The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors

Life-history trade-offs and limitations associated with phenotypic adaptation under future ocean warming and elevated salinity

(2019) Michael D. Jarrold et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Understanding interactions between plasticity, adaptation and range shifts in response to marine environmental change

(2019) Jennifer M. Donelson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Patterns of alternative splicing in response to cold acclimation in fish

(2019) Timothy M. Healy et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex

(2019) Clément Rougeux et al.   MOLECULAR ECOLOGY

Similarities in temperature-dependent gene expression plasticity across timescales in threespine stickleback (Gasterosteus aculeatus )

(2018) David C. H. Metzger et al.   MOLECULAR ECOLOGY

R(NA)-tistic expression: The art of matching unknown mRNA and proteins to environmental response in ecological genomics

(2018) Brenna C. M. Stanford et al.   MOLECULAR ECOLOGY

Maladaptive phenotypic plasticity in cardiac muscle growth is suppressed in high‐altitude deer mice

(2018) Jonathan P. Velotta et al.   EVOLUTION

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial genotype and phenotypic plasticity of gene expression in response to cold acclimation in killifish

(2017) Timothy M. Healy et al.   MOLECULAR ECOLOGY

Gene expression plasticity in response to salinity acclimation in threespine stickleback ecotypes from different salinity habitats

(2017) Taylor C. Gibbons et al.   MOLECULAR ECOLOGY

Early transcriptional response pathways in Daphnia magna are coordinated in networks of crustacean-specific genes

(2017) Luisa Orsini et al.   MOLECULAR ECOLOGY

Detecting gene subnetworks under selection in biological pathways

(2017) Alexandre Gouy et al.   NUCLEIC ACIDS RESEARCH

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Transcriptomic Analysis of Thermally Stressed Symbiodinium Reveals Differential Expression of Stress and Metabolism Genes

(2017) Sarah L. Gierz et al.   Frontiers in Plant Science

Responses to simulated winter conditions differ between threespine stickleback ecotypes

(2016) Taylor C. Gibbons et al.   MOLECULAR ECOLOGY

The power and promise of RNA-seq in ecology and evolution

(2016) Erica V. Todd et al.   MOLECULAR ECOLOGY

Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

(2016) Stefan Dennenmoser et al.   MOLECULAR ECOLOGY

How plasticity, genetic assimilation and cryptic genetic variation may contribute to adaptive radiations

(2016) Ralf F. Schneider et al.   MOLECULAR ECOLOGY

Convergent local adaptation to climate in distantly related conifers

(2016) S. Yeaman et al.   SCIENCE

A single generation of domestication heritably alters the expression of hundreds of genes

(2016) Mark R. Christie et al.   Nature Communications

Overcoming maladaptive plasticity through plastic compensation

(2016) Matthew R.J. Morris et al.   Current Zoology

Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress

(2015) Noah H. Rose et al.   Genome Biology and Evolution

The effects of temperature on aerobic metabolism: towards a mechanistic understanding of the responses of ectotherms to a changing environment

(2015) P. M. Schulte   JOURNAL OF EXPERIMENTAL BIOLOGY

Molecular mechanism of PPARα action and its impact on lipid metabolism, inflammation and fibrosis in non-alcoholic fatty liver disease

(2015) Michal Pawlak et al.   JOURNAL OF HEPATOLOGY

Reproductive workers show queenlike gene expression in an intermediately eusocial insect, the buff-tailed bumble beeBombus terrestris

(2015) Mark C. Harrison et al.   MOLECULAR ECOLOGY

The role of transcriptome resilience in resistance of corals to bleaching

(2015) Francois O. Seneca et al.   MOLECULAR ECOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

The BioMart community portal: an innovative alternative to large, centralized data repositories

(2015) Damian Smedley et al.   NUCLEIC ACIDS RESEARCH

The utility of protein and mRNA correlation

(2015) Samuel H. Payne   TRENDS IN BIOCHEMICAL SCIENCES

Zebrafish as a Model to Study the Role of Peroxisome Proliferating-Activated Receptors in Adipogenesis and Obesity

(2015) Marjo J. Den Broeder et al.   PPAR Research

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice

(2014) Meritxell Rosell et al.   AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM

Skeletal muscle plasticity induced by seasonal acclimatization involves IGF1 signaling: Implications in ribosomal biogenesis and protein synthesis

(2014) Eduardo N. Fuentes et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

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

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

Towards a gene regulatory network perspective on phenotypic plasticity, genetic accommodation and genetic assimilation

(2014) David W. Pfennig et al.   MOLECULAR ECOLOGY

Analyzing Cold Tolerance Mechanism in Transgenic Zebrafish (Danio rerio)

(2014) Qian Wang et al.   PLoS One

Temperature-dependent differential transcriptomes during formation of an epigenetic memory in Norway spruce embryogenesis

(2014) Igor A. Yakovlev et al.   Tree Genetics & Genomes

Structures of mitochondrial oxidative phosphorylation supercomplexes and mechanisms for their stabilisation

(2013) Yuriy Chaban et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

Transcriptomic characterization of cold acclimation in larval zebrafish

(2013) Yong Long et al.   BMC GENOMICS

Environmental metabolomics: an emerging approach to study organism responses to environmental stressors

(2013) Brian P. Lankadurai et al.   ENVIRONMENTAL REVIEWS

Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

(2013) Marie Filteau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements

(2012) Lucy W. Barrett et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

GENETIC SIGNATURE OF ADAPTIVE PEAK SHIFT IN THREESPINE STICKLEBACK

(2012) Sean M. Rogers et al.   EVOLUTION

The genomic basis of adaptive evolution in threespine sticklebacks

(2012) Felicity C. Jones et al.   NATURE

Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

(2012) Christine Vogel et al.   NATURE REVIEWS GENETICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish

(2012) G. R. Scott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

What is needed for next-generation ecological and evolutionary genomics?

(2012) Scott A. Pavey et al.   TRENDS IN ECOLOGY & EVOLUTION

Thermal tolerance and the global redistribution of animals

(2012) Jennifer M. Sunday et al.   Nature Climate Change

Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges

(2012) Purvesh Khatri et al.   PLoS Computational Biology

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

(2011) P. Gaudet et al.   BRIEFINGS IN BIOINFORMATICS

The molecular basis of aerobic metabolic remodeling differs between oxidative muscle and liver of threespine sticklebacks in response to cold acclimation

(2010) J. I. Orczewska et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

The role of gene expression in ecological speciation

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

Mitochondrial biogenesis in cold-bodied fishes

(2010) K. M. O'Brien   JOURNAL OF EXPERIMENTAL BIOLOGY

The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'

(2010) G. N. Somero   JOURNAL OF EXPERIMENTAL BIOLOGY

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

Rapid evolution of cold tolerance in stickleback

(2010) R. D. H. Barrett et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

From ‘differential expression’ to ‘differential networking’ – identification of dysfunctional regulatory networks in diseases

(2010) Alberto de la Fuente   TRENDS IN GENETICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

A flexible whole-genome microarray for transcriptomics in three-spine stickleback (Gasterosteus aculeatus)

(2009) Erica H Leder et al.   BMC GENOMICS

ADAPTIVE DIVERGENCE BETWEEN FRESHWATER AND MARINE STICKLEBACKS: INSIGHTS INTO THE ROLE OF PHENOTYPIC PLASTICITY FROM AN INTEGRATED ANALYSIS OF CANDIDATE GENE EXPRESSION

(2009) R. J. Scott McCairns et al.   EVOLUTION

Stress and fish reproduction: The roles of allostasis and hormesis

(2009) Carl B. Schreck   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Protein synthesis is lowered while 20S proteasome activity is maintained following acclimation to low temperature in juvenile spotted wolffish (Anarhichas minor Olafsen)

(2009) S. G. Lamarre et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Genomic reaction norms: using integrative biology to understand molecular mechanisms of phenotypic plasticity

(2009) NADIA AUBIN-HORTH et al.   MOLECULAR ECOLOGY

Linking genotypes to phenotypes and fitness: how mechanistic biology can inform molecular ecology

(2009) ANNE C. DALZIEL et al.   MOLECULAR ECOLOGY

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

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

(2009) Y. F. Chan et al.   SCIENCE

The transcriptomics of life-history trade-offs in whitefish species pairs (Coregonussp.)

(2008) J. ST-CYR et al.   MOLECULAR ECOLOGY