Contrasting gene expression programs correspond with predator-induced phenotypic plasticity within and across generations in Daphnia

Local adaptation in transgenerational responses to predators

(2016) Matthew R. Walsh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Evolution of Transgenerational Integration of Information in Heterogeneous Environments

(2015) Olof Leimar et al.   AMERICAN NATURALIST

When to rely on maternal effects and when on phenotypic plasticity?

(2015) Bram Kuijper et al.   EVOLUTION

Transcriptional profiling of predator-induced phenotypic plasticity in Daphnia pulex

(2015) Andrey Rozenberg et al.   Frontiers in Zoology

Differential transcriptomic responses of ancient and modernDaphniagenotypes to phosphorus supply

(2015) Priyanka Roy Chowdhury et al.   MOLECULAR ECOLOGY

Interclonal proteomic responses to predator exposure inDaphnia magnamay depend on predator composition of habitats

(2015) Kathrin A. Otte et al.   MOLECULAR ECOLOGY

Epigenetic Basis of Morphological Variation and Phenotypic Plasticity inArabidopsis thaliana

(2015) Rik Kooke et al.   PLANT CELL

The Up-Regulation of Ribosomal Proteins Further Regulates Protein Expression Profile in Female Schistosoma japonicum after Pairing

(2015) Jun Sun et al.   PLoS One

When is incomplete epigenetic resetting in germ cells favoured by natural selection?

(2015) Tobias Uller et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Ribosomal proteins: functions beyond the ribosome

(2015) Xiang Zhou et al.   Journal of Molecular Cell Biology

EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

(2015) Drew R. Schield et al.   Methods in Ecology and Evolution

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Predator-induced phenotypic plasticity within- and across-generations: a challenge for theory?

(2014) M. R. Walsh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Evolution of Multivariate Maternal Effects

(2014) Bram Kuijper et al.   PLoS Computational Biology

Expression changes of ribosomal proteins in phosphate- and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition

(2013) Jinyan Wang et al.   BMC GENOMICS

NATURAL VARIATION IN EPIGENETIC GENE REGULATION AND ITS EFFECTS ON PLANT DEVELOPMENTAL TRAITS

(2013) Franziska Turck et al.   EVOLUTION

HOW STABLE ‘SHOULD’ EPIGENETIC MODIFICATIONS BE? INSIGHTS FROM ADAPTIVE PLASTICITY AND BET HEDGING

(2013) Jacob J. Herman et al.   EVOLUTION

The fitness costs of adaptation via phenotypic plasticity and maternal effects

(2013) Thomas H. G. Ezard et al.   FUNCTIONAL ECOLOGY

The benefits of maternal effects in novel and in stable environments

(2012) R. B. Hoyle et al.   Journal of the Royal Society Interface

Epigenetic variation creates potential for evolution of plant phenotypic plasticity

(2012) Yuan-Ye Zhang et al.   NEW PHYTOLOGIST

Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

(2012) B. E. Miner et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Unified Approach to the Evolutionary Consequences of Genetic and Nongenetic Inheritance

(2011) Troy Day et al.   AMERICAN NATURALIST

B2G-FAR, a species-centered GO annotation repository

(2011) Stefan Götz et al.   BIOINFORMATICS

Thermal legacies: transgenerational effects of temperature on growth in a vertebrate

(2011) Santiago Salinas et al.   ECOLOGY LETTERS

Epigenetics and its implications for ecotoxicology

(2011) Michiel B. Vandegehuchte et al.   ECOTOXICOLOGY

The implications of nongenetic inheritance for evolution in changing environments

(2011) Russell Bonduriansky et al.   Evolutionary Applications

The impact of intraspecific variation in a fish predator on the evolution of phenotypic plasticity and investment in sex in Daphnia ambigua

(2011) M. R. WALSH et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Three epigenetic information channels and their different roles in evolution

(2011) N. SHEA et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Jack of all nectars, master of most: DNA methylation and the epigenetic basis of niche width in a flower-living yeast

(2011) C. M. HERRERA et al.   MOLECULAR ECOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Interpopulation variation in a fish predator drives evolutionary divergence in prey in lakes

(2011) M. R. Walsh et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Ensembl BioMarts: a hub for data retrieval across taxonomic space

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

Ecological genomics: steps towards unraveling the genetic basis of inducible defenses in Daphnia

(2010) Ralph Tollrian et al.   BMC BIOLOGY

Gene up-regulation in response to predator kairomones in the water flea, Daphnia pulex

(2010) Hitoshi Miyakawa et al.   BMC DEVELOPMENTAL BIOLOGY

Paternally Induced Transgenerational Environmental Reprogramming of Metabolic Gene Expression in Mammals

(2010) Benjamin R. Carone et al.   CELL

Gene transcription profiles, global DNA methylation and potential transgenerational epigenetic effects related to Zn exposure history in Daphnia magna

(2010) Michiel B. Vandegehuchte et al.   ENVIRONMENTAL POLLUTION

SYNTHESIS: The role of adaptive trans-generational plasticity in biological invasions of plants

(2010) Andrew R. Dyer et al.   Evolutionary Applications

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis

(2010) Carlos M. Herrera et al.   NEW PHYTOLOGIST

Environmental context determines within- and potential between-generation consequences of herbivory

(2010) Susan M. Lin et al.   OECOLOGIA

How to balance the offspring quality-quantity tradeoff when environmental cues are unreliable

(2010) Barbara Fischer et al.   OIKOS

Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins

(2010) Alex Boyko et al.   PLoS One

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Contrasting patterns of transgenerational plasticity in ecologically distinct congeners

(2009) Sonia E. Sultan et al.   ECOLOGY

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

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

Plasticity to canopy shade in a monocarpic herb: within- and between-generation effects

(2009) Laura F. Galloway et al.   NEW PHYTOLOGIST

Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution

(2009) Eva Jablonka et al.   QUARTERLY REVIEW OF BIOLOGY

TRANSGENERATIONAL PLASTICITY IN THE SEA: CONTEXT-DEPENDENT MATERNAL EFFECTS ACROSS THE LIFE HISTORY

(2008) Dustin J. Marshall   ECOLOGY

INTRASPECIFIC VARIATION IN A PREDATOR AFFECTS COMMUNITY STRUCTURE AND CASCADING TROPHIC INTERACTIONS

(2008) David M. Post et al.   ECOLOGY

Adaptive Phenotypic Plasticity in Response to Climate Change in a Wild Bird Population

(2008) A. Charmantier et al.   SCIENCE

Developmental plasticity and the evolution of parental effects

(2008) T ULLER   TRENDS IN ECOLOGY & EVOLUTION