A house finch (Haemorhous mexicanus) spleen transcriptome reveals intra- and interspecific patterns of gene expression, alternative splicing and genetic diversity in passerines

Evidence from a House Finch (Haemorhous mexicanus) Spleen Transcriptome for Adaptive Evolution and Biased Gene Conversion in Passerine Birds

(2013) Niclas Backström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cis-regulatory sequence variation and association withMycoplasmaload in natural populations of the house finch (Carpodacus mexicanus)

(2013) Niclas Backström et al.   Ecology and Evolution

Parallel Patterns of Increased Virulence in a Recently Emerged Wildlife Pathogen

(2013) Dana M. Hawley et al.   PLOS BIOLOGY

De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system

(2012) Mark P Peterson et al.   BMC GENOMICS

Innate immunity and the evolution of resistance to an emerging infectious disease in a wild bird

(2012) CAMILLE BONNEAUD et al.   MOLECULAR ECOLOGY

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensivein silicoassessment of RNA-seq experiments

(2012) Nagarjun Vijay et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Contrasting Epidemic Histories Reveal Pathogen-Mediated Balancing Selection on Class II MHC Diversity in a Wild Songbird

(2012) Dana M. Hawley et al.   PLoS One

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

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

(2012) B. Wang et al.   Open Biology

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

(2011) Anna W Santure et al.   BMC GENOMICS

Independent Effects of Alternative Splicing and Structural Constraint on the Evolution of Mammalian Coding Exons

(2011) F.-C. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular Evolution of the Toll-Like Receptor Multigene Family in Birds

(2011) M. Alcaide et al.   MOLECULAR BIOLOGY AND EVOLUTION

ConDeTri - A Content Dependent Read Trimmer for Illumina Data

(2011) Linnéa Smeds et al.   PLoS One

Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird

(2011) C. Bonneaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

(2010) Rita Gemayel et al.   Annual Review of Genetics

Digital gene expression analysis of the zebra finch genome

(2010) Robert Ekblom et al.   BMC GENOMICS

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

(2010) R Ekblom et al.   HEREDITY

Individuals and populations: the role of long-term, individual-based studies of animals in ecology and evolutionary biology

(2010) Tim Clutton-Brock et al.   TRENDS IN ECOLOGY & EVOLUTION

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Genetic basis of fitness differences in natural populations

(2008) Hans Ellegren et al.   NATURE