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

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

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

Protein Insertions and Deletions Enabled by Neutral Roaming in Sequence Space

(2013) Ágnes Tóth-Petróczy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

The genetic code constrains yet facilitates Darwinian evolution

(2013) Elad Firnberg et al.   NUCLEIC ACIDS 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

The Innate Growth Bistability and Fitness Landscapes of Antibiotic-Resistant Bacteria

(2013) J. B. Deris et al.   SCIENCE

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

(2013) D. B. Goodman et al.   SCIENCE

Positively Charged Residues Are the Major Determinants of Ribosomal Velocity

(2013) Catherine A. Charneski et al.   PLOS BIOLOGY

CBDB: The codon bias database

(2012) Adam Hilterbrand et al.   BMC BIOINFORMATICS

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

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

Protein Quality Control Acts on Folding Intermediates to Shape the Effects of Mutations on Organismal Fitness

(2012) Shimon Bershtein et al.   MOLECULAR CELL

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

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

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

Small changes in enzyme function can lead to surprisingly large fitness effects during adaptive evolution of antibiotic resistance

(2012) K. Walkiewicz 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

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality

(2011) Yves Dehouck et al.   BMC BIOINFORMATICS

A biophysical protein folding model accounts for most mutational fitness effects in viruses

(2011) C. S. Wylie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta

(2010) S. Chaudhury et al.   BIOINFORMATICS

On Relevance of Codon Usage to Expression of Synthetic and Natural Genes in Escherichia coli

(2010) F. Supek et al.   GENETICS

Distribution of Fitness Effects Caused by Single-Nucleotide Substitutions in Bacteriophage f1

(2010) J. B. Peris et al.   GENETICS

Evidence that the supE44 Mutation of Escherichia coli Is an Amber Suppressor Allele of glnX and that It Also Suppresses Ochre and Opal Nonsense Mutations

(2010) B. Singaravelan et al.   JOURNAL OF BACTERIOLOGY

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Mutational effects and the evolution of new protein functions

(2010) Misha Soskine et al.   NATURE REVIEWS GENETICS

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

Chaperonin overexpression promotes genetic variation and enzyme evolution

(2009) Nobuhiko Tokuriki et al.   NATURE

An externally tunable bacterial band-pass filter

(2009) T. Sohka et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry