The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits

Local adaptation and spatiotemporal patterns of genetic diversity revealed by repeated sampling of Caenorhabditis elegans across the Hawaiian Islands

(2022) Timothy A. Crombie et al.   MOLECULAR ECOLOGY

Evaluating the power and limitations of genome-wide association studies in Caenorhabditis elegan s 

(2022) Samuel J Widmayer et al.   G3-Genes Genomes Genetics

The Dfam community resource of transposable element families, sequence models, and genome annotations

(2021) Jessica Storer et al.   Mobile DNA

Natural variation in fecundity is correlated with species-wide levels of divergence in Caenorhabditis elegans

(2021) Gaotian Zhang et al.   G3-Genes Genomes Genetics

Two novel loci underlie natural differences in Caenorhabditis elegans abamectin responses

(2021) Kathryn S. Evans et al.   PLoS Pathogens

Whole-organism eQTL mapping at cellular resolution with single-cell sequencing

(2021) Eyal Ben-David et al.   eLife

Balancing selection maintains hyper-divergent haplotypes in Caenorhabditis elegans

(2021) Daehan Lee et al.   Nature Ecology & Evolution

The genetics of gene expression in a Caenorhabditis elegans multiparental recombinant inbred line population

(2021) Basten L Snoek et al.   G3-Genes Genomes Genetics

Natural variation in Caenorhabditis elegans responses to the anthelmintic emodepside

(2021) Janneke Wit et al.   International Journal for Parasitology-Drugs and Drug Resistance

From QTL to gene: C. elegans facilitates discoveries of the genetic mechanisms underlying natural variation

(2021) Kathryn S. Evans et al.   TRENDS IN GENETICS

Newly identified parasitic nematode beta-tubulin alleles confer resistance to benzimidazoles

(2021) Clayton M. Dilks et al.   International Journal for Parasitology-Drugs and Drug Resistance

The Gene scb-1 Underlies Variation in Caenorhabditis elegans Chemotherapeutic Responses

(2020) Kathryn S. Evans et al.   G3-Genes Genomes Genetics

The GTEx Consortium atlas of genetic regulatory effects across human tissues

(2020)   SCIENCE

Natural variation in a glucuronosyltransferase modulates propionate sensitivity in a C. elegans propionic acidemia model

(2020) Huimin Na et al.   PLoS Genetics

Molecular and evolutionary processes generating variation in gene expression

(2020) Mark S. Hill et al.   NATURE REVIEWS GENETICS

Quantitative benzimidazole resistance and fitness effects of parasitic nematode beta-tubulin alleles

(2020) Clayton M. Dilks et al.   International Journal for Parasitology-Drugs and Drug Resistance

Natural variation in C. elegans arsenic toxicity is explained by differences in branched chain amino acid metabolism

(2019) Stefan Zdraljevic et al.   eLife

A Novel Gene Underlies Bleomycin-Response Variation in Caenorhabditis elegans

(2019) Shannon C. Brady et al.   GENETICS

Gephebase, a database of genotype–phenotype relationships for natural and domesticated variation in Eukaryotes

(2019) Virginie Courtier-Orgogozo et al.   NUCLEIC ACIDS RESEARCH

Selection and gene flow shape niche-associated variation in pheromone response

(2019) Daehan Lee et al.   Nature Ecology & Evolution

WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data

(2019) Amy D. Holdorf et al.   GENETICS

WormQTL2: an interactive platform for systems genetics in Caenorhabditis elegans

(2019) Basten L Snoek et al.   Database-The Journal of Biological Databases and Curation

Deep sampling of Hawaiian Caenorhabditis elegans reveals high genetic diversity and admixture with global populations

(2019) Tim A Crombie et al.   eLife

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Genetics of trans-regulatory variation in gene expression

(2018) Frank Wolfgang Albert et al.   eLife

Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles

(2018) Steffen R. Hahnel et al.   PLoS Pathogens

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds ofDrosophilaandCaenorhabditis elegansTranscription Factors

(2017) Michelle M. Kudron et al.   GENETICS

The Natural Biotic Environment ofCaenorhabditis elegans

(2017) Hinrich Schulenburg et al.   GENETICS

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

High-resolution mapping ofcis-regulatory variation in budding yeast

(2017) Ryosuke Kita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans

(2017) Mark G. Sterken et al.   G3-Genes Genomes Genetics

Widespread epistasis regulates glucose homeostasis and gene expression

(2017) Anlu Chen et al.   PLoS Genetics

Natural variation in a single amino acid substitution underlies physiological responses to topoisomerase II poisons

(2017) Stefan Zdraljevic et al.   PLoS Genetics

The ModERN Resource: Genome-Wide Binding Profiles for Hundreds ofDrosophilaandCaenorhabditis elegansTranscription Factors

(2017) Michelle M. Kudron et al.   GENETICS

The Natural Biotic Environment ofCaenorhabditis elegans

(2017) Hinrich Schulenburg et al.   GENETICS

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

(2016) Daniel E. Cook et al.   GENETICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

CeNDR, theCaenorhabditis elegansnatural diversity resource

(2016) Daniel E. Cook et al.   NUCLEIC ACIDS RESEARCH

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Genetic Regulation of Transcriptional Variation in Natural Arabidopsis thaliana Accessions

(2016) Yanjun Zan et al.   G3-Genes Genomes Genetics

The Genetic Basis of Natural Variation in Caenorhabditis elegans Telomere Length

(2016) Daniel E. Cook et al.   GENETICS

Genome-Assisted Prediction of Quantitative Traits Using the R Package sommer

(2016) Giovanny Covarrubias-Pazaran   PLoS One

Co-expression of the transcription factors CEH-14 and TTX-1 regulates AFD neuron-specific genes gcy-8 and gcy-18 in C. elegans

(2015) Hiroshi Kagoshima et al.   DEVELOPMENTAL BIOLOGY

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

The laboratory domestication of Caenorhabditis elegans

(2015) Mark G. Sterken et al.   TRENDS IN GENETICS

Why we need more ecology for genetic models such as C. elegans

(2015) Carola Petersen et al.   TRENDS IN GENETICS

C. elegans outside the Petri dish

(2015) Lise Frézal et al.   eLife

Remarkably Divergent Regions Punctuate the Genome Assembly of the Caenorhabditis elegans Hawaiian Strain CB4856

(2015) Owen A. Thompson et al.   GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

mediation:RPackage for Causal Mediation Analysis

(2015) Dustin Tingley et al.   Journal of Statistical Software

Regulatory analysis of the C. elegans genome with spatiotemporal resolution

(2014) Carlos L. Araya et al.   NATURE

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

A Variant in the Neuropeptide Receptor npr-1 is a Major Determinant of Caenorhabditis elegans Growth and Physiology

(2014) Erik C. Andersen et al.   PLoS Genetics

Finding the sources of missing heritability in a yeast cross

(2013) Joshua S. Bloom et al.   NATURE

The diversity outbred mouse population

(2012) Gary A. Churchill et al.   MAMMALIAN GENOME

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity

(2012) Erik C Andersen et al.   NATURE GENETICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Caenorhabditis elegans as a platform for molecular quantitative genetics and the systems biology of natural variation

(2011) BRYN E. GAERTNER et al.   Genetics Research

Controlling gene expression in response to stress

(2011) Eulàlia de Nadal et al.   NATURE REVIEWS GENETICS

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Global Genetic Robustness of the Alternative Splicing Machinery in Caenorhabditis elegans

(2010) Yang Li et al.   GENETICS

Genome-wide gene expression regulation as a function of genotype and age in C. elegans

(2010) A. Vinuela et al.   GENOME RESEARCH

Selection at Linked Sites Shapes Heritable Phenotypic Variation in C. elegans

(2010) M. V. Rockman et al.   SCIENCE

ETS-4 Is a Transcriptional Regulator of Life Span in Caenorhabditis elegans

(2010) Bargavi Thyagarajan et al.   PLoS Genetics

Recombinational Landscape and Population Genomics of Caenorhabditis elegans

(2009) Matthew V. Rockman et al.   PLoS Genetics

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS