Avian Genomes Revisited: Hidden Genes Uncovered and the Rates versus Traits Paradox in Birds

Genome sequence of a diabetes-prone rodent reveals a mutation hotspot around the ParaHox gene cluster

(2017) Adam D. Hargreaves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

(2016) Joana Damas et al.   GENOME RESEARCH

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

(2016) Emeric Figuet et al.   MOLECULAR BIOLOGY AND EVOLUTION

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

(2016) Wesley C. Warren et al.   G3-Genes Genomes Genetics

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

Stable recombination hotspots in birds

(2015) S. Singhal et al.   SCIENCE

SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads

(2014) Y. Xie et al.   BIOINFORMATICS

Finding the missing honey bee genes: lessons learned from a genome upgrade

(2014) Christine G Elsik et al.   BMC GENOMICS

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

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

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

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

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

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

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

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

(2012) Jonathan Romiguier et al.   PLoS One

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

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

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

(2011) Vincent Ranwez et al.   PLoS One

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

(2010) J. Romiguier 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

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

Evolutionary stasis: the stable chromosomes of birds

(2010) Hans Ellegren   TRENDS IN ECOLOGY & EVOLUTION

Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis

(2010) Rami A. Dalloul et al.   PLOS BIOLOGY

Hotspots of Biased Nucleotide Substitutions in Human Genes

(2009) Jonas Berglund et al.   PLOS BIOLOGY

Accelerated Evolution of the Prdm9 Speciation Gene across Diverse Metazoan Taxa

(2009) Peter L. Oliver et al.   PLoS Genetics

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

(2008) Nicolas Galtier et al.   TRENDS IN GENETICS