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

Comparative venomics of the Prairie Rattlesnake (Crotalus viridis viridis) from Colorado: Identification of a novel pattern of ontogenetic changes in venom composition and assessment of the immunoreactivity of the commercial antivenom CroFab®

(2015) Anthony J. Saviola et al.   Journal of Proteomics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Transcriptomic Analysis of Tail Regeneration in the Lizard Anolis carolinensis Reveals Activation of Conserved Vertebrate Developmental and Repair Mechanisms

(2014) Elizabeth D. Hutchins et al.   PLoS One

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

A Common Cellular Basis for Muscle Regeneration in Arthropods and Vertebrates

(2014) N. Konstantinides et al.   SCIENCE

Ecological Epigenetics: Beyond MS-AFLP

(2013) A. W. Schrey et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

(2013) B. Arnold et al.   MOLECULAR ECOLOGY

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Rainbow: an integrated tool for efficient clustering and assembling RAD-seq reads

(2012) Z. Chong et al.   BIOINFORMATICS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

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

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

(2012) Jordana T. Bell et al.   PLoS Genetics

DNA methylation: A source of random variation in natural populations

(2011) Rachel Massicotte et al.   Epigenetics

Genome-wide analysis identifies changes in histone retention and epigenetic modifications at developmental and imprinted gene loci in the sperm of infertile men

(2011) S. S. Hammoud et al.   HUMAN REPRODUCTION

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

The role of epigenetic processes in controlling flowering time in plants exposed to stress

(2011) M. W. Yaish et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

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

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

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

Direct and transgenerational impact on Daphnia magna of chemicals with a known effect on DNA methylation

(2009) Michiel B. Vandegehuchte et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Testosterone, growth and the evolution of sexual size dimorphism

(2009) R. M. COX et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

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

DNA methylation is widespread across social Hymenoptera

(2008) Marcus R. Kronforst et al.   CURRENT BIOLOGY

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

(2008) David M. Post et al.   ECOLOGY

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS