Natural selection and the genetic basis of osmoregulation in heteromyid rodents as revealed by RNA-seq

A comparison of methods for differential expression analysis of RNA-seq data

(2013) Charlotte Soneson et al.   BMC BIOINFORMATICS

The ABCs of membrane transporters in health and disease (SLC series): Introduction

(2013) Matthias A. Hediger et al.   MOLECULAR ASPECTS OF MEDICINE

A priori and a posteriori approaches for finding genes of evolutionary interest in non-model species: Osmoregulatory genes in the kidney transcriptome of the desert rodent Dipodomys spectabilis (banner-tailed kangaroo rat)

(2012) Nicholas J. Marra et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

(2011) Soo Hyung Eo et al.   GENE

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Detecting signatures of positive selection in partial sequences generated on a large scale: pitfalls, procedures and resources

(2011) MARINE S. O. BRIEUC et al.   Molecular Ecology Resources

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

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

(2010) R Ekblom et al.   HEREDITY

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): the relative merits of normalization and rarefaction in gene discovery

(2009) Matthew C Hale et al.   BMC GENOMICS

From evolutionary genetics to human immunology: how selection shapes host defence genes

(2009) Luis B. Barreiro et al.   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Sequencing breakthroughs for genomic ecology and evolutionary biology

(2007) MATTHEW E. HUDSON   Molecular Ecology Resources