Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution

Reference-assisted chromosome assembly

(2013) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing of the core MHC region of black grouse (Tetrao tetrix) and comparative genomics of the galliform MHC

(2012) Biao Wang et al.   BMC GENOMICS

Molecular evolutionary and population genomic analysis of the nine-spined stickleback using a modified restriction-site-associated DNA tag approach

(2012) Matthieu Bruneaux et al.   MOLECULAR ECOLOGY

Consistent divergence times and allele sharing measured from cross-species application of SNP chips developed for three domestic species

(2012) J. M. Miller et al.   Molecular Ecology Resources

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Identification of Genes Related to White and Black Plumage Formation by RNA-Seq from White and Black Feather Bulbs in Ducks

(2012) Shijun Li et al.   PLoS One

Increased divergence but reduced variation on the Z chromosome relative to autosomes inFicedulaflycatchers: differential introgression or the faster-Z effect?

(2012) Silje Hogner et al.   Ecology and Evolution

Transcriptome sequencing of black grouse (Tetrao tetrix) for immune gene discovery and microsatellite development

(2012) B. Wang et al.   Open Biology

A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education

(2012) Taras K Oleksyk et al.   GigaScience

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

A Genome Sequence Resource for the Aye-Aye (Daubentonia madagascariensis), a Nocturnal Lemur from Madagascar

(2011) George H. Perry et al.   Genome Biology and Evolution

Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

(2011) Louise Teixeira Cerdeira et al.   JOURNAL OF BACTERIOLOGY

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

The genome sequence of Atlantic cod reveals a unique immune system

(2011) Bastiaan Star et al.   NATURE

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil)

(2011) W. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

(2011) K. Schneeberger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Introduction into the analysis of high-throughput-sequencing based epigenome data

(2010) M. Huss   BRIEFINGS IN BIOINFORMATICS

Next generation sequencing in functional genomics

(2010) T. Werner   BRIEFINGS IN BIOINFORMATICS

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

An EST-based genome scan using 454 sequencing in the marine snail Littorina saxatilis

(2010) J. GALINDO et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The genome of a songbird

(2010) Wesley C. Warren et al.   NATURE

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

(2009) Dietmar Schwarz et al.   BMC GENOMICS

Comparison of the transcriptomes of American chestnut (Castanea dentata) and Chinese chestnut (Castanea mollissima) in response to the chestnut blight infection

(2009) Abdelali Barakat et al.   BMC PLANT BIOLOGY

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

(2009) Judith E. Mank et al.   EVOLUTION

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

Faster-Z Evolution Is Predominantly Due to Genetic Drift

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

New methods to identify conserved microsatellite loci and develop primer sets of high cross-species utility - as demonstrated for birds

(2009) DEBORAH A. DAWSON et al.   Molecular Ecology Resources

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

Assisted assembly: how to improve a de novo genome assembly by using related species

(2009) Sante Gnerre et al.   GENOME BIOLOGY

Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing

(2008) J. CRISTOBAL VERA et al.   MOLECULAR ECOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS