Are Synonymous Sites in Primates and Rodents Functionally Constrained?

Translational Selection Frequently Overcomes Genetic Drift in Shaping Synonymous Codon Usage Patterns in Vertebrates

(2013) Aoife Doherty et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

DNA Replication Timing

(2013) N. Rhind et al.   Cold Spring Harbor Perspectives in Biology

Strong Purifying Selection at Synonymous Sites in D. melanogaster

(2013) David S. Lawrie et al.   PLoS Genetics

The evolution, impact and properties of exonic splice enhancers

(2013) Eva Cáceres et al.   GENOME BIOLOGY

Differential Relationship of DNA Replication Timing to Different Forms of Human Mutation and Variation

(2012) Amnon Koren et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human

(2012) Qiaoping Yuan et al.   BMC GENETICS

Selection on Synonymous Sites for Increased Accessibility around miRNA Binding Sites in Plants

(2012) Wanjun Gu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Purifying Selection in Mammalian Mitochondrial Protein-Coding Genes Is Highly Effective and Congruent with Evolution of Nuclear Genes

(2012) K. Y. Popadin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Adaptive Evolution and Effective Population Size in Wild House Mice

(2012) M. Phifer-Rixey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomic Evidence for Large, Long-Lived Ancestors to Placental Mammals

(2012) J. Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Inference of Site Frequency Spectra From High-Throughput Sequence Data: Quantification of Selection on Nonsynonymous and Synonymous Sites in Humans

(2011) Peter D. Keightley et al.   GENETICS

Inference of Mutation Parameters and Selective Constraint in Mammalian Coding Sequences by Approximate Bayesian Computation

(2011) P. D. Keightley et al.   GENETICS

Faster than Neutral Evolution of Constrained Sequences: The Complex Interplay of Mutational Biases and Weak Selection

(2011) David S. Lawrie et al.   Genome Biology and Evolution

Impact of replication timing on non-CpG and CpG substitution rates in mammalian genomes

(2010) C. L. Chen et al.   GENOME RESEARCH

Detecting Positive and Purifying Selection at Synonymous Sites in Yeast and Worm

(2010) T. Zhou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Detecting positive selection within genomes: the problem of biased gene conversion

(2010) A. Ratnakumar et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Timing of Replication Is a Determinant of Neutral Substitution Rates but Does Not Explain Slow Y Chromosome Evolution in Rodents

(2009) C. J. Pink et al.   MOLECULAR 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

Human mutation rate associated with DNA replication timing

(2009) John A Stamatoyannopoulos et al.   NATURE GENETICS

Effective population size and patterns of molecular evolution and variation

(2009) Brian Charlesworth   NATURE REVIEWS GENETICS

Hotspots of Biased Nucleotide Substitutions in Human Genes

(2009) Jonas Berglund et al.   PLOS BIOLOGY

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

(2008) D. Allan Drummond et al.   CELL

The Impact of Recombination on Nucleotide Substitutions in the Human Genome

(2008) Laurent Duret et al.   PLoS Genetics

Human-macaque comparisons illuminate variation in neutral substitution rates

(2008) Svitlana Tyekucheva et al.   GENOME BIOLOGY