Plastic and Evolved Responses to Global Change: What Can We Learn from Comparative Transcriptomics?: Table 1.

Transcriptomic response to heat stress among ecologically divergent populations of redband trout

(2015) Shawn R Narum et al.   BMC GENOMICS

Low evolutionary potential for egg-to-adult viability inDrosophila melanogasterat high temperatures

(2015) Torsten N. Kristensen et al.   EVOLUTION

Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus

(2015) R. S. Brennan et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Rapid acclimation of juvenile corals to CO2-mediated acidification by upregulation of heat shock protein and Bcl-2 genes

(2015) A. Moya et al.   MOLECULAR ECOLOGY

Transcriptome sequencing reveals both neutral and adaptive genome dynamics in a marine invader

(2015) C. K. Tepolt et al.   MOLECULAR ECOLOGY

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

RNA-seq reveals regional differences in transcriptome response to heat stress in the marine snailChlorostoma funebralis

(2015) Lani U. Gleason et al.   MOLECULAR ECOLOGY

SNP genotyping and population genomics from expressed sequences - current advances and future possibilities

(2015) Pierre De Wit et al.   MOLECULAR ECOLOGY

The role of transcriptome resilience in resistance of corals to bleaching

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

Building coral reef resilience through assisted evolution

(2015) Madeleine J. H. van Oppen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution

(2015) Rori V. Rohlfs et al.   SYSTEMATIC BIOLOGY

Polyribosomal RNA-Seq Reveals the Decreased Complexity and Diversity of the Arabidopsis Translatome

(2015) Xingtan Zhang et al.   PLoS One

Transcriptomic responses to heat stress and nickel in the mussel Mytilus galloprovincialis

(2014) Banni Mohamed et al.   AQUATIC TOXICOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Climate Change: Many Ways to Beat the Heat for Reef Corals

(2014) Andrew C. Baker   CURRENT BIOLOGY

TraitCapture: genomic and environment modelling of plant phenomic data

(2014) Tim B Brown et al.   CURRENT OPINION IN PLANT BIOLOGY

Using genomics to characterize evolutionary potential for conservation of wild populations

(2014) Katherine A. Harrisson et al.   Evolutionary Applications

Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms

(2014) D. Berger et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genome-wide transcriptomic responses of the seagrasses Zostera marina and Nanozostera noltii under a simulated heatwave confirm functional types

(2014) Susanne U. Franssen et al.   Marine Genomics

Spatial analysis of gene regulation reveals new insights into the molecular basis of upper thermal limits

(2014) Marina Telonis-Scott et al.   MOLECULAR ECOLOGY

Reverse genetics in the tide pool: knock-down of target gene expression via RNA interference in the copepodTigriopus californicus

(2014) Felipe S. Barreto et al.   Molecular Ecology Resources

Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

The rise of regulatory RNA

(2014) Kevin V. Morris et al.   NATURE REVIEWS GENETICS

Inferring Regulatory Networks by Combining Perturbation Screens and Steady State Gene Expression Profiles

(2014) Ali Shojaie et al.   PLoS One

Thermal Stress Triggers Broad Pocillopora damicornis Transcriptomic Remodeling, while Vibrio coralliilyticus Infection Induces a More Targeted Immuno-Suppression Response

(2014) Jeremie Vidal-Dupiol et al.   PLoS One

Genomic and Genotoxic Responses to Controlled Weathered-Oil Exposures Confirm and Extend Field Studies on Impacts of the Deepwater Horizon Oil Spill on Native Killifish

(2014) Whitney Pilcher et al.   PLoS One

Gene expression changes in the coccolithophore Emiliania huxleyi after 500 generations of selection to ocean acidification

(2014) K. T. Lohbeck et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Assisted Gene Flow to Facilitate Local Adaptation to Climate Change

(2013) Sally N. Aitken et al.   Annual Review of Ecology Evolution and Systematics

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

(2013) Camila Granados-Cifuentes et al.   BMC GENOMICS

The complex transcriptional landscape of the anucleate human platelet

(2013) Paul F Bray et al.   BMC GENOMICS

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Transcriptomics in the RNA-seq era

(2013) Paul A McGettigan   CURRENT OPINION IN CHEMICAL BIOLOGY

Multitissue Molecular, Genomic, and Developmental Effects of the Deepwater Horizon Oil Spill on Resident Gulf Killifish (Fundulus grandis)

(2013) Benjamin Dubansky et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Genetic Variation for Life History Sensitivity to Seasonal Warming in Arabidopsis thaliana

(2013) Y. Li et al.   GENETICS

Natural variation and the capacity to adapt to ocean acidification in the keystone sea urchinStrongylocentrotus purpuratus

(2013) Morgan W. Kelly et al.   GLOBAL CHANGE BIOLOGY

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

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

Annotated genes and nonannotated genomes: cross-species use of Gene Ontology in ecology and evolution research

(2013) C. R. Primmer et al.   MOLECULAR ECOLOGY

Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides ) from different thermal environments

(2013) C. D. Kenkel et al.   MOLECULAR ECOLOGY

Common functional targets of adaptive micro- and macro-evolutionary divergence in killifish

(2013) Andrew Whitehead et al.   MOLECULAR ECOLOGY

Accuracy of allele frequency estimation using pooled RNA-Seq

(2013) M. Konczal et al.   Molecular Ecology Resources

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

Transcriptomics of salinity tolerance capacity in Arctic charr (Salvelinus alpinus): a comparison of gene expression profiles between divergent QTL genotypes

(2013) Joseph D. Norman et al.   PHYSIOLOGICAL GENOMICS

Analysis of Genome-Wide Changes in the Translatome of Arabidopsis Seedlings Subjected to Heat Stress

(2013) Emilio Yángüez et al.   PLoS One

Space can substitute for time in predicting climate-change effects on biodiversity

(2013) Jessica L. Blois et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture

(2013) C. N. Topp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic basis for coral resilience to climate change

(2013) Daniel J. Barshis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temperature and CO2 additively regulate physiology, morphology and genomic responses of larval sea urchins, Strongylocentrotus purpuratus

(2013) J. L. Padilla-Gamino et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Primate Transcript and Protein Expression Levels Evolve Under Compensatory Selection Pressures

(2013) Z. Khan et al.   SCIENCE

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data

(2013) Franck Rapaport et al.   GENOME BIOLOGY

Investigating the molecular basis of local adaptation to thermal stress: population differences in gene expression across the transcriptome of the copepod Tigriopus californicus

(2012) Sean D Schoville et al.   BMC EVOLUTIONARY BIOLOGY

How do genetic correlations affect species range shifts in a changing environment?

(2012) Anne Duputié et al.   ECOLOGY LETTERS

The evolution of salinity tolerance inDaphnia: a functional genomics approach

(2012) Leigh C. Latta et al.   ECOLOGY LETTERS

The functional genomics of an eco-evolutionary feedback loop: linking gene expression, trait evolution, and community dynamics

(2012) Lutz Becks et al.   ECOLOGY LETTERS

GENETIC CONSTRAINTS ON ADAPTATION TO A CHANGING ENVIRONMENT

(2012) Luis-Miguel Chevin   EVOLUTION

DIFFERENCES IN THE REGULATION OF GROWTH AND BIOMINERALIZATION GENES REVEALED THROUGH LONG-TERM COMMON-GARDEN ACCLIMATION AND EXPERIMENTAL GENOMICS IN THE PURPLE SEA URCHIN

(2012) Melissa H. Pespeni et al.   EVOLUTION

Adaptation and the physiology of ocean acidification

(2012) Morgan W. Kelly et al.   FUNCTIONAL ECOLOGY

Long-term and trans-life-cycle effects of exposure to ocean acidification in the green sea urchin Strongylocentrotus droebachiensis

(2012) S. Dupont et al.   MARINE BIOLOGY

The transcriptomic response to thermal stress is immediate, transient and potentiated by ultraviolet radiation in the sea anemoneAnemonia viridis

(2012) A. MOYA et al.   MOLECULAR ECOLOGY

Mapping phenotypic, expression and transmission ratio distortion QTL using RAD markers in the Lake Whitefish(Coregonus clupeaformis)

(2012) Pierre-Alexandre Gagnaire et al.   MOLECULAR ECOLOGY

Transcriptome-wide polymorphisms of red abalone (Haliotis rufescens) reveal patterns of gene flow and local adaptation

(2012) Pierre De Wit et al.   MOLECULAR ECOLOGY

Genetics of gene expression responses to temperature stress in a sea urchin gene network

