Exploring local immunological adaptation of two stickleback ecotypes by experimental infection and transcriptome-wide digital gene expression analysis

A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data

(2012) Vanessa M. Kvam et al.   AMERICAN JOURNAL OF BOTANY

Divergent selection on locally adapted major histocompatibility complex immune genes experimentally proven in the field

(2012) Christophe Eizaguirre et al.   ECOLOGY LETTERS

Genome divergence during evolutionary diversification as revealed in replicate lake-stream stickleback population pairs

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach

(2012) Marvin Mundry et al.   PLoS One

Disease Tolerance as a Defense Strategy

(2012) R. Medzhitov et al.   SCIENCE

Rapid and adaptive evolution of MHC genes under parasite selection in experimental vertebrate populations

(2012) Christophe Eizaguirre et al.   Nature Communications

Genome-wide Transcriptional Profiling of Appressorium Development by the Rice Blast Fungus Magnaporthe oryzae

(2012) Darren M. Soanes et al.   PLoS Pathogens

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

PARALLEL AND NONPARALLEL ASPECTS OF ECOLOGICAL, PHENOTYPIC, AND GENETIC DIVERGENCE ACROSS REPLICATE POPULATION PAIRS OF LAKE AND STREAM STICKLEBACK

(2011) Renaud Kaeuffer et al.   EVOLUTION

Extent and scale of local adaptation in salmonid fishes: review and meta-analysis

(2011) D J Fraser et al.   HEREDITY

Digital gene expression analysis of gastrointestinal helminth resistance in Scottish blackface lambs

(2011) J. M. PEMBERTON et al.   MOLECULAR ECOLOGY

Ensembl BioMarts: a hub for data retrieval across taxonomic space

(2011) R. J. Kinsella et al.   Database-The Journal of Biological Databases and Curation

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Parasite diversity, patterns of MHC II variation and olfactory based mate choice in diverging three-spined stickleback ecotypes

(2010) Christophe Eizaguirre et al.   EVOLUTIONARY ECOLOGY

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

(2010) R Ekblom et al.   HEREDITY

Major histocompatibility complex polymorphism: dynamics and consequences of parasite-mediated local adaptation in fishes

(2010) C. Eizaguirre et al.   JOURNAL OF FISH BIOLOGY

The transcriptomics of sympatric dwarf and normal lake whitefish (Coregonus clupeaformis spp., Salmonidae) divergence as revealed by next-generation sequencing

(2010) JULIE JEUKENS et al.   MOLECULAR ECOLOGY

Next Generation Molecular Ecology

(2010) DIETHARD TAUTZ et al.   MOLECULAR ECOLOGY

Transcriptomic response of red grouse to gastro-intestinal nematode parasites and testosterone: implications for population dynamics

(2010) L. M. I. WEBSTER et al.   MOLECULAR ECOLOGY

A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush)

(2010) FREDERICK GOETZ et al.   MOLECULAR ECOLOGY

Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonusspp. Salmonidae)

(2010) SÉBASTIEN RENAUT et al.   MOLECULAR ECOLOGY

Rapid evolution and selection inferred from the transcriptomes of sympatric crater lake cichlid fishes

(2010) K. R. ELMER et al.   MOLECULAR ECOLOGY

On the origin of species: insights from the ecological genomics of lake whitefish

(2010) L. Bernatchez et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Apomictic and Sexual Ovules of Boechera Display Heterochronic Global Gene Expression Patterns

(2010) T. F. Sharbel et al.   PLANT CELL

Digital Gene Expression Signatures for Maize Development

(2010) A. L. Eveland et al.   PLANT PHYSIOLOGY

High-Throughput SuperSAGE for Digital Gene Expression Analysis of Multiple Samples Using Next Generation Sequencing

(2010) Hideo Matsumura et al.   PLoS One

The evolution of sex-specific immune defences

(2010) O. Restif et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

A Quantitative Survey of Local Adaptation and Fitness Trade‐Offs

(2009) Joe Hereford   AMERICAN NATURALIST

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

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

Divergence in gene regulation at young life history stages of whitefish (Coregonus sp.) and the emergence of genomic isolation

(2009) Arne W Nolte et al.   BMC EVOLUTIONARY BIOLOGY

VARIABLE PROGRESS TOWARD ECOLOGICAL SPECIATION IN PARAPATRY: STICKLEBACK ACROSS EIGHT LAKE-STREAM TRANSITIONS

(2009) Daniel Berner et al.   EVOLUTION

Pathogens as potential selective agents in the wild

(2009) MÉLANIE DIONNE   MOLECULAR ECOLOGY

MHC-based mate choice combines good genes and maintenance of MHC polymorphism

(2009) C. EIZAGUIRRE et al.   MOLECULAR ECOLOGY

Genetics and ecological speciation

(2009) D. Schluter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speciation accelerated and stabilized by pleiotropic major histocompatibility complex immunogenes

(2008) Christophe Eizaguirre et al.   ECOLOGY LETTERS

Sequencing goes 454 and takes large-scale genomics into the wild

(2008) HANS ELLEGREN   MOLECULAR ECOLOGY

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

(2008) Peter A. C. 't Hoen et al.   NUCLEIC ACIDS RESEARCH

Introduction. Ecological immunology

(2008) H. Schulenburg et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES