Sort-seq under the hood: implications of design choices on large-scale characterization of sequence-function relations

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

(2015) Michael A. Stiffler et al.   CELL

High-throughput cellular RNA device engineering

(2015) Brent Townshend et al.   NATURE METHODS

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

MicroRNA control of protein expression noise

(2015) J. M. Schmiedel et al.   SCIENCE

Pervasive degeneracy and epistasis in a protein-protein interface

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

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

(2015) Ophir Shalem et al.   PLoS Genetics

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

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

Probing the effect of promoters on noise in gene expression using thousands of designed sequences

(2014) Eilon Sharon et al.   GENOME RESEARCH

A Systematic Survey of an Intragenic Epistatic Landscape

(2014) Claudia Bank et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quantitative analysis of mammalian translation initiation sites by FACS-seq

(2014) W. L. Noderer et al.   Molecular Systems Biology

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

Massively parallel functional annotation of 3′ untranslated regions

(2014) Wenxue Zhao et al.   NATURE BIOTECHNOLOGY

Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

(2014) Jason D Buenrostro et al.   NATURE BIOTECHNOLOGY

Function-based identification of mammalian enhancers using site-specific integration

(2014) Diane E Dickel et al.   NATURE METHODS

Large-scale de novo DNA synthesis: technologies and applications

(2014) Sriram Kosuri et al.   NATURE METHODS

FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells

(2014) Matthew Murtha et al.   NATURE METHODS

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Empirical fitness landscapes and the predictability of evolution

(2014) J. Arjan G.M. de Visser et al.   NATURE REVIEWS GENETICS

Parametric Inference in the Large Data Limit Using Maximally Informative Models

(2014) Justin B. Kinney et al.   NEURAL COMPUTATION

Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity

(2014) Neil Peterman et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

Comparison of the theoretical and real-world evolutionary potential of a genetic circuit

(2014) M Razo-Mejia et al.   PHYSICAL BIOLOGY

Inferring fitness landscapes by regression produces biased estimates of epistasis

(2014) J. Otwinowski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Identification of Regulatory Elements in Conserved 3′ UTRs of Human Transcripts

(2014) Panos Oikonomou et al.   Cell Reports

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

(2014) Arnaud R Krebs et al.   eLife

Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos

(2013) Stephen S Gisselbrecht et al.   NATURE METHODS

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

(2013) Erik Holmqvist et al.   NUCLEIC ACIDS RESEARCH

Genotype to Phenotype Mapping and the Fitness Landscape of the E. coli lac Promoter

(2013) Jakub Otwinowski et al.   PLoS One

Composability of regulatory sequences controlling transcription and translation inEscherichia coli

(2013) Sriram Kosuri 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

Causes and Effects of N-Terminal Codon Bias in Bacterial Genes

(2013) D. B. Goodman et al.   SCIENCE

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

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

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

Universal Protein Fluctuations in Populations of Microorganisms

(2012) Hanna Salman et al.   PHYSICAL REVIEW LETTERS

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

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

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

Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene

(2010) Chenghang Zong et al.   Molecular Systems Biology

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

Rapid Construction of Empirical RNA Fitness Landscapes

(2010) J. N. Pitt et al.   SCIENCE

Quantitative phenotyping via deep barcode sequencing

(2009) A. M. Smith et al.   GENOME RESEARCH

Analysis of a complete DNA-protein affinity landscape

(2009) W. Rowe et al.   Journal of the Royal Society Interface