(2012) DANIEL E. RUNCIE et al.   MOLECULAR ECOLOGY

Proteomics in evolutionary ecology: linking the genotype with the phenotype

(2012) ANGEL P. DIZ et al.   MOLECULAR ECOLOGY

Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change

(2012) T. G. Evans et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genome-Wide Analyses of Changes in Translation State Caused by Elevated Temperature in Oryza sativa

(2012) Kiyotaka Ueda et al.   PLANT AND CELL PHYSIOLOGY

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

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

Phenotypic Plasticity of the Drosophila Transcriptome

(2012) Shanshan Zhou et al.   PLoS Genetics

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Venom gland transcriptomes of two elapid snakes (Bungarus multicinctus and Naja atra) and evolution of toxin genes

(2011) Yu Jiang et al.   BMC GENOMICS

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution

(2011) R. DHAR et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Global change ecotoxicology: Identification of early life history bottlenecks in marine invertebrates, variable species responses and variable experimental approaches

(2011) M. Byrne   MARINE ENVIRONMENTAL RESEARCH

The transcriptomic responses of the eastern oyster, Crassostrea virginica, to environmental conditions

(2011) ROBERT W. CHAPMAN et al.   MOLECULAR ECOLOGY

Climate change and evolutionary adaptation

(2011) Ary A. Hoffmann et al.   NATURE

From expression QTLs to personalized transcriptomics

(2011) Stephen B. Montgomery et al.   NATURE REVIEWS GENETICS

Comparison of salt stress resistance genes in transgenic Arabidopsis thaliana indicates that extent of transcriptomic change may not predict secondary phenotypic or fitness effects

(2011) Zhulong Chan et al.   PLANT BIOTECHNOLOGY JOURNAL

Quantifying Rates of Evolutionary Adaptation in Response to Ocean Acidification

(2011) Jennifer M. Sunday et al.   PLoS One

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

The evolution of gene expression and the transcriptome–phenotype relationship

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

Phenomics – technologies to relieve the phenotyping bottleneck

(2011) Robert T. Furbank et al.   TRENDS IN PLANT SCIENCE

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Statistical Design and Analysis of RNA Sequencing Data

(2010) P. L. Auer et al.   GENETICS

Functional Genomics of Physiological Plasticity and Local Adaptation in Killifish

(2010) A. Whitehead et al.   JOURNAL OF HEREDITY

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

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

Phenotypic plasticity and population viability: the importance of environmental predictability

(2010) T. E. Reed et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TRIM5 Suppresses Cross-Species Transmission of a Primate Immunodeficiency Virus and Selects for Emergence of Resistant Variants in the New Species

(2010) Andrea Kirmaier et al.   PLOS BIOLOGY

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

(2009) Jacob F. Degner et al.   BIOINFORMATICS

Evolutionary rescue can prevent extinction following environmental change

(2009) Graham Bell et al.   ECOLOGY LETTERS

Thermotolerance and gene expression following heat stress in the whitefly Bemisia tabaci B and Q biotypes

(2009) Assaf Mahadav et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Variation in gene expression ofAndropogon gerardiiin response to altered environmental conditions associated with climate change

(2009) Steven E. Travers et al.   JOURNAL OF ECOLOGY

Ocean acidification alters skeletogenesis and gene expression in larval sea urchins

(2009) MJ O’Donnell et al.   MARINE ECOLOGY PROGRESS SERIES

Betulin Is a Potent Anti-Tumor Agent that Is Enhanced by Cholesterol

(2009) Franziska B. Mullauer et al.   PLoS One

Stress-Dependent Coordination of Transcriptome and Translatome in Yeast

(2009) Regula E Halbeisen et al.   PLOS BIOLOGY

Ocean Acidification: The Other CO2Problem

(2008) Scott C. Doney et al.   Annual Review of Marine Science

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Predicted impact of ocean acidification on a marine invertebrate: elevated CO2 alters response to thermal stress in sea urchin larvae

(2008) Michael J. O’Donnell et al.   MARINE BIOLOGY

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

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Evidence for Upwelling of Corrosive "Acidified" Water onto the Continental Shelf

(2008) R. A. Feely et al.   SCIENCE

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

(2008) Yoav Gilad et al.   TRENDS IN GENETICS