Multiplexed assays of variant effects contribute to a growing genotype–phenotype atlas

A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation

(2018) Eran Kotler et al.   MOLECULAR CELL

Multiplexed gene synthesis in emulsions for exploring protein functional landscapes

(2018) Calin Plesa et al.   SCIENCE

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data

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

Saturation mutagenesis reveals manifold determinants of exon definition

(2017) Shengdong Ke et al.   GENOME RESEARCH

The ubiquity of pleiotropy in human disease

(2017) Kevin Chesmore et al.   HUMAN GENETICS

A framework for exhaustively mapping functional missense variants

(2017) Jochen Weile et al.   Molecular Systems Biology

A platform for functional assessment of large variant libraries in mammalian cells

(2017) Kenneth A. Matreyek et al.   NUCLEIC ACIDS RESEARCH

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

(2017) Justin R. Klesmith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Cas9–mediated saturated mutagenesis screen predicts clinical drug resistance with improved accuracy

(2017) Leyuan Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A method of high-throughput functional evaluation of EGFR gene variants of unknown significance in cancer

(2017) Shinji Kohsaka et al.   Science Translational Medicine

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

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

Deconstruction of the Ras switching cycle through saturation mutagenesis

(2017) Pradeep Bandaru et al.   eLife

Evaluation of ACMG-Guideline-Based Variant Classification of Cancer Susceptibility and Non-Cancer-Associated Genes in Families Affected by Breast Cancer

(2016) Kara N. Maxwell et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing

(2016) Tian-Hao Zhang et al.   BMC GENOMICS

An extended set of yeast-based functional assays accurately identifies human disease mutations

(2016) Song Sun et al.   GENOME RESEARCH

Shifting Fitness and Epistatic Landscapes Reflect Trade-offs along an Evolutionary Pathway

(2016) Barrett Steinberg et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data

(2016) Arti Tripathi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Local fitness landscape of the green fluorescent protein

(2016) Karen S. Sarkisyan et al.   NATURE

Prospective functional classification of all possible missense variants in PPARG

(2016) Amit R Majithia et al.   NATURE GENETICS

A genome-integrated massively parallel reporter assay reveals DNA sequence determinants ofcis-regulatory activity in neural cells

(2016) Brett B. Maricque et al.   NUCLEIC ACIDS RESEARCH

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

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

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

High Throughput Analyses of Budding Yeast ARSs Reveal New DNA Elements Capable of Conferring Centromere-Independent Plasmid Propagation

(2016) Timothy Hoggard et al.   G3-Genes Genomes Genetics

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

(2016) David Mavor et al.   eLife

Software for the analysis and visualization of deep mutational scanning data

(2015) Jesse D Bloom   BMC BIOINFORMATICS

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

(2015) Michael A. Stiffler et al.   CELL

Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders

(2015) Nidhi Sahni et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

SORTCERY—A High–Throughput Method to Affinity Rank Peptide Ligands

(2015) Lothar “Luther” Reich et al.   JOURNAL OF MOLECULAR BIOLOGY

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

(2015) Michael B. Doud et al.   MOLECULAR BIOLOGY AND EVOLUTION

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

High-throughput identification of protein mutant stability computed from a double mutant fitness landscape

(2015) Nicholas C. Wu et al.   PROTEIN SCIENCE

Gene essentiality and synthetic lethality in haploid human cells

(2015) V. A. Blomen 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

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

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

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

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

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

Selecting causal genes from genome-wide association studies via functionally coherent subnetworks

(2014) Murat Taşan et al.   NATURE METHODS

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

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

Variants of uncertain significance in BRCA: a harbinger of ethical and policy issues to come?

(2014) Jae Yeon Cheon et al.   Genome Medicine

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

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A rapid, efficient, and economical inverse polymerase chain reaction-based method for generating a site saturation mutant library

(2013) Pankaj C. Jain et al.   ANALYTICAL BIOCHEMISTRY

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

(2013) Ryan T. Hietpas et al.   EVOLUTION

Computational Design of a Protein-Based Enzyme Inhibitor

(2013) Erik Procko 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

Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing

(2013) Charles M. Forsyth et al.   mAbs

High-throughput Analysis ofin vivoProtein Stability

(2013) Ikjin Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Computational design of ligand-binding proteins with high affinity and selectivity

(2013) Christine E. Tinberg et al.   NATURE

Resistance to vemurafenib resulting from a novel mutation in the BRAFV600E kinase domain

(2013) Timothy R. Wagenaar et al.   Pigment Cell & Melanoma Research

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

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

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Latent Effects of Hsp90 Mutants Revealed at Reduced Expression Levels

(2013) Li Jiang et al.   PLoS Genetics

Robust in vitro affinity maturation strategy based on interface-focused high-throughput mutational scanning

(2012) Yasuhiro Fujino et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

High-resolution mapping, characterization, and optimization of autonomously replicating sequences in yeast

(2012) I. Liachko et al.   GENOME RESEARCH

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

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

(2012) Zhifeng Deng 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

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

PFunkel: Efficient, Expansive, User-Defined Mutagenesis

(2012) Elad Firnberg et al.   PLoS One

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

Complex effects of nucleotide variants in a mammalian cis-regulatory element

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

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

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

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Protein Model Discrimination Using Mutational Sensitivity Derived from Deep Sequencing

(2012) Bharat V. Adkar et al.   STRUCTURE

Enrich: software for analysis of protein function by enrichment and depletion of variants

(2011) Douglas M. Fowler et al.   BIOINFORMATICS

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

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

(2010) Andreas Ernst et al.   Molecular BioSystems

Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips

(2010) Sriram Kosuri et al.   NATURE BIOTECHNOLOGY

Parallel, tag-directed assembly of locally derived short sequence reads

(2010) Joseph B Hiatt et al.   NATURE METHODS

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS