Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead (Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment

Age at Release, Size, and Maturation Status Influence Residualism in Hatchery Steelhead

(2019) Christopher P. Tatara et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Long-Term Conservation of Ohnologs Through Partial Tetrasomy Following Whole-Genome Duplication in Salmonidae

(2019) Matthew A. Campbell et al.   G3-Genes Genomes Genetics

DNA methylation profiles correlated to striped bass sperm fertility

(2018) L. Curry Woods III et al.   BMC GENOMICS

The DNA Methylation Landscape of Stickleback Reveals Patterns of Sex Chromosome Evolution and Effects of Environmental Salinity

(2018) David C H Metzger et al.   Genome Biology and Evolution

Egg incubation temperature affects the timing of the Atlantic salmon Salmo salar homing migration

(2018) B. Jonsson et al.   JOURNAL OF FISH BIOLOGY

Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding

(2018) R. D. Houston et al.   ANIMAL GENETICS

The role of DNA methylation in epigenetics of aging

(2018) Archana Unnikrishnan et al.   PHARMACOLOGY & THERAPEUTICS

Characterization of Genetic and Epigenetic Variation in Sperm and Red Blood Cells from Adult Hatchery and Natural-Origin Steelhead, Oncorhynchus mykiss

(2018) Mackenzie R. Gavery et al.   G3-Genes Genomes Genetics

Transcriptional shifts during juvenile Coho salmon (Oncorhynchus kisutch) life stage changes in freshwater and early marine environments

(2018) Aimee Lee S. Houde et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Age and Method of Release Affect Migratory Performance of Hatchery Steelhead

(2017) Christopher P. Tatara et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon

(2017) Jérémy Le Luyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Persistent and plastic effects of temperature on DNA methylation across the genome of threespine stickleback ( Gasterosteus aculeatus )

(2017) David C. H. Metzger et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epigenetic considerations in aquaculture

(2017) Mackenzie R. Gavery et al.   PeerJ

Measuring Animal Age with DNA Methylation: From Humans to Wild Animals

(2017) Ricardo De Paoli-Iseppi et al.   Frontiers in Genetics

Maximizing ecological and evolutionary insight in bisulfite sequencing data sets

(2017) Amanda J. Lea et al.   Nature Ecology & Evolution

Genetic background and embryonic temperature affect DNA methylation and expression of myogenin and muscle development in Atlantic salmon (Salmo salar)

(2017) Erik Burgerhout et al.   PLoS One

Factors associated with aberrant imprint methylation and oligozoospermia

(2017) Norio Kobayashi et al.   Scientific Reports

Impacts of Early Life Stress on the Methylome and Transcriptome of Atlantic Salmon

(2017) Hooman K. Moghadam et al.   Scientific Reports

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

(2016) Mukundh N. Balasubramanian et al.   BMC GENOMICS

RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout ( Oncorhynchus mykiss )

(2016) Matthew C. Hale et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Genetic contribution to variation in DNA methylation at maternal smoking-sensitive loci in exposed neonates

(2016) Semira Gonseth et al.   Epigenetics

Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus)

(2016) Amanda J. Lea et al.   MOLECULAR ECOLOGY

Broodstock History Strongly Influences Natural Spawning Success in Hatchery Steelhead (Oncorhynchus mykiss)

(2016) Michael J. Ford et al.   PLoS One

A single generation of domestication heritably alters the expression of hundreds of genes

(2016) Mark R. Christie et al.   Nature Communications

Analysis of a four generation family reveals the widespread sequence-dependent maintenance of allelic DNA methylation in somatic and germ cells

(2016) Aifa Tang et al.   Scientific Reports

Coping with a changing environment: the effects of early life stress

(2016) Marco A. Vindas et al.   Royal Society Open Science

BS-SNPer: SNP calling in bisulfite-seq data

(2015) Shengjie Gao et al.   BIOINFORMATICS

Anadromy and residency in steelhead and rainbow trout (Oncorhynchus mykiss): a review of the processes and patterns

(2015) Neala W. Kendall et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Dynamics of epigenetic phenomena: intergenerational and intragenerational phenotype 'washout'

(2015) W. W. Burggren   JOURNAL OF EXPERIMENTAL BIOLOGY

Migration-related phenotypic divergence is associated with epigenetic modifications in rainbow trout

(2015) Melinda R. Baerwald et al.   MOLECULAR ECOLOGY

Developmental windows of susceptibility for epigenetic inheritance through the male germline

(2015) Lundi Ly et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A Flexible, Efficient Binomial Mixed Model for Identifying Differential DNA Methylation in Bisulfite Sequencing Data

(2015) Amanda J. Lea et al.   PLoS Genetics

Overexpression of the Heterochromatinization Factor BAHD1 in HEK293 Cells Differentially Reshapes the DNA Methylome on Autosomes and X Chromosome

(2015) Emanuele Libertini et al.   Frontiers in Genetics

Epigenetic modification and inheritance in sexual reversal of fish

(2014) C. Shao et al.   GENOME RESEARCH

The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes

(2014) A. L. Teh et al.   GENOME RESEARCH

Early environment influences later performance in fishes

(2014) B. Jonsson et al.   JOURNAL OF FISH BIOLOGY

Early Life Nutrition, Epigenetics and Programming of Later Life Disease

(2014) Mark Vickers   Nutrients

Epigenetic Regulation of Individual Modules of the immunoglobulin heavy chain locus 3′ Regulatory Region

(2014) Barbara K. Birshtein   