A genetic mechanism for sexual dichromatism in birds

Genetic Basis of De Novo Appearance of Carotenoid Ornamentation in Bare Parts of Canaries

(2020) Małgorzata Anna Gazda et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

(2019) Pedro Andrade et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput sequencing is revealing genetic associations with avian plumage color

(2019) Erik R Funk et al.   AUK

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Carotenoid metabolism strengthens the link between feather coloration and individual quality

(2018) Ryan J. Weaver et al.   Nature Communications

What maintains signal honesty in animal colour displays used in mate choice?

(2017) Ryan J. Weaver et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

High-density lipoprotein receptor SCARB1 is required for carotenoid coloration in birds

(2017) Matthew B. Toomey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plumage Genes and Little Else Distinguish the Genomes of Hybridizing Warblers

(2016) David P.L. Toews et al.   CURRENT BIOLOGY

Substrate Specificity of Purified Recombinant Chicken β-Carotene 9′,10′-Oxygenase (BCO2)

(2016) Carlo dela Seña et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The effects of life history and sexual selection on male and female plumage colouration

(2015) James Dale et al.   NATURE

A cost-effective RNA sequencing protocol for large-scale gene expression studies

(2015) Zhonggang Hou et al.   Scientific Reports

Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds

(2015) Carolina Frankl-Vilches et al.   GENOME BIOLOGY

Rcorrector: efficient and accurate error correction for Illumina RNA-seq reads

(2015) Li Song et al.   GigaScience

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes involved in avian photoreceptor diversification

(2014) Jennifer M. Enright et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci

(2014) Simon H. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Different modes of evolution in males and females generate dichromatism in fairy-wrens (Maluridae)

(2013) Allison E. Johnson et al.   Ecology and Evolution

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Carotenoid-based signals in behavioural ecology: a review

(2011) Svensson et al.   BEHAVIOUR

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The phylogenetic relationships and generic limits of finches (Fringillidae)

(2011) Dario Zuccon et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A mitochondrial enzyme degrades carotenoids and protects against oxidative stress

(2010) Jaume Amengual et al.   FASEB JOURNAL

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

(2010) A. McKenna et al.   GENOME RESEARCH

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genetic and molecular insights into the development and evolution of sexual dimorphism

(2009) Thomas M. Williams et al.   NATURE REVIEWS GENETICS

The liver but not the skin is the site for conversion of a red carotenoid in a passerine bird

(2009) Esther del Val et al.   NATURWISSENSCHAFTEN

Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken

(2008) Jonas Eriksson et al.   PLoS Genetics