The architecture of an empirical genotype-phenotype map

Structural properties of genotype–phenotype maps

(2017) S. E. Ahnert   Journal of the Royal Society Interface

Systematic Investigation of Transcription Factor Activity in the Context of Chromatin Using Massively Parallel Binding and Expression Assays

(2017) Michal Levo et al.   MOLECULAR CELL

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

(2017) Alina Isakova et al.   NATURE METHODS

The genotype-phenotype map of an evolving digital organism

(2017) Miguel A. Fortuna et al.   PLoS Computational Biology

The ground truth about metadata and community detection in networks

(2017) Leto Peel et al.   Science Advances

A thousand empirical adaptive landscapes and their navigability

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

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Network of epistatic interactions within a yeast snoRNA

(2016) O. Puchta et al.   SCIENCE

The fitness landscape of a tRNA gene

(2016) C. Li et al.   SCIENCE

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

(2016) Philippe Julien et al.   Nature Communications

Intrinsic limits to gene regulation by global crosstalk

(2016) Tamar Friedlander et al.   Nature Communications

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

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

High-Resolution Phenotypic Landscape of the RNA Polymerase II Trigger Loop

(2016) Chenxi Qiu et al.   PLoS Genetics

Unraveling determinants of transcription factor binding outside the core binding site

(2015) Michal Levo et al.   GENOME RESEARCH

Mistranslation drives the evolution of robustness in TEM-1 β-lactamase

(2015) Sinisa Bratulic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-base pair differences in a shared motif determine differential Rhodopsin expression

(2015) J. Rister et al.   SCIENCE

Pervasive degeneracy and epistasis in a protein-protein interface

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

Mutational Robustness Accelerates the Origin of Novel RNA Phenotypes through Phenotypic Plasticity

(2014) Andreas Wagner   BIOPHYSICAL JOURNAL

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

A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure

(2014) S. F. Greenbury et al.   Journal of the Royal Society Interface

Evolution on neutral networks accelerates the ticking rate of the molecular clock

(2014) S. Manrubia et al.   Journal of the Royal Society Interface

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima

(2014) Steffen Schaper et al.   PLoS One

Mapping and Dynamics of Regulatory DNA and Transcription Factor Networks in A. thaliana

(2014) Alessandra M. Sullivan et al.   Cell Reports

The Amino Acid Alphabet and the Architecture of the Protein Sequence-Structure Map. I. Binary Alphabets

(2014) Evandro Ferrada   PLoS Computational Biology

Evolutionary systems biology: What it is and why it matters

(2013) Orkun S. Soyer et al.   BIOESSAYS

ON THE FINDABILITY OF GENOTYPES

(2013) David M. McCandlish   EVOLUTION

Adaptive dynamics under development-based genotype–phenotype maps

(2013) Isaac Salazar-Ciudad et al.   NATURE

A latent capacity for evolutionary innovation through exaptation in metabolic systems

(2013) Aditya Barve et al.   NATURE

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

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

DNA-binding specificity changes in the evolution of forkhead transcription factors

(2013) S. Nakagawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of a polymorphism in a Hox/Pax-responsive enhancer in the evolution of the vertebrate spine

(2013) I. Guerreiro 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

Constraint and Contingency in Multifunctional Gene Regulatory Circuits

(2013) Joshua L. Payne et al.   PLoS Computational Biology

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

Evolutionary dynamics on multiple scales: a quantitative analysis of the interplay between genotype, phenotype, and fitness in linear genetic programming

(2012) Ting Hu et al.   Genetic Programming and Evolvable Machines

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

The pleiotropic structure of the genotype–phenotype map: the evolvability of complex organisms

(2011) Günter P. Wagner et al.   NATURE REVIEWS GENETICS

Silencing chromatin: comparing modes and mechanisms

(2011) Christian Beisel et al.   NATURE REVIEWS GENETICS

Topological Structure of the Space of Phenotypes: The Case of RNA Neutral Networks

(2011) Jacobo Aguirre et al.   PLoS One

The evolvability of programmable hardware

(2010) K. Raman et al.   Journal of the Royal Society Interface

An atlas of gene regulatory networks reveals multiple three-gene mechanisms for interpreting morphogen gradients

(2010) James Cotterell et al.   Molecular Systems Biology

Mutational robustness can facilitate adaptation

(2010) Jeremy A. Draghi et al.   NATURE

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Analysis of a complete DNA-protein affinity landscape

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

Variation in the Ratio of Nucleotide Substitution and Indel Rates across Genomes in Mammals and Bacteria

(2009) J.-Q. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks

(2009) João F. Matias Rodrigues et al.   PLoS Computational Biology

Problems and Solutions for Estimating Indel Rates and Length Distributions

(2008) Reed A. Cartwright   MOLECULAR BIOLOGY AND EVOLUTION

UniPROBE: an online database of protein binding microarray data on protein-DNA interactions

(2008) D. E. Newburger et al.   NUCLEIC ACIDS RESEARCH

The Ascent of the Abundant: How Mutational Networks Constrain Evolution

(2008) Matthew C. Cowperthwaite et al.   PLoS Computational Biology

Robustness and evolvability: a paradox resolved

(2007) A. Wagner   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES