Disentangling the Causes for Faster-X Evolution in Aphids

Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid

(2017) Gautier Richard et al.   Epigenetics & Chromatin

De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms

(2016) Claude Rispe et al.   BMC GENOMICS

Misassembly detection using paired-end sequence reads and optical mapping data

(2015) Martin D. Muggli et al.   BIOINFORMATICS

The effects of sex-biased gene expression and X-linkage on rates of adaptive protein sequence evolution in Drosophila

(2015) V. Avila et al.   Biology Letters

Gene expression, chromosome heterogeneity and the fast-X effect in mammals

(2015) L.-P. Nguyen et al.   Biology Letters

Evaluation of variant detection software for pooled next-generation sequence data

(2015) Howard W. Huang et al.   BMC BIOINFORMATICS

Variation in the X:Autosome Distribution of Male-Biased Genes amongDrosophila melanogasterTissues and Its Relationship with Dosage Compensation

(2015) Ann Kathrin Huylmans et al.   Genome Biology and Evolution

The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression

(2015) Arka Pal et al.   Genome Biology and Evolution

Genetic characterisation of new host-specialised biotypes and novel associations with bacterial symbionts in the pea aphid complex

(2015) Jean Peccoud et al.   Insect Conservation and Diversity

DrosophilaX-Linked Genes Have Lower Translation Rates than Autosomal Genes

(2015) Zhenguo Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Determinants of the rate of protein sequence evolution

(2015) Jianzhi Zhang et al.   NATURE REVIEWS GENETICS

Sequencing the Mouse Y Chromosome Reveals Convergent Gene Acquisition and Amplification on Both Sex Chromosomes

(2014) Y.Q. Shirleen Soh et al.   CELL

Faster-X Effects in Two Drosophila Lineages

(2014) Victoria Ávila et al.   Genome Biology and Evolution

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

(2014) A Gouin et al.   HEREDITY

Accelerated Evolution of Morph-Biased Genes in Pea Aphids

(2014) Swapna R. Purandare et al.   MOLECULAR BIOLOGY AND EVOLUTION

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

Genetic Control of Contagious Asexuality in the Pea Aphid

(2014) Julie Jaquiéry et al.   PLoS Genetics

Faster-X Adaptive Protein Evolution in House Mice

(2013) Athanasios Kousathanas et al.   GENETICS

Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping

(2013) Mathieu Gautier et al.   MOLECULAR ECOLOGY

The evolutionary causes and consequences of sex-biased gene expression

(2013) John Parsch et al.   NATURE REVIEWS GENETICS

The faster-X effect: integrating theory and data

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

Widespread Selection Across Coding and Noncoding DNA in the Pea Aphid Genome

(2013) Ryan D. Bickel et al.   G3-Genes Genomes Genetics

Masculinization of the X Chromosome in the Pea Aphid

(2013) Julie Jaquiéry et al.   PLoS Genetics

The genetics of sex chromosomes: evolution and implications for hybrid incompatibility

(2012) Norman A. Johnson et al.   Annals of the New York Academy of Sciences

Genomic Variation in Natural Populations of Drosophila melanogaster

(2012) C. H. Langley et al.   GENETICS

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

(2012) J. Jaquiéry et al.   MOLECULAR ECOLOGY

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

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

Accelerated Evolution of Sex Chromosomes in Aphids, an X0 System

(2011) J. Jaquiery et al.   MOLECULAR BIOLOGY AND EVOLUTION

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

Facultative Symbiont Infections Affect Aphid Reproduction

(2011) Jean-Christophe Simon et al.   PLoS One

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Are all sex chromosomes created equal?

(2011) Doris Bachtrog et al.   TRENDS IN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Estimation of the Neutrality Index

(2010) N. Stoletzki et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

FrameDP: sensitive peptide detection on noisy matured sequences

(2009) J. Gouzy et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Host races of the pea aphid Acyrthosiphon pisum differ in male wing phenotypes

(2009) A. Frantz et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

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

Faster-Z Evolution Is Predominantly Due to Genetic Drift

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

A role for a neo-sex chromosome in stickleback speciation

(2009) Jun Kitano et al.   NATURE

A continuum of genetic divergence from sympatric host races to species in the pea aphid complex

(2009) J. Peccoud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts

(2009) J. Peccoud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic conflict and sex chromosome evolution

(2009) Colin D. Meiklejohn et al.   TRENDS IN ECOLOGY & EVOLUTION

CAIcal: A combined set of tools to assess codon usage adaptation

(2008) Pere Puigbò et al.   Biology Direct

Testing for Neutrality in Samples With Sequencing Errors

(2008) G. Achaz   GENETICS

Effects of X-Linkage and Sex-Biased Gene Expression on the Rate of Adaptive Protein Evolution in Drosophila

(2008) J. F. Baines et al.   MOLECULAR BIOLOGY AND EVOLUTION

Host range expansion of an introduced insect pest through multiple colonizations of specialized clones

(2008) J. PECCOUD et al.   MOLECULAR ECOLOGY

Rarity of Males in Pea Aphids Results in Mutational Decay

(2008) J. A. Brisson et al.   SCIENCE