The genetic theory of adaptation: a brief history

HA Orr - Nature reviews genetics, 2005‏ - nature.com
Theoretical studies of adaptation have exploded over the past decade. This work has been
inspired by recent, surprising findings in the experimental study of adaptation. For example …

A comprehensive survey on fitness landscape analysis

E Pitzer, M Affenzeller - Recent advances in intelligent engineering …, 2012‏ - Springer
In the past, the notion of fitness landscapes has found widespread adoption. Many different
methods have been developed that provide a general and abstract framework applicable to …

[PDF][PDF] Fast folding and comparison of RNA secondary structures

IL Hofacker, W Fontana, PF Stadler… - Monatshefte fur …, 1994‏ - academia.edu
Computer codes for computation and comparison of RNA secondary structures, the Vienna
RNA paCKage, are presented, that are based on dynamic programming algorithms and aim …

Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals

X **e, J Lu, EJ Kulbokas, TR Golub, V Mootha… - Nature, 2005‏ - nature.com
Comprehensive identification of all functional elements encoded in the human genome is a
fundamental need in biomedical research. Here, we present a comparative analysis of the …

From sequences to shapes and back: a case study in RNA secondary structures

P Schuster, W Fontana, PF Stadler… - Proceedings of the …, 1994‏ - royalsocietypublishing.org
RNA folding is viewed here as a map assigning secondary structures to sequences. At fixed
chain length the number of sequences far exceeds the number of structures. Frequencies of …

A survey of techniques for characterising fitness landscapes and some possible ways forward

KM Malan, AP Engelbrecht - Information Sciences, 2013‏ - Elsevier
Real-world optimisation problems are often very complex. Metaheuristics have been
successful in solving many of these problems, but the difficulty in choosing the best …

[ספר][B] Introduction to artificial life

C Adami - 1998‏ - books.google.com
Developed from a lab-orientated multidisciplinary course, this book and CD-ROM package
brings together the theoretical groundwork for understanding the dynamics of systems of self …

Neutral evolution of mutational robustness

E Van Nimwegen, JP Crutchfield, M Huynen - Proceedings of the National …, 1999‏ - pnas.org
We introduce and analyze a general model of a population evolving over a network of
selectively neutral genotypes. We show that the population's limit distribution on the neutral …

Biophysics of protein evolution and evolutionary protein biophysics

T Sikosek, HS Chan - Journal of The Royal Society …, 2014‏ - royalsocietypublishing.org
The study of molecular evolution at the level of protein-coding genes often entails comparing
large datasets of sequences to infer their evolutionary relationships. Despite the importance …

Plasticity, evolvability, and modularity in RNA

LW Ancel, W Fontana - Journal of Experimental Zoology, 2000‏ - Wiley Online Library
RNA folding from sequences into secondary structures is a simple yet powerful,
biophysically grounded model of a genotype–phenotype map in which concepts like …