Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals

Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection

(2019) Iakov I Davydov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Modelling structural constraints on protein evolution via side-chain conformational states

(2019) Umberto Perron et al.   MOLECULAR BIOLOGY AND EVOLUTION

Measuring intolerance to mutation in human genetics

(2019) Zachary L. Fuller et al.   NATURE GENETICS

Positive selection in dNTPase SAMHD1 throughout mammalian evolution

(2019) Christopher Monit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Datamonkey 2.0: A Modern Web Application for Characterizing Selective and Other Evolutionary Processes

(2018) Steven Weaver et al.   MOLECULAR BIOLOGY AND EVOLUTION

UniProt: the universal protein knowledgebase

(2018) The UniProt Consortium   NUCLEIC ACIDS RESEARCH

Human carboxylesterases: a comprehensive review

(2018) Dandan Wang et al.   Acta Pharmaceutica Sinica B

An optimized prediction framework to assess the functional impact of pharmacogenetic variants

(2018) Yitian Zhou et al.   PHARMACOGENOMICS JOURNAL

A map of constrained coding regions in the human genome

(2018) James M. Havrilla et al.   NATURE GENETICS

Ensembl 2019

(2018) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins

(2018) Jose M Dana et al.   NUCLEIC ACIDS RESEARCH

Positive diversifying selection is a pervasive adaptive force throughout the Drosophila radiation

(2017) Francesco Cicconardi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

PDBe: towards reusable data delivery infrastructure at protein data bank in Europe

(2017) Saqib Mir et al.   NUCLEIC ACIDS RESEARCH

High rate of adaptation of mammalian proteins that interact with Plasmodium and related parasites

(2017) Emily R. Ebel et al.   PLoS Genetics

Protein-structure-guided discovery of functional mutations across 19 cancer types

(2016) Beifang Niu et al.   NATURE GENETICS

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Multidimensional structure-function relationships in human β-cardiac myosin from population-scale genetic variation

(2016) Julian R. Homburger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ensembl comparative genomics resources

(2016) Javier Herrero et al.   Database-The Journal of Biological Databases and Curation

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes

(2016) Benjamin R. Jack et al.   PLOS BIOLOGY

Viruses are a dominant driver of protein adaptation in mammals

(2016) David Enard et al.   eLife

The aldo-keto reductases (AKRs): Overview

(2015) Trevor M. Penning   CHEMICO-BIOLOGICAL INTERACTIONS

Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response

(2015) Andrew E. Webb et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atomic structure of human γ-secretase

(2015) Xiao-chen Bai et al.   NATURE

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

(2015) Carlos L Araya et al.   NATURE GENETICS

Evolutionary insights into host–pathogen interactions from mammalian sequence data

(2015) Manuela Sironi et al.   NATURE REVIEWS GENETICS

The energy landscape of adenylate kinase during catalysis

(2015) S Jordan Kerns et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comprehensive assessment of cancer missense mutation clustering in protein structures

(2015) Atanas Kamburov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The energy landscape of adenylate kinase during catalysis

(2015) S Jordan Kerns et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

(2015) Martin L. Miller et al.   Cell Systems

Evolution in an Ancient Detoxification Pathway Is Coupled with a Transition to Herbivory in the Drosophilidae

(2014) Andrew D. Gloss et al.   MOLECULAR BIOLOGY AND EVOLUTION

Divergent Positive Selection in Rhodopsin from Lake and Riverine Cichlid Fishes

(2014) Ryan K. Schott et al.   MOLECULAR BIOLOGY AND EVOLUTION

Patterns of Positive Selection in Seven Ant Genomes

(2014) Julien Roux et al.   MOLECULAR BIOLOGY AND EVOLUTION

Crystal structure of the γ-secretase component nicastrin

(2014) Tian Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synonymous Constraint Elements Show a Tendency to Encode Intrinsically Disordered Protein Segments

(2014) Mauricio Macossay-Castillo et al.   PLoS Computational Biology

Structural and Functional Evolution of Positively Selected Sites in Pine GlutathioneS-Transferase Enzyme Family

(2013) Ting Lan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes

(2013) Nicholas Furnham et al.   NUCLEIC ACIDS RESEARCH

Dual Host-Virus Arms Races Shape an Essential Housekeeping Protein

(2013) Ann Demogines et al.   PLOS BIOLOGY

Looking for Darwin in Genomic Sequences—Validity and Success of Statistical Methods

(2012) Weiwei Zhai et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity

(2011) Fuyuan Jing et al.   BMC BIOCHEMISTRY

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

The Effects of Alignment Error and Alignment Filtering on the Sitewise Detection of Positive Selection

(2011) G. Jordan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Slow protein evolutionary rates are dictated by surface-core association

(2011) A. Toth-Petroczy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular evolution and the role of oxidative stress in the expansion and functional diversification of cytosolic glutathione transferases

(2010) Rute R da Fonseca et al.   BMC EVOLUTIONARY BIOLOGY

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

SERPINB3, apoptosis and autoimmunity

(2009) Laura Vidalino et al.   AUTOIMMUNITY REVIEWS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Estimates of Positive Darwinian Selection Are Inflated by Errors in Sequencing, Annotation, and Alignment

(2009) Adrian Schneider et al.   Genome Biology and Evolution

Distributions of Selectively Constrained Sites and Deleterious Mutation Rates in the Hominid and Murid Genomes

(2009) L. Eory et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution of Digestive RNASE1 Genes in Leaf-Eating Monkeys Revisited: New Insights from Ten Additional Colobines

(2009) Li Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

In defense of statistical methods for detecting positive selection

(2009) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recent progress in understanding the diversity of the human ov-serpin/clade B serpin family

(2008) K. Izuhara et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Aldo-Keto Reductase Superfamily and its Role in Drug Metabolism and Detoxification

(2008) Oleg A. Barski et al.   DRUG METABOLISM REVIEWS

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

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

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics

Understanding the molecular machinery of genetics through 3D structures

(2007) Roman A. Laskowski et al.   NATURE REVIEWS GENETICS