RAD sequencing reveals within-generation polygenic selection in response to anthropogenic organic and metal contamination in North Atlantic Eels

Pollutants and fish predator/prey behavior: A review of laboratory and field approaches

(2016) Judith S. Weis et al.   Current Zoology

RAD Sequencing Highlights Polygenic Discrimination of Habitat Ecotypes in the Panmictic American Eel

(2015) Scott A. Pavey et al.   CURRENT BIOLOGY

Transcriptional and physiological response of fathead minnows (Pimephales promelas) exposed to urban waters entering into wildlife protected areas

(2015) Ignacio A. Rodriguez-Jorquera et al.   ENVIRONMENTAL POLLUTION

Signatures of positive selection: from selective sweeps at individual loci to subtle allele frequency changes in polygenic adaptation

(2015) Wolfgang Stephan   MOLECULAR ECOLOGY

Integration of Random Forest with population-based outlier analyses provides insight on the genomic basis and evolution of run timing in Chinook salmon (Oncorhynchus tshawytscha)

(2015) Marine S. O. Brieuc et al.   MOLECULAR ECOLOGY

RAD genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species, the American lobster (Homarus americanus)

(2015) Laura Benestan et al.   MOLECULAR ECOLOGY

Fifteen years of genomewide scans for selection: trends, lessons and unaddressed genetic sources of complication

(2015) Ryan J. Haasl et al.   MOLECULAR ECOLOGY

RAD-QTL Mapping Reveals Both Genome-Level Parallelism and Different Genetic Architecture Underlying the Evolution of Body Shape in Lake Whitefish ( Coregonus clupeaformis ) Species Pairs

(2015) Martin Laporte et al.   G3-Genes Genomes Genetics

In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)

(2014) Caroline L Côté et al.   BMC GENOMICS

Genotyping by sequencing for genomic prediction in a soybean breeding population

(2014) Diego Jarquín et al.   BMC GENOMICS

Liver transcriptome analysis of Atlantic cod (Gadus morhua) exposed to PCB 153 indicates effects on cell cycle regulation and lipid metabolism

(2014) Fekadu Yadetie et al.   BMC GENOMICS

Letter to the Editor: On the term 'interaction' and related phrases in the literature on Random Forests

(2014) A.-L. Boulesteix et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptome profile analysis reveals specific signatures of pollutants in Atlantic eels

(2014) Lucie Baillon et al.   ECOTOXICOLOGY

Transcriptomic responses to emamectin benzoate in Pacific and Atlantic Canada salmon liceLepeophtheirus salmoniswith differing levels of drug resistance

(2014) Ben J. G. Sutherland et al.   Evolutionary Applications

Detecting genotypic changes associated with selective mortality at sea in Atlantic salmon: polygenic multilocus analysis surpasses genome scan

(2014) Vincent Bourret et al.   MOLECULAR ECOLOGY

Genomic footprints of speciation in Atlantic eels (Anguilla anguillaandA. rostrata)

(2014) Magnus W. Jacobsen et al.   MOLECULAR ECOLOGY

Evaluation of demographic history and neutral parameterization on the performance ofFSToutlier tests

(2014) Katie E. Lotterhos et al.   MOLECULAR ECOLOGY

How does exposure to nickel and cadmium affect the transcriptome of yellow perch (Perca flavescens) – Results from a 1000 candidate-gene microarray

(2013) Bérénice Bougas et al.   AQUATIC TOXICOLOGY

Detecting genome-wide gene transcription profiles associated with high pollution burden in the critically endangered European eel

(2013) J.M. Pujolar et al.   AQUATIC TOXICOLOGY

Assessment of Heavy Metal Contamination in Various Tissues of Six Ray Species from İskenderun Bay, Northeastern Mediterranean Sea

(2013) Mustafa Türkmen et al.   BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY

Detecting anthropogenic effects on a vulnerable species, the freshwater blenny (Salaria fluviatilis): The importance of considering key ecological variables

(2013) M. Laporte et al.   ECOLOGICAL INDICATORS

Evolutionary change driven by metal exposure as revealed by coding SNP genome scan in wild yellow perch (Perca flavescens)

(2013) Sébastien Bélanger-Deschênes et al.   ECOTOXICOLOGY

Contaminant driven genetic erosion and associated hypotheses on alleles loss, reduced population growth rate and increased susceptibility to future stressors: an essay

(2013) Rui Ribeiro et al.   ECOTOXICOLOGY

Effect of Low-Dose Cadmium Exposure on DNA Methylation in the Endangered European Eel

(2013) Fabien Pierron et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Testing for Associations between Loci and Environmental Gradients Using Latent Factor Mixed Models

(2013) Eric Frichot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Gene–environment interactions in heavy metal and pesticide carcinogenesis

(2013) Shams Tabrez et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Population genomics of rapid adaptation by soft selective sweeps

(2013) Philipp W. Messer et al.   TRENDS IN ECOLOGY & EVOLUTION

Predicting Adaptive Phenotypes From Multilocus Genotypes in Sitka Spruce ( Picea sitchensis ) Using Random Forest

(2013) Jason A. Holliday et al.   G3-Genes Genomes Genetics

PCB153-induced oxidative stress and cell apoptosis on cultured rat Sertoli cells

(2013) Ming Gao et al.   Toxicology Research

Surviving in a toxic world: transcriptomics and gene expression profiling in response to environmental pollution in the critically endangered European eel

(2012) Jose Pujolar et al.   BMC GENOMICS

Protective and antioxidant role of selenium on arsenic trioxide-induced oxidative stress and genotoxicity in the fish hepatoma cell line PLHC-1

(2012) Vellaisamy Selvaraj et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Random forests for genomic data analysis

(2012) Xi Chen et al.   GENOMICS

Correction for population stratification in random forest analysis

(2012) Yang Zhao et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Population genetics of the American eel (Anguilla rostrata):FST = 0 and North Atlantic Oscillation effects on demographic fluctuations of a panmictic species

(2012) Caroline L. Côté et al.   MOLECULAR ECOLOGY

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Overview of random forest methodology and practical guidance with emphasis on computational biology and bioinformatics

(2012) Anne-Laure Boulesteix et al.   Wiley Interdisciplinary Reviews-Data Mining and Knowledge Discovery

Applications for next-generation sequencing in fish ecotoxicogenomics

(2012) Alvine C. Mehinto et al.   Frontiers in Genetics

Postnatal exposure to PCB 153 and PCB 180, but not to PCB 52, produces changes in activity level and stimulus control in outbred male Wistar Kyoto rats

(2011) Espen Johansen et al.   Behavioral and Brain Functions

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Genome Wide Association Study to predict severe asthma exacerbations in children using random forests classifiers

(2011) Mousheng Xu et al.   BMC Medical Genetics

PBDE and PCB contamination of eels from the Gironde estuary: From glass eels to silver eels

(2011) Nathalie Tapie et al.   CHEMOSPHERE

Effects of chronic metal exposure on wild fish populations revealed by high-throughput cDNA sequencing

(2011) Fabien Pierron et al.   ECOTOXICOLOGY

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus)

(2011) Emma E. Lind et al.   ECOTOXICOLOGY

The effect of metal pollution on the population genetic structure of brown trout (Salmo trutta L.) residing in the River Hayle, Cornwall, UK

(2011) Christopher J. Durrant et al.   ENVIRONMENTAL POLLUTION

The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel ( Anguilla rostrata )

(2011) Pierre-Alexandre Gagnaire et al.   GENETICS

All roads lead to home: panmixia of European eel in the Sargasso Sea

(2011) THOMAS D. ALS et al.   MOLECULAR ECOLOGY

Random Forests for Genetic Association Studies

(2011) Benjamin A Goldstein et al.   Statistical Applications in Genetics and Molecular Biology

p,p′-Dichlorodiphenoxydichloroethylene induced apoptosis of Sertoli cells through oxidative stress-mediated p38 MAPK and mitochondrial pathway

(2011) Yang Song et al.   TOXICOLOGY LETTERS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

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

Genomic approaches with natural fish populations from polluted environments

(2010) Goran Bozinovic et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

The consequences of phenotypic plasticity for ecological speciation

(2010) X. THIBERT-PLANTE et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Phenotypic plasticity's impacts on diversification and speciation

(2010) David W. Pfennig et al.   TRENDS IN ECOLOGY & EVOLUTION

The effects of contaminants in European eel: a review

(2009) Caroline Geeraerts et al.   ECOTOXICOLOGY

Transcriptional responses to environmental metal exposure in wild yellow perch (Perca flavescens) collected in lakes with differing environmental metal concentrations (Cd, Cu, Ni)

(2009) Fabien Pierron et al.   ECOTOXICOLOGY

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

How Cadmium Could Compromise the Completion of the European Eel’s Reproductive Migration

(2008) Fabien Pierron et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A Genome-Scan Method to Identify Selected Loci Appropriate for Both Dominant and Codominant Markers: A Bayesian Perspective

(2008) M. Foll et al.   GENETICS

Spatial analysis method (sam): a software tool combining molecular and environmental data to identify candidate loci for selection

(2008) STÉPHANE JOOST et al.   Molecular Ecology Resources

Evolutionary ecotoxicology of wild yellow perch (Perca flavescens) populations chronically exposed to a polymetallic gradient

(2007) Vincent Bourret et al.   AQUATIC TOXICOLOGY

Evidence of population genetic effects of long-term exposure to contaminated sediments—A multi-endpoint study with copepods

(2007) Johanna Gardeström et al.   AQUATIC TOXICOLOGY

Evolutionary change in human-altered environments

(2007) THOMAS B. SMITH et al.   MOLECULAR ECOLOGY