Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks

Lake-Stream Divergence in Stickleback Life History: A Plastic Response to Trophic Niche Differentiation?

(2015) Dario Moser et al.   Evolutionary Biology

Transcription in space - environmental vs. genetic effects on differential immune gene expression

(2015) Tobias L. Lenz   MOLECULAR ECOLOGY

Among-lake reciprocal transplants induce convergent expression of immune genes in threespine stickleback

(2015) William E. Stutz et al.   MOLECULAR ECOLOGY

Genomics of Divergence along a Continuum of Parapatric Population Differentiation

(2015) Philine G. D. Feulner et al.   PLoS Genetics

Divergent Macroparasite Infections in Parapatric Swiss Lake-Stream Pairs of Threespine Stickleback (Gasterosteus aculeatus)

(2015) Anssi Karvonen et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

SPECIES-SPECIFIC DIFFERENCES IN ADAPTIVE PHENOTYPIC PLASTICITY IN AN ECOLOGICALLY RELEVANT TROPHIC TRAIT: HYPERTROPHIC LIPS IN MIDAS CICHLID FISHES

(2014) Gonzalo Machado-Schiaffino et al.   EVOLUTION

NLRC3, a Member of the NLR Family of Proteins, Is a Negative Regulator of Innate Immune Signaling Induced by the DNA Sensor STING

(2014) Lu Zhang et al.   IMMUNITY

Contemporary ecotypic divergence during a recent range expansion was facilitated by adaptive introgression

(2014) K. Lucek et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

The Evolution and Adaptive Potential of Transcriptional Variation in Sticklebacks—Signatures of Selection and Widespread Heritability

(2014) Erica H. Leder et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene expression plasticity evolves in response to colonization of freshwater lakes in threespine stickleback

(2014) Matthew R. J. Morris et al.   MOLECULAR ECOLOGY

Major Histocompatibility Complex class IIb polymorphism influences gut microbiota composition and diversity

(2014) Daniel I. Bolnick et al.   MOLECULAR ECOLOGY

Specific Gene Expression Responses to Parasite Genotypes Reveal Redundancy of Innate Immunity in Vertebrates

(2014) David Haase et al.   PLoS One

Extensive Copy-Number Variation of Young Genes across Stickleback Populations

(2014) Frédéric J. J. Chain et al.   PLoS Genetics

PARALLEL EVOLUTION OF LOCAL ADAPTATION AND REPRODUCTIVE ISOLATION IN THE FACE OF GENE FLOW

(2013) Roger K. Butlin et al.   EVOLUTION

Gene expression drives local adaptation in humans

(2013) H. B. Fraser   GENOME RESEARCH

Impacts of Variation in the Human Genome on Gene Regulation

(2013) Rajini R. Haraksingh et al.   JOURNAL OF MOLECULAR BIOLOGY

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

Ecological genomics of local adaptation

(2013) Outi Savolainen et al.   NATURE REVIEWS GENETICS

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Convergent Evolution within an Adaptive Radiation of Cichlid Fishes

(2012) Moritz Muschick et al.   CURRENT BIOLOGY

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

(2012) Christophe Eizaguirre et al.   ECOLOGY LETTERS

Genome-wide Association Study of Periodontal Pathogen Colonization

(2012) K. Divaris et al.   JOURNAL OF DENTAL RESEARCH

Comparative genomics in ecological physiology: toward a more nuanced understanding of acclimation and adaptation

(2012) A. Whitehead   JOURNAL OF EXPERIMENTAL BIOLOGY

Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua

(2012) Tereza Manousaki et al.   MOLECULAR ECOLOGY

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

(2012) Tobias L. Lenz et al.   MOLECULAR ECOLOGY

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

(2012) MARIUS ROESTI et al.   MOLECULAR ECOLOGY

The ecological and genetic basis of convergent thick-lipped phenotypes in cichlid fishes

(2012) Marco Colombo et al.   MOLECULAR ECOLOGY

The innate immune sensor NLRC3 attenuates Toll-like receptor signaling via modification of the signaling adaptor TRAF6 and transcription factor NF-κB

(2012) Monika Schneider et al.   NATURE IMMUNOLOGY

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

(2012) Christophe Eizaguirre et al.   Nature Communications

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

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Are fish immune systems really affected by parasites? an immunoecological study of common carp (Cyprinus carpio)

(2011) Karolína Rohlenová et al.   Parasites & Vectors

Transcriptomic resilience to global warming in the seagrass Zostera marina, a marine foundation species

(2011) S. U. Franssen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions

(2011) B. E. Deagle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Developmental Role of Agouti in Color Pattern Evolution

(2011) M. Manceau et al.   SCIENCE

The evolution of gene expression and the transcriptome–phenotype relationship

(2011) Peter W. Harrison et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Adaptation in the age of ecological genomics: insights from parallelism and convergence

(2011) Kathryn R. Elmer et al.   TRENDS IN ECOLOGY & EVOLUTION

Ecological transcriptomics of lake-type and riverine sockeye salmon (Oncorhynchus nerka)

(2011) Scott A Pavey et al.   BMC ECOLOGY

The role of gene expression in ecological speciation

(2010) Scott A. Pavey et al.   Annals of the New York Academy of Sciences

Variable Tandem Repeats Accelerate Evolution of Coding and Regulatory Sequences

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

The Genetics of Human Adaptation: Hard Sweeps, Soft Sweeps, and Polygenic Adaptation

(2010) Jonathan K. Pritchard et al.   CURRENT BIOLOGY

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

Constraints on speciation suggested by comparing lake-stream stickleback divergence across two continents

(2010) DANIEL BERNER et al.   MOLECULAR ECOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

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

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

Identification of LRRc17 as a Negative Regulator of Receptor Activator of NF-κB Ligand (RANKL)-induced Osteoclast Differentiation

(2009) Taesoo Kim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genetics of human gene expression: mapping DNA variants that influence gene expression

(2009) Vivian G. Cheung et al.   NATURE REVIEWS GENETICS

Stepwise Modification of a Modular Enhancer Underlies Adaptation in a Drosophila Population

(2009) M. Rebeiz et al.   SCIENCE

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Speciation accelerated and stabilized by pleiotropic major histocompatibility complex immunogenes

(2008) Christophe Eizaguirre et al.   ECOLOGY LETTERS

Natural selection drives patterns of lake-stream divergence in stickleback foraging morphology

(2008) D. BERNER et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Transcriptomic variation and plasticity in rufous-collared sparrows (Zonotrichia capensis) along an altitudinal gradient

(2008) ZACHARY A. CHEVIRON et al.   MOLECULAR ECOLOGY

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

Revealing the architecture of gene regulation: the promise of eQTL studies

(2008) Yoav Gilad et al.   TRENDS IN GENETICS

Adaptation from standing genetic variation

(2007) R BARRETT et al.   TRENDS IN ECOLOGY & EVOLUTION