The causes of evolvability and their evolution

Pairwise and higher-order genetic interactions during the evolution of a tRNA

(2018) Júlia Domingo et al.   NATURE

Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice

(2018) Zoë N. Rogers et al.   NATURE GENETICS

RNA-mediated gene regulation is less evolvable than transcriptional regulation

(2018) Joshua L. Payne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Destabilizing mutations encode nongenetic variation that drives evolutionary innovation

(2018) Katherine L. Petrie et al.   SCIENCE

Phase separation of a yeast prion protein promotes cellular fitness

(2018) Titus M. Franzmann et al.   SCIENCE

Quantitative characterization of all single amino acid variants of a viral capsid-based drug delivery vehicle

(2018) Emily C. Hartman et al.   Nature Communications

Innovation in an E. coli evolution experiment is contingent on maintaining adaptive potential until competition subsides

(2018) Dacia Leon et al.   PLoS Genetics

Mapping mutational effects along the evolutionary landscape of HIV envelope

(2018) Hugh K Haddox et al.   eLife

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Computing the Extended Synthesis: Mapping the Dynamics and Conceptual Structure of the Evolvability Research Front

(2017) Laura Nuño de la Rosa   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Deletion of a mycobacterial divisome factor collapses single-cell phenotypic heterogeneity

(2017) E. Hesper Rego et al.   NATURE

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Alternative evolutionary histories in the sequence space of an ancient protein

(2017) Tyler N. Starr et al.   NATURE

Scaling by shrinking: empowering single-cell 'omics' with microfluidic devices

(2017) Sanjay M. Prakadan et al.   NATURE REVIEWS GENETICS

Epigenetic plasticity and the hallmarks of cancer

(2017) William A. Flavahan et al.   SCIENCE

Gene duplication can impart fragility, not robustness, in the yeast protein interaction network

(2017) Guillaume Diss et al.   SCIENCE

A bacterial global regulator forms a prion

(2017) Andy H. Yuan et al.   SCIENCE

Antibiotic tolerance facilitates the evolution of resistance

(2017) Irit Levin-Reisman et al.   SCIENCE

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

Pioneer cells established by the [SWI+] prion can promote dispersal and out-crossing in yeast

(2017) Gregory A. Newby et al.   PLOS BIOLOGY

High-order epistasis shapes evolutionary trajectories

(2017) Zachary R. Sailer et al.   PLoS Computational Biology

Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator

(2017) Isabel Nocedal et al.   eLife

Genetic variation in adaptability and pleiotropy in budding yeast

(2017) Elizabeth R Jerison et al.   eLife

Attenuation of RNA viruses by redirecting their evolution in sequence space

(2017) Gonzalo Moratorio et al.   Nature Microbiology

A thousand empirical adaptive landscapes and their navigability

(2017) José Aguilar-Rodríguez et al.   Nature Ecology & Evolution

Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory

(2017) Andrea Wünsche et al.   Nature Ecology & Evolution

Origins of Allostery and Evolvability in Proteins: A Case Study

(2016) Arjun S. Raman et al.   CELL

Ribosome Footprint Profiling of Translation throughout the Genome

(2016) Nicholas T. Ingolia   CELL

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

(2016) Sohini Chakrabortee et al.   CELL

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

Epistatic interactions between ancestral genotype and beneficial mutations shape evolvability in Pseudomonas aeruginosa

(2016) Danna R. Gifford et al.   EVOLUTION

The Molecular Chaperone DnaK Is a Source of Mutational Robustness

(2016) José Aguilar-Rodríguez et al.   Genome Biology and Evolution

Gap Gene Regulatory Dynamics Evolve along a Genotype Network

(2016) Anton Crombach et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary Dynamics of Abundant Stop Codon Readthrough

(2016) Irwin Jungreis et al.   MOLECULAR BIOLOGY AND EVOLUTION

How Good Are Statistical Models at Approximating Complex Fitness Landscapes?

(2016) Louis du Plessis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Sex speeds adaptation by altering the dynamics of molecular evolution

(2016) Michael J. McDonald et al.   NATURE

On the (un)predictability of a large intragenic fitness landscape

(2016) Claudia Bank et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Luminidependens (LD) is an Arabidopsis protein with prion behavior

(2016) Sohini Chakrabortee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network of epistatic interactions within a yeast snoRNA

(2016) O. Puchta et al.   SCIENCE

The linker histone H1.0 generates epigenetic and functional intratumor heterogeneity

(2016) C. M. Torres et al.   SCIENCE

The fitness landscape of a tRNA gene

(2016) C. Li et al.   SCIENCE

Mechanisms of bacterial persistence during stress and antibiotic exposure

(2016) Alexander Harms et al.   SCIENCE

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

(2016) Michael Doud et al.   Viruses-Basel

The complete local genotype–phenotype landscape for the alternative splicing of a human exon

(2016) Philippe Julien et al.   Nature Communications

Prevalent mutator genotype identified in fungal pathogen Candida glabrata promotes multi-drug resistance

(2016) Kelley R. Healey et al.   Nature Communications

Diverse drug-resistance mechanisms can emerge from drug-tolerant cancer persister cells

(2016) Michael Ramirez et al.   Nature Communications

Selection Transforms the Landscape of Genetic Variation Interacting with Hsp90

(2016) Kerry A. Geiler-Samerotte et al.   PLOS BIOLOGY

Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture

(2016) Hugh K. Haddox et al.   PLoS Pathogens

Environmental changes bridge evolutionary valleys

(2016) B. Steinberg et al.   Science Advances

Competition along trajectories governs adaptation rates towards antimicrobial resistance

(2016) C. Brandon Ogbunugafor et al.   Nature Ecology & Evolution

Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates

(2015) Christopher D. Aakre et al.   CELL

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

(2015) Michael A. Stiffler et al.   CELL

A functional perspective on phenotypic heterogeneity in microorganisms

(2015) Martin Ackermann   NATURE REVIEWS MICROBIOLOGY

Generating new prions by targeted mutation or segment duplication

(2015) Kacy R. Paul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Translational readthrough potential of natural termination codons in eucaryotes – The impact of RNA sequence

(2015) Maciej Dabrowski et al.   RNA Biology

Pervasive degeneracy and epistasis in a protein-protein interface

(2015) A. I. Podgornaia et al.   SCIENCE

The origins of mutational robustness

(2015) Mario A. Fares   TRENDS IN GENETICS

The Evolutionary Potential of Phenotypic Mutations

(2015) Hayato Yanagida et al.   PLoS Genetics

Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

(2015) Dave W Anderson et al.   eLife

Expression noise facilitates the evolution of gene regulation

(2015) Luise Wolf et al.   eLife

Cross-Kingdom Chemical Communication Drives a Heritable, Mutually Beneficial Prion-Based Transformation of Metabolism

(2014) Daniel F. Jarosz et al.   CELL

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

The Impact of Macroscopic Epistasis on Long-Term Evolutionary Dynamics

(2014) B. H. Good et al.   GENETICS

Preservation of genetic and regulatory robustness in ancient gene duplicates ofSaccharomyces cerevisiae

(2014) Orla M. Keane et al.   GENOME RESEARCH

A Systematic Survey of an Intragenic Epistatic Landscape

(2014) Claudia Bank et al.   MOLECULAR BIOLOGY AND EVOLUTION

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Empirical fitness landscapes and the predictability of evolution

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

Inferring fitness landscapes by regression produces biased estimates of epistasis

(2014) J. Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance

(2014) B. Javid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Robustness and Evolvability of Transcription Factor Binding Sites

(2014) J. L. Payne et al.   SCIENCE

A Promiscuous Intermediate Underlies the Evolution of LEAFY DNA Binding Specificity

(2014) C. Sayou et al.   SCIENCE

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

Promoter architecture dictates cell-to-cell variability in gene expression

(2014) Daniel L. Jones et al.   SCIENCE

Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network

(2014) Ksenia Pougach et al.   Nature Communications

Genome-wide Translational Changes Induced by the Prion [PSI+]

(2014) Agnès Baudin-Baillieu et al.   Cell Reports

Comprehensive experimental fitness landscape and evolutionary network for small RNA

(2013) J. I. Jimenez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of phenotypic heterogeneity to adaptive antibiotic resistance

(2013) M. A. Sanchez-Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deep mutational scanning of an RRM domain of the Saccharomyces cerevisiae poly(A)-binding protein

(2013) D. Melamed et al.   RNA

Cryptic Variation in Morphological Evolution: HSP90 as a Capacitor for Loss of Eyes in Cavefish

