animate world and deciphering the language of evolution is the key towards understanding nature. The dynamics of evolution is simplified by considering it as a superposition of three less sophisticated processes: population dynamics, population support dynamics, and genotypephenotype mapping. Evolution of molecules in laboratory assays provides a sufficiently simple system for the quantitative analysis of the three phenomena. Coarsegrained notions of structures like RNA secondary structures are used as model phenotypes. They provide an excellent tool for a comprehensive analysis of the entire complex of molecular evolution. The mapping from RNA genotypes into secondary structures is highly redundant. In order to find at least one sequence for every common structures one need only search a (relatively) small part of sequence space. The existence of selectively neutral phenotypes plays an important role for the the success and the efficiency ...
Random Field Models For Fitness Landscapes
, 1996
"... In many cases fitness landscapes are obtained as particular instances of random fields by assigning a large number of random parameters. Models of this type are often characterized reasonably well by their covariance matrices. We characterize isotropic random fields on finite graphs in terms of thei ..."
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Cited by 21 (6 self)
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In many cases fitness landscapes are obtained as particular instances of random fields by assigning a large number of random parameters. Models of this type are often characterized reasonably well by their covariance matrices. We characterize isotropic random fields on finite graphs in terms of their Fourier series expansions and investigate the relation between the covariance matrix of the random field model and the correlation structure of the individual landscapes constructed from this random field. Our formalism suggests to approximate landscape with known autocorrelation function by a random field model that has the same correlation structure.