DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction

Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

(2020) Vikas Pejaver et al.   Nature Communications

VIPdb, a genetic Variant Impact Predictor Database

(2019) Zhiqiang Hu et al.   HUMAN MUTATION

GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects

(2019) Elodie Laine et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning

(2018) Jeremiah D. Heredia et al.   JOURNAL OF IMMUNOLOGY

Multiplex assessment of protein variant abundance by massively parallel sequencing

(2018) Kenneth A. Matreyek et al.   NATURE GENETICS

Predicting the clinical impact of human mutation with deep neural networks

(2018) Laksshman Sundaram et al.   NATURE GENETICS

Structure and mutagenic analysis of the lipid II flippase MurJ fromEscherichia coli

(2018) Sanduo Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping mutational effects along the evolutionary landscape of HIV envelope

(2018) Hugh K Haddox et al.   eLife

The genetic landscape of a physical interaction

(2018) Guillaume Diss et al.   eLife

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

(2018) Vanessa E. Gray et al.   Cell Systems

Accurate classification of BRCA1 variants with saturation genome editing

(2018) Gregory M. Findlay et al.   NATURE

Mutational processes shape the landscape of TP53 mutations in human cancer

(2018) Andrew O. Giacomelli et al.   NATURE GENETICS

Deep generative models of genetic variation capture the effects of mutations

(2018) Adam J. Riesselman et al.   NATURE METHODS

Improved mutant function prediction via PACT: Protein Analysis and Classifier Toolkit

(2018) Justin R Klesmith et al.   BIOINFORMATICS

The phylogenomics of evolving virus virulence

(2018) Jemma L. Geoghegan et al.   NATURE REVIEWS GENETICS

A framework for exhaustively mapping functional missense variants

(2017) Jochen Weile et al.   Molecular Systems Biology

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

Depth dependent amino acid substitution matrices and their use in predicting deleterious mutations

(2017) Nida Farheen et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

(2017) Yvonne H. Chan et al.   Nature Communications

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

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

Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

(2017) Orr Ashenberg et al.   PLoS Pathogens

Deconstruction of the Ras switching cycle through saturation mutagenesis

(2017) Pradeep Bandaru et al.   eLife

Rational design of non-resistant targeted cancer therapies

(2017) Francisco Martínez-Jiménez et al.   Scientific Reports

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

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

(2016) Michael Doud et al.   Viruses-Basel

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

(2016) Parul Mishra et al.   Cell Reports

Phenotypic Characterization of a Comprehensive Set of MAPK1 /ERK2 Missense Mutants

(2016) Lisa Brenan et al.   Cell Reports

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

(2016) David Mavor et al.   eLife

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq

(2016) Eric D. Kelsic et al.   Cell Systems

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

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

(2015) Michael A. Stiffler et al.   CELL

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification

(2015) Massimo Andreatta et al.   IMMUNOGENETICS

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

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

Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli

(2015) Justin R. Klesmith et al.   ACS Synthetic Biology

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

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

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

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

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

A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

(2014) Panagiotis Katsonis et al.   GENOME RESEARCH

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

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   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

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

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Towards Precision Medicine: Advances in Computational Approaches for the Analysis of Human Variants

(2013) Thomas A. Peterson 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

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

The spatial architecture of protein function and adaptation

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

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

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

Musite, a Tool for Global Prediction of General and Kinase-specific Phosphorylation Sites

(2010) Jianjiong Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols