Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks

The number of accessible paths in the hypercube

(2016) Julien Berestycki et al.   BERNOULLI

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Biophysical principles predict fitness landscapes of drug resistance

(2016) João V. Rodrigues et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability

(2016) Sam F. Greenbury et al.   PLoS Computational Biology

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Breaking evolutionary constraint with a tradeoff ratchet

(2015) Marjon G. J. de Vos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lower glycolysis carries a higher flux than any biochemically possible alternative

(2015) Steven J. Court et al.   Nature Communications

Delayed commitment to evolutionary fate in antibiotic resistance fitness landscapes

(2015) Adam C. Palmer et al.   Nature Communications

On the existence of accessible paths in various models of fitness landscapes

(2014) Peter Hegarty et al.   ANNALS OF APPLIED PROBABILITY

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Kinetic modelling indicates that fast-translating codons can coordinate cotranslational protein folding by avoiding misfolded intermediates

(2014) Edward P. O’Brien et al.   Nature Communications

Quantifying the Role of Population Subdivision in Evolution on Rugged Fitness Landscapes

(2014) Anne-Florence Bitbol et al.   PLoS Computational Biology

Accessibility percolation on n-trees

(2013) S. Nowak et al.   EPL

Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

(2013) Gordon M. Bennett et al.   Genome Biology and Evolution

Quantitative analyses of empirical fitness landscapes

(2013) Ivan G Szendro et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Hidden specificity in an apparently nonspecific RNA-binding protein

(2013) Ulf-Peter Guenther et al.   NATURE

Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter

(2013) Jakub Otwinowski et al.   PLoS One

Mutational Pathway Determines Whether Drug Gradients Accelerate Evolution of Drug-Resistant Cells

(2012) Philip Greulich et al.   PHYSICAL REVIEW LETTERS

Predictability of evolution depends nonmonotonically on population size

(2012) I. G. Szendro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speeding with control: codon usage, tRNAs, and ribosomes

(2012) Eva Maria Novoa et al.   TRENDS IN GENETICS

Exploring the Complexity of the HIV-1 Fitness Landscape

(2012) Roger D. Kouyos et al.   PLoS Genetics

In Silico Evolution of Early Metabolism

(2011) Alexander Ullrich et al.   ARTIFICIAL LIFE

Evolutionary paths to antibiotic resistance under dynamically sustained drug selection

(2011) Erdal Toprak et al.   NATURE GENETICS

Acceleration of Emergence of Bacterial Antibiotic Resistance in Connected Microenvironments

(2011) Q. Zhang et al.   SCIENCE

Evolutionary Accessibility of Mutational Pathways

(2011) Jasper Franke et al.   PLoS Computational Biology

Multiple peaks and reciprocal sign epistasis in an empirically determined genotype-phenotype landscape

(2010) Alexandre Dawid et al.   CHAOS

Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes

(2010) Frank J. Poelwijk et al.   JOURNAL OF THEORETICAL BIOLOGY

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

Constraints and plasticity in genome and molecular-phenome evolution

(2010) Eugene V. Koonin et al.   NATURE REVIEWS GENETICS

Synonymous codon usage influences the local protein structure observed

(2010) Rhodri Saunders et al.   NUCLEIC ACIDS RESEARCH

Evolutionary Trajectories of Beta-Lactamase CTX-M-1 Cluster Enzymes: Predicting Antibiotic Resistance

(2010) Ângela Novais et al.   PLoS Pathogens

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface

Stepwise acquisition of pyrimethamine resistance in the malaria parasite

(2009) E. R. Lozovsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive landscapes and protein evolution

(2009) M. Carneiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interplay in the Selection of Fluoroquinolone Resistance and Bacterial Fitness

(2009) Linda L. Marcusson et al.   PLoS Pathogens

Molecular Evolution under Fitness Fluctuations

(2008) Ville Mustonen et al.   PHYSICAL REVIEW LETTERS