Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences

(2015) Krystyna Nadachowska-Brzyska et al.   CURRENT BIOLOGY

Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associatedcis-Motifs

(2015) XianMing Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill–Robertson Interference, in an Avian System

(2015) Paulina Bolívar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Q&A: Karl Grammer

(2015) Kristin Lynn Sainani   NATURE

Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

(2014) Emeric Figuet et al.   Genome Biology and Evolution

Highly Variable Recombinational Landscape Modulates Efficacy of Natural Selection in Birds

(2014) Toni I. Gossmann et al.   Genome Biology and Evolution

Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals

(2014) E. Figuet et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

(2014) Takeshi Kawakami et al.   MOLECULAR ECOLOGY

Comparative population genomics in animals uncovers the determinants of genetic diversity

(2014) J. Romiguier et al.   NATURE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy

(2014) Saskia Hiltemann et al.   GigaScience

New approaches for unravelling reassortment pathways

(2013) Victoria Svinti et al.   BMC EVOLUTIONARY BIOLOGY

Population Size Dependence of Fitness Effect Distribution and Substitution Rate Probed by Biophysical Model of Protein Thermostability

(2013) Richard A. Goldstein   Genome Biology and Evolution

Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

(2013) Benoit Nabholz et al.   Genome Biology and Evolution

Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species

(2012) J. J. Wiens et al.   Biology Letters

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Weak Selection and Protein Evolution

(2012) H. Akashi et al.   GENETICS

The Population Genomics of a Fast Evolver: High Levels of Diversity, Functional Constraint, and Molecular Adaptation in the Tunicate Ciona intestinalis

(2012) Georgia Tsagkogeorga et al.   Genome Biology and Evolution

The determinants of the molecular substitution process in turtles

(2012) J. M. LourençO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Efficient Selection of Branch-Specific Models of Sequence Evolution

(2012) Julien Y. Dutheil et al.   MOLECULAR BIOLOGY AND EVOLUTION

Interaction between Selection and Biased Gene Conversion in Mammalian Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance Analysis

(2012) N. Lartillot   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles

(2012) Daniel G. Mulcahy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fast and Robust Characterization of Time-Heterogeneous Sequence Evolutionary Processes Using Substitution Mapping

(2012) Jonathan Romiguier et al.   PLoS One

JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL

(2011) Nicolas Lartillot et al.   EVOLUTION

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

(2011) G. H. Perry et al.   GENOME RESEARCH

Dynamic Evolution of Base Composition: Causes and Consequences in Avian Phylogenomics

(2011) B. Nabholz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Crocodilian phylogeny inferred from twelve mitochondrial protein-coding genes, with new complete mitochondrial genomic sequences for Crocodylus acutus and Crocodylus novaeguineae

(2011) Zhang Man et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Contrasting GC-content dynamics across 33 mammalian genomes: Relationship with life-history traits and chromosome sizes

(2010) J. Romiguier et al.   GENOME RESEARCH

The recombination landscape of the zebra finch Taeniopygia guttata genome

(2010) N. Backstrom et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

(2010) N. Lartillot 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

Mutation rate is linked to diversification in birds

(2010) R. Lanfear et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bats and birds: Exceptional longevity despite high metabolic rates

(2009) Jason Munshi-South et al.   AGEING RESEARCH REVIEWS

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A database of vertebrate longevity records and their relation to other life-history traits

(2009) J. P. DE MAGALHÃES et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

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

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates

(2008) Nicolas Galtier et al.   TRENDS IN GENETICS