Experimental Evolution of Gene Expression and Plasticity in Alternative Selective Regimes

Does Genetic Variation Maintained by Environmental Heterogeneity Facilitate Adaptation to Novel Selection?

(2016) Yuheng Huang et al.   AMERICAN NATURALIST

Quantitative genetic variance in experimental fly populations evolving with or without environmental heterogeneity

(2015) Yuheng Huang et al.   EVOLUTION

Differences in performance and transcriptome-wide gene expression associated withRhagoletis(Diptera: Tephritidae) larvae feeding in alternate host fruit environments

(2015) Gregory J. Ragland et al.   MOLECULAR ECOLOGY

Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations ofFundulus heteroclitus

(2015) David I. Dayan et al.   MOLECULAR ECOLOGY

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature

(2015) Cameron K. Ghalambor et al.   NATURE

Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster

(2015) Jun Chen et al.   PLoS Genetics

Genetic Architecture of Ethanol-Responsive Transcriptome Variation in Saccharomyces cerevisiae Strains

(2014) Jeffrey A. Lewis et al.   GENETICS

Genome-Wide Patterns of Genetic Variation within and among Alternative Selective Regimes

(2014) Yuheng Huang et al.   PLoS Genetics

The Effects of Selective History and Environmental Heterogeneity on Inbreeding Depression in Experimental Populations of Drosophila melanogaster

(2013) Tristan A. F. Long et al.   AMERICAN NATURALIST

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

(2013) Simon Anders et al.   Nature Protocols

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

The genetics of phenotypic plasticity. XII. Temporal and spatial heterogeneity

(2013) Samuel M. Scheiner   Ecology and Evolution

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Evolution of gene expression and expression plasticity in long-term experimental populations ofDrosophila melanogastermaintained under constant and variable ethanol stress

(2012) LEV Y. YAMPOLSKY et al.   MOLECULAR ECOLOGY

Genomic Variation and Its Impact on Gene Expression in Drosophila melanogaster

(2012) Andreas Massouras et al.   PLoS Genetics

PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)

(2011) R. Kofler et al.   BIOINFORMATICS

Whole-Genome Expression Plasticity across Tropical and Temperate Drosophila melanogaster Populations from Eastern Australia

(2010) M. T. Levine et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Covariance between Genetic and Environmental Influences across Ecological Gradients

(2009) David O. Conover et al.   Annals of the New York Academy of Sciences

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

Adaptive differences in gene expression associated with heavy metal tolerance in the soil arthropodOrchesella cincta

(2009) DICK ROELOFS et al.   MOLECULAR ECOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Evolving gene expression: from G to E to G×E

(2009) Andrea Hodgins-Davis et al.   TRENDS IN ECOLOGY & EVOLUTION

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

The environmental contribution to gene expression profiles

(2008) Greg Gibson   NATURE REVIEWS GENETICS

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Gene–Environment Interaction in Yeast Gene Expression

(2008) Erin N Smith et al.   PLOS BIOLOGY