Covariation Is a Poor Measure of Molecular Coevolution

Amino acid coevolution reveals three-dimensional structure and functional domains of insect odorant receptors

(2015) Thomas A. Hopf et al.   Nature Communications

Epistasis Constrains Mutational Pathways of Hemoglobin Adaptation in High-Altitude Pikas

(2014) Danielle M. Tufts et al.   MOLECULAR BIOLOGY AND EVOLUTION

Empirical fitness landscapes and the predictability of evolution

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

Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information

(2014) Sergey Ovchinnikov et al.   eLife

Prediction of contacts from correlated sequence substitutions

(2013) William R Taylor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era

(2013) H. Kamisetty et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

(2012) Sharon H. Ackerman et al.   PLoS One

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees

(2011) Fernando Izquierdo-Carrasco et al.   BMC BIOINFORMATICS

Hot Spots for Allosteric Regulation on Protein Surfaces

(2011) Kimberly A. Reynolds et al.   CELL

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein topology from predicted residue contacts

(2011) William R. Taylor et al.   PROTEIN SCIENCE

GUIDANCE: a web server for assessing alignment confidence scores

(2010) O. Penn et al.   NUCLEIC ACIDS RESEARCH

Validation of Coevolving Residue Algorithms via Pipeline Sensitivity Analysis: ELSC and OMES and ZNMI, Oh My!

(2010) Christopher A. Brown et al.   PLoS One

Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways

(2010) Emily J. Capra et al.   PLoS Genetics

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH