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Fast folding and comparison of RNA secondary structures
SummaryComputer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of…
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From sequences to shapes and back: a case study in RNA secondary structures
TLDR
Using an algorithm for inverse folding, it is shown that sequences sharing the same structure are distributed randomly over sequence space, which means that finding a particular structure by mutation and selection is much simpler than expected.
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Plasticity, evolvability, and modularity in RNA.
TLDR
Analytical models of neutral confinement, made tractable by the assumption of perfect plastogenetic congruence, formally connect mutation rate, the topography of phenotype space, and evolvability to suggest a possible evolutionary origin of modularity as a side effect of environmental canalization.
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Complete suboptimal folding of RNA and the stability of secondary structures.
TLDR
It is shown that sequences whose ground state structure is thermodynamically well defined show a significant tendency to buffer single point mutations, which can have evolutionary implications, since selection pressure to improve the definition of ground states with biological function may result in increased neutrality.
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Curvature in metabolic scaling
TLDR
It is shown that the relationship between mass and metabolic rate has convex curvature on a logarithmic scale, and is therefore not a pure power law, even after accounting for body temperature.
View on Nature
Continuity in evolution: on the nature of transitions.
TLDR
The simulation of replicating and mutating RNA populations under selection shows that sudden adaptive progress coincides mostly, but not always, with discontinuous shape transformations in RNA.
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Smoothness within ruggedness: the role of neutrality in adaptation.
TLDR
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure, on which the success of phenotypic adaptation becomes much less sensitive to the initial conditions in genotype space.
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RNA folding at elementary step resolution.
TLDR
This work studies the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs based on artificial and natural sequences.
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Rule-Based Modelling of Cellular Signalling
TLDR
It is shown how causality enables the formalization of the colloquial concept of pathway and, perhaps more surprisingly, how conflict can be used to dissect the signalling dynamics to obtain a qualitative handle on the range of system behaviours.
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PERSPECTIVE:EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS
TLDR
This work focuses on the first kind of robustness—genetic robustness)—and survey three growing avenues of research: measuring genetic robustness in nature and in the laboratory; understanding the evolution of genetic robusts; and exploring the implications of genetic resilientness for future evolution.
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