Temporal genomic evolution of bird sex chromosomes

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

(2014) Y. Xie et al.   BIOINFORMATICS

Origins and functional evolution of Y chromosomes across mammals

(2014) Diego Cortez et al.   NATURE

Complex evolutionary trajectories of sex chromosomes across bird taxa

(2014) Q. Zhou et al.   SCIENCE

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

Expansion of the Pseudo-autosomal Region and Ongoing Recombination Suppression in the Silene latifolia Sex Chromosomes

(2013) R. Bergero et al.   GENETICS

Progressive Recombination Suppression and Differentiation in Recently Evolved Neo-sex Chromosomes

(2013) Heini M. Natri et al.   MOLECULAR BIOLOGY AND EVOLUTION

Lack of Dosage Compensation Accompanies the Arrested Stage of Sex Chromosome Evolution in Ostriches

(2013) Sofia Adolfsson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination in the threespine stickleback genome-patterns and consequences

(2013) Marius Roesti et al.   MOLECULAR ECOLOGY

Sex-biased gene expression at homomorphic sex chromosomes in emus and its implication for sex chromosome evolution

(2013) B. Vicoso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The faster-X effect: integrating theory and data

(2013) Richard P. Meisel et al.   TRENDS IN GENETICS

Comparative Sex Chromosome Genomics in Snakes: Differentiation, Evolutionary Strata, and Lack of Global Dosage Compensation

(2013) Beatriz Vicoso et al.   PLOS BIOLOGY

RNA sequencing reveals sexually dimorphic gene expression before gonadal differentiation in chicken and allows comprehensive annotation of the W-chromosome

(2013) Katie L Ayers et al.   GENOME BIOLOGY

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

(2012) Pablo Cingolani et al.   FLY

Trade-off Between Selection for Dosage Compensation and Masculinization on the Avian Z Chromosome

(2012) Alison E. Wright et al.   GENETICS

Rate of Amino Acid Substitution Is Influenced by the Degree and Conservation of Male-Biased Transcription Over 50 Myr of Drosophila Evolution

(2012) Sonja Grath et al.   Genome Biology and Evolution

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Extensive X-linked adaptive evolution in central chimpanzees

(2012) C. Hvilsom et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila

(2012) Q. Zhou et al.   SCIENCE

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

Error-Prone ZW Pairing and No Evidence for Meiotic Sex Chromosome Inactivation in the Chicken Germ Line

(2012) Silvana Guioli et al.   PLoS Genetics

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Buffering and the evolution of chromosome-wide gene regulation

(2011) Per Stenberg et al.   CHROMOSOMA

Mutation Bias is the Driving Force of Codon Usage in the Gallus gallus genome

(2011) Y. Rao et al.   DNA RESEARCH

DO VARIATIONS IN SUBSTITUTION RATES AND MALE MUTATION BIAS CORRELATE WITH LIFE-HISTORY TRAITS? A STUDY OF 32 MAMMALIAN GENOMES

(2011) Melissa A. Wilson Sayres et al.   EVOLUTION

LINEAGE-SPECIFIC VARIATION IN SLOW- AND FAST-X EVOLUTION IN PRIMATES

(2011) Ke Xu et al.   EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Sex-chromosome evolution: recent progress and the influence of male and female heterogamety

(2011) Hans Ellegren   NATURE REVIEWS GENETICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Dosage Compensation and Demasculinization of X Chromosomes in Drosophila

(2010) Doris Bachtrog et al.   CURRENT BIOLOGY

Synteny Conservation of Chicken Macrochromosomes 1–10 in Different Avian Lineages Revealed by Cross-Species Chromosome Painting

(2010) I. Nanda et al.   CYTOGENETIC AND GENOME RESEARCH

Sex bias and dosage compensation in the zebra finch versus chicken genomes: General and specialized patterns among birds

(2010) Y. Itoh et al.   GENOME RESEARCH

Patterns of Codon Usage Bias in Silene latifolia

(2010) S. Qiu et al.   MOLECULAR BIOLOGY AND EVOLUTION

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition

(2010) Daniel W. Bellott et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

EFFECTIVE POPULATION SIZE AND THE FASTER-X EFFECT: AN EXTENDED MODEL

(2009) Beatriz Vicoso et al.   EVOLUTION

EFFECTIVE POPULATION SIZE AND THE FASTER-X EFFECT: EMPIRICAL RESULTS AND THEIR INTERPRETATION

(2009) Judith E. Mank et al.   EVOLUTION

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

The Deficit of Male-Biased Genes on the D. melanogaster X Chromosome Is Expression-Dependent: A Consequence of Dosage Compensation?

(2009) Beatriz Vicoso et al.   JOURNAL OF MOLECULAR EVOLUTION

Faster-Z Evolution Is Predominantly Due to Genetic Drift

(2009) J. E. Mank et al.   MOLECULAR BIOLOGY AND EVOLUTION

The avian Z-linked gene DMRT1 is required for male sex determination in the chicken

(2009) Craig A. Smith et al.   NATURE

Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees

(2009) K. Liu et al.   SCIENCE

Female Meiotic Sex Chromosome Inactivation in Chicken

(2009) Sam Schoenmakers et al.   PLoS Genetics

Characterization of chromosome structures of Falconinae (Falconidae, Falconiformes, Aves) by chromosome painting and delineation of chromosome rearrangements during their differentiation

(2008) Chizuko Nishida et al.   CHROMOSOME RESEARCH

Ecological factors affect the level and scaling of avian BMR

(2008) Brian Keith McNab   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Synteny conservation of the Z chromosome in 14 avian species (11 families) supports a role for Z dosage in avian sex determination

(2008) I. Nanda et al.   CYTOGENETIC AND GENOME RESEARCH

The Chicken (Gallus gallus) Z Chromosome Contains at Least Three Nonlinear Evolutionary Strata

(2008) K. Nam et al.   GENETICS

Natural selection in avian protein-coding genes expressed in brain

(2008) ERIK AXELSSON et al.   MOLECULAR ECOLOGY

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes

(2008) Lukasz Potrzebowski et al.   PLOS BIOLOGY