(2013) N. Rohner et al.   SCIENCE

Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

(2013) Christopher R. Baker et al.   SCIENCE

Long-Term Dynamics of Adaptation in Asexual Populations

(2013) M. J. Wiser et al.   SCIENCE

Candida albicans CUG Mistranslation Is a Mechanism To Create Cell Surface Variation

(2013) I. Miranda et al.   mBio

Bet-hedging-a triple trade-off between means, variances and correlations

(2012) Jostein Starrfelt et al.   BIOLOGICAL REVIEWS

Cryptic peroxisomal targeting via alternative splicing and stop codon read-through in fungi

(2012) Johannes Freitag et al.   NATURE

Prions are a common mechanism for phenotypic inheritance in wild yeasts

(2012) Randal Halfmann et al.   NATURE

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load

(2012) S. Wielgoss et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Yeast Prion, Mod5, Promotes Acquired Drug Resistance and Cell Survival Under Environmental Stress

(2012) G. Suzuki et al.   SCIENCE

Nonheritable Cellular Variability Accelerates the Evolutionary Processes of Cancer

(2012) Steven A. Frank et al.   PLOS BIOLOGY

Structure and Age Jointly Influence Rates of Protein Evolution

(2012) Macarena Toll-Riera et al.   PLoS Computational Biology

Natural selection. II. Developmental variability and evolutionary rate*

(2011) S. A. FRANK   JOURNAL OF EVOLUTIONARY BIOLOGY

The genetical theory of kin selection

(2011) A. GARDNER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

(2011) Eric J. Hayden et al.   NATURE

Experimental illumination of a fitness landscape

(2011) R. T. Hietpas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences

(2011) M. Rebeiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Diminishing Returns Epistasis Among Beneficial Mutations Decelerates Adaptation

(2011) H.-H. Chou et al.   SCIENCE

Second-Order Selection for Evolvability in a Large Escherichia coli Population

(2011) R. J. Woods et al.   SCIENCE

Initial Mutations Direct Alternative Pathways of Protein Evolution

(2011) Merijn L. M. Salverda et al.   PLoS Genetics

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

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

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

Messy biology and the origins of evolutionary innovations

(2010) Dan S Tawfik   Nature Chemical Biology

Hsp90 and Environmental Stress Transform the Adaptive Value of Natural Genetic Variation

(2010) D. F. Jarosz et al.   SCIENCE

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

(2010) Matthew T. Weirauch et al.   TRENDS IN GENETICS

Robustness and Evolvability

(2010) Joanna Masel et al.   TRENDS IN GENETICS

The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts

(2010) Ryan K. Shultzaberger et al.   PLoS Genetics

RNA editing: a driving force for adaptive evolution?

(2009) Willemijn M. Gommans et al.   BIOESSAYS

Effects of Recombination on Complex Regulatory Circuits

(2009) O. C. Martin et al.   GENETICS

Analysis of a complete DNA-protein affinity landscape

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

Congruent Evolution of Genetic and Environmental Robustness in Micro-RNA

(2009) G. J. Szollosi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Positive selection for elevated gene expression noise in yeast

(2009) Zhihua Zhang et al.   Molecular Systems Biology

The Beagle in a bottle

(2009) Angus Buckling et al.   NATURE

Experimental evolution of bet hedging

(2009) Hubertus J. E. Beaumont et al.   NATURE

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

Chaperonin overexpression promotes genetic variation and enzyme evolution

(2009) Nobuhiko Tokuriki et al.   NATURE

The evolutionary consequences of erroneous protein synthesis

(2009) D. Allan Drummond et al.   NATURE REVIEWS GENETICS

The dynamics of adaptation on correlated fitness landscapes

(2009) S. Kryazhimskiy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential role of phenotypic mutations in the evolution of protein expression and stability

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

Protein Dynamism and Evolvability

(2009) N. Tokuriki et al.   SCIENCE

Positive Epistasis Drives the Acquisition of Multidrug Resistance

(2009) Sandra Trindade et al.   PLoS Genetics

Complex Adaptations Can Drive the Evolution of the Capacitor [PSI+], Even with Realistic Rates of Yeast Sex

(2009) Cortland K. Griswold et al.   PLoS Genetics

The look-ahead effect of phenotypic mutations

(2008) Dion J Whitehead et al.   Biology Direct

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Prion Switching in Response to Environmental Stress

(2008) Jens Tyedmers et al.   PLOS BIOLOGY

Is evolvability evolvable?

(2007) Massimo Pigliucci   NATURE REVIEWS GENETICS