Mutation effects predicted from sequence co-variation

Structured States of Disordered Proteins from Genomic Sequences

(2016) Agnes Toth-Petroczy et al.   CELL

Epistasis and the Dynamics of Reversion in Molecular Evolution

(2016) D. M. McCandlish et al.   GENETICS

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

The power of multiplexed functional analysis of genetic variants

(2016) Molly Gasperini et al.   Nature Protocols

Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

(2016) Jeffrey I. Boucher et al.   PROTEIN SCIENCE

Design, synthesis, and testing toward a 57-codon genome

(2016) N. Ostrov et al.   SCIENCE

The fitness landscape of a tRNA gene

(2016) C. Li et al.   SCIENCE

The Genome Project-Write

(2016) J. D. Boeke et al.   SCIENCE

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

(2016) Philippe Julien et al.   Nature Communications

Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function

(2016) Parul Mishra et al.   Cell Reports

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

(2016) Erik van Nimwegen   PLoS Computational Biology

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

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

(2015) Andrew Currin et al.   CHEMICAL SOCIETY REVIEWS

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

The Evaluation of Tools Used to Predict the Impact of Missense Variants Is Hindered by Two Types of Circularity

(2015) Dominik G. Grimm et al.   HUMAN MUTATION

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

(2015) A. H. Kachroo et al.   SCIENCE

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

(2015) Liat Rockah-Shmuel et al.   PLoS Computational Biology

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

(2015) Nicholas C. Wu et al.   PLoS Genetics

Large-scale determination of previously unsolved protein structures using evolutionary information

(2015) Sergey Ovchinnikov et al.   eLife

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Systematic Exploration of Ubiquitin Sequence, E1 Activation Efficiency, and Experimental Fitness in Yeast

(2014) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Comprehensive mutational scanning of a kinasein vivoreveals substrate-dependent fitness landscapes

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

De Novo Structure Prediction of Globular Proteins Aided by Sequence Variation-Derived Contacts

(2014) Tomasz Kosciolek et al.   PLoS One

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity

(2014) Hangfei Qi et al.   PLoS Pathogens

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Sequence co-evolution gives 3D contacts and structures of protein complexes

(2014) Thomas A Hopf et al.   eLife

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

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

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

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

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty 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

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Deep Sequencing of Systematic Combinatorial Libraries Reveals β-Lactamase Sequence Constraints at High Resolution

(2012) Zhifeng Deng et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations

(2012) S. Bershtein 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

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Discussion of: Brownian distance covariance

(2010) Peter J. Bickel et al.   Annals of Applied Statistics

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Robustness and evolvability in the functional anatomy of a PER-ARNT-SIM (PAS) domain

(2010) A. F. Philip et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

SNAP predicts effect of mutations on protein function

(2008) Yana Bromberg et al.   BIOINFORMATICS