Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations

Effects of new mutations on fitness: insights from models and data

(2014) Thomas Bataillon et al.   Annals of the New York Academy of Sciences

EFIN: predicting the functional impact of nonsynonymous single nucleotide polymorphisms in human genome

(2014) Shuai Zeng et al.   BMC GENOMICS

Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge

(2014) Karan S Hingorani et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

(2014) J. I. Boucher et al.   GENETICS

SuSPect: Enhanced Prediction of Single Amino Acid Variant (SAV) Phenotype Using Network Features

(2014) Christopher M. Yates et al.   JOURNAL OF MOLECULAR BIOLOGY

Biophysics of protein evolution and evolutionary protein biophysics

(2014) T. Sikosek et al.   Journal of the Royal Society Interface

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

PredictProtein—an open resource for online prediction of protein structural and functional features

(2014) Guy Yachdav et al.   NUCLEIC ACIDS RESEARCH

Exploring the Functional Residues in a Flavin-Binding Fluorescent Protein Using Deep Mutational Scanning

(2014) HyeonSeok Shin et al.   PLoS One

Single nucleotide variations: Biological impact and theoretical interpretation

(2014) Panagiotis Katsonis et al.   PROTEIN SCIENCE

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

(2014) Jaroslav Bendl et al.   PLoS Computational Biology

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

(2013) Romain A. Studer et al.   BIOCHEMICAL JOURNAL

Congruency in the prediction of pathogenic missense mutations: state-of-the-art web-based tools

(2013) S. Castellana et al.   BRIEFINGS IN BIOINFORMATICS

Predicting phenotypic variation from genotypes, phenotypes and a combination of the two

(2013) Alejandro Burga et al.   CURRENT OPINION IN BIOTECHNOLOGY

Strong Mutational Bias Toward Deletions in the Drosophila melanogaster Genome Is Compensated by Selection

(2013) Evgeny V. Leushkin et al.   Genome Biology and Evolution

News from the Protein Mutability Landscape

(2013) Maximilian Hecht et al.   JOURNAL OF MOLECULAR BIOLOGY

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

Contribution of Selection for Protein Folding Stability in Shaping the Patterns of Polymorphisms in Coding Regions

(2013) Adrian W.R. Serohijos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutational and fitness landscapes of an RNA virus revealed through population sequencing

(2013) Ashley Acevedo et al.   NATURE

Genotype to phenotype: lessons from model organisms for human genetics

(2013) Ben Lehner   NATURE REVIEWS GENETICS

SPACER: server for predicting allosteric communication and effects of regulation

(2013) Alexander Goncearenco et al.   NUCLEIC ACIDS RESEARCH

Neutral and weakly nonneutral sequence variants may define individuality

(2013) Y. Bromberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

(2013) L. M. Starita 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

Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels

(2013) Li Jiang et al.   PLoS Genetics

Mechanisms of Protein Sequence Divergence and Incompatibility

(2013) Alon Wellner et al.   PLoS Genetics

Correlated Occurrence and Bypass of Frame-Shifting Insertion-Deletions (InDels) to Give Functional Proteins

(2013) Liat Rockah-Shmuel et al.   PLoS Genetics

Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing

(2012) Yali Xue et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Performance of computational tools in evaluating the functional impact of laboratory-induced amino acid mutations

(2012) V. E. Gray et al.   BIOINFORMATICS

Dynamic Mutation-Selection Balance as an Evolutionary Attractor

(2012) S. Goyal et al.   GENETICS

Construction of a Stability Landscape of the CH3 Domain of Human IgG1 by Combining Directed Evolution with High Throughput Sequencing

(2012) Michael W. Traxlmayr et al.   JOURNAL OF MOLECULAR BIOLOGY

Systematic Identification of H274Y Compensatory Mutations in Influenza A Virus Neuraminidase by High-Throughput Screening

(2012) N. C. Wu et al.   JOURNAL OF VIROLOGY

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Epistasis as the primary factor in molecular evolution

(2012) Michael S. Breen et al.   NATURE

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Critical features for biosynthesis, stability, and functionality of a G protein-coupled receptor uncovered by all-versus-all mutations

(2012) K. M. Schlinkmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing

(2012) H. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A fundamental protein property, thermodynamic stability, revealed solely from large-scale measurements of protein function

(2012) C. L. Araya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing

(2012) Bharat V. Adkar et al.   STRUCTURE

Prediction of Mutational Tolerance in HIV-1 Protease and Reverse Transcriptase Using Flexible Backbone Protein Design

(2012) Elisabeth Humphris-Narayanan et al.   PLoS Computational Biology

Predicting disease-associated substitution of a single amino acid by analyzing residue interactions

(2011) Yizhou Li et al.   BMC BIOINFORMATICS

Inference of Site Frequency Spectra From High-Throughput Sequence Data: Quantification of Selection on Nonsynonymous and Synonymous Sites in Humans

(2011) Peter D. Keightley et al.   GENETICS

Genomic island variability facilitates Prochlorococcus–virus coexistence

(2011) Sarit Avrani et al.   NATURE

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Mutation Detection with Next-Generation Resequencing through a Mediator Genome

(2011) Omri Wurtzel et al.   PLoS One

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

In vitro evolution goes deep

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

Slow protein evolutionary rates are dictated by surface-core association

(2011) A. Toth-Petroczy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The functional spectrum of low-frequency coding variation

(2011) Gabor T Marth et al.   GENOME BIOLOGY

SNP detection and genotyping from low-coverage sequencing data on multiple diploid samples

(2010) S. Q. Le et al.   GENOME RESEARCH

Coevolution of PDZ domain–ligand interactions analyzed by high-throughput phage display and deep sequencing

(2010) Andreas Ernst et al.   Molecular BioSystems

Sequence space and the ongoing expansion of the protein universe

(2010) Inna S. Povolotskaya et al.   NATURE

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?

(2010) P. D. Keightley et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A geometry-based generic predictor for catalytic and allosteric sites

(2010) S. Mitternacht et al.   PROTEIN ENGINEERING DESIGN & SELECTION

The Use of Orthologous Sequences to Predict the Impact of Amino Acid Substitutions on Protein Function

(2010) Nicholas J. Marini et al.   PLoS Genetics

Pervasive Cryptic Epistasis in Molecular Evolution

(2010) Mark Lunzer et al.   PLoS Genetics

Stability effects of mutations and protein evolvability

(2009) Nobuhiko Tokuriki et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

(2009) Richard J. Roberts et al.   NUCLEIC ACIDS RESEARCH

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Intense Neutral Drifts Yield Robust and Evolvable Consensus Proteins

(2008) Shimon Bershtein et al.   JOURNAL OF MOLECULAR BIOLOGY

Real-time kinetics of restriction–modification gene expression after entry into a new host cell

(2008) Iwona Mruk et al.   NUCLEIC ACIDS RESEARCH

How Protein Stability and New Functions Trade Off

(2008) Nobuhiko Tokuriki et al.   PLoS Computational Biology