High Levels of Gene Expression Explain the Strong Evolutionary Constraint of Mitochondrial Protein-Coding Genes

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Protein misinteraction avoidance causes highly expressed proteins to evolve slowly

(2012) J.-R. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reactome pathway analysis to enrich biological discovery in proteomics data sets

(2011) Robin Haw et al.   PROTEOMICS

The Neutral Theory of Molecular Evolution in the Genomic Era

(2010) Masatoshi Nei et al.   Annual Review of Genomics and Human Genetics

Expression Level, Evolutionary Rate, and the Cost of Expression

(2010) J. L. Cherry   Genome Biology and Evolution

Chaperonin-Dependent Accelerated Substitution Rates in Prokaryotes

(2010) David Bogumil et al.   Genome Biology and Evolution

The Effect of Chaperonin Buffering on Protein Evolution

(2010) Tom A. Williams et al.   Genome Biology and Evolution

Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia

(2010) J D Gibson et al.   HEREDITY

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species

(2010) AXEL KÜNSTNER et al.   MOLECULAR ECOLOGY

Nucleotide divergence vs. gene expression differentiation: comparative transcriptome sequencing in natural isolates from the carrion crow and its hybrid zone with the hooded crow

(2010) JOCHEN B. W. WOLF et al.   MOLECULAR ECOLOGY

GroEL dependency affects codon usage—support for a critical role of misfolding in gene evolution

(2010) Tobias Warnecke et al.   Molecular Systems Biology

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

The Relationship among Gene Expression, the Evolution of Gene Dosage, and the Rate of Protein Evolution

(2010) Jean-François Gout et al.   PLoS Genetics

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

The rapid evolution of signal peptides is mainly caused by relaxed selection on non-synonymous and synonymous sites

(2009) Yu-Dong Li et al.   GENE

Nonlinear Dynamics of Nonsynonymous (dN) and Synonymous (dS) Substitution Rates Affects Inference of Selection

(2009) Jochen B. W. Wolf et al.   Genome Biology and Evolution

Comparative Genomics of Drosophila mtDNA: Novel Features of Conservation and Change Across Functional Domains and Lineages

(2009) Kristi L. Montooth et al.   JOURNAL OF MOLECULAR EVOLUTION

Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins

(2009) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolutionary consequences of erroneous protein synthesis

(2009) D. Allan Drummond et al.   NATURE REVIEWS GENETICS

Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing

(2009) Tatiana Teixeira Torres et al.   NUCLEIC ACIDS RESEARCH

The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages

(2009) Y. I. Wolf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Impact of Natural Selection on the Genome: Emerging Patterns in Drosophila and Arabidopsis

(2008) Stephen I. Wright et al.   Annual Review of Ecology Evolution and Systematics

Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution

(2008) D. Allan Drummond et al.   CELL

Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species

(2008) C Gissi et al.   HEREDITY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Transcriptional Paradigms in Mammalian Mitochondrial Biogenesis and Function

(2008) Richard C. Scarpulla   PHYSIOLOGICAL REVIEWS