The power of multiplexed functional analysis of genetic variants

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

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2016) Ryan Tewhey et al.   CELL

Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae

(2016) Matthew S. Rich 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

Comprehensive Analysis of the SUL1 Promoter of Saccharomyces cerevisiae

(2016) Matthew S. Rich et al.   GENETICS

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

Learning the Sequence Determinants of Alternative Splicing from Millions of Random Sequences

(2015) Alexander B. Rosenberg et al.   CELL

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

(2015) Christopher M. Vockley et al.   GENOME RESEARCH

Understanding how cis -regulatory function is encoded in DNA sequence using massively parallel reporter assays and designed sequences

(2015) Michael A. White   GENOMICS

Decoding enhancers using massively parallel reporter assays

(2015) Fumitaka Inoue et al.   GENOMICS

Conformation-Dependent Epitopes Recognized by Prion Protein Antibodies Probed Using Mutational Scanning and Deep Sequencing

(2015) Kyle M. Doolan et al.   JOURNAL OF MOLECULAR BIOLOGY

Precise and Efficient Antibody Epitope Determination through Library Design, Yeast Display and Next-Generation Sequencing

(2015) Thomas Van Blarcom 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

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

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

Pervasive degeneracy and epistasis in a protein-protein interface

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

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Combining Natural Sequence Variation with High Throughput Mutational Data to Reveal Protein Interaction Sites

(2015) Daniel Melamed et al.   PLoS Genetics

Systematic Dissection of the Sequence Determinants of Gene 3’ End Mediated Expression Control

(2015) Ophir Shalem et al.   PLoS Genetics

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

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

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

High-throughput mutagenesis reveals functional determinants for DNA targeting by activation-induced deaminase

(2014) Kiran S. Gajula et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Alexandre Melnikov 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

Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes

(2014) A. R. Majithia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human splicing code reveals new insights into the genetic determinants of disease

(2014) H. Y. Xiong et al.   SCIENCE

Systematic Dissection of Coding Exons at Single Nucleotide Resolution Supports an Additional Role in Cell-Specific Transcriptional Regulation

(2014) Ramon Y. Birnbaum et al.   PLoS Genetics

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

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

ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing

(2013) Robert C. Green et al.   GENETICS IN MEDICINE

Computational Design of a Protein-Based Enzyme Inhibitor

(2013) Erik Procko 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

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Massive functional mapping of a 5′-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing

(2013) Erik Holmqvist et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Massively parallel in vivo enhancer assay reveals that highly local features determine the cis-regulatory function of ChIP-seq peaks

(2013) M. A. White 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

Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast

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

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

RNA-programmed genome editing in human cells

(2013) Martin Jinek et al.   eLife

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Timothy A Whitehead et al.   NATURE BIOTECHNOLOGY

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

PFunkel: Efficient, Expansive, User-Defined Mutagenesis

(2012) Elad Firnberg 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

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

Quantitative evaluation of all hexamers as exonic splicing elements

(2011) Shengdong Ke et al.   GENOME RESEARCH

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

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

Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence

(2010) J. B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational Robustness of Ribosomal Protein Genes

(2010) P. A. Lind et al.   SCIENCE

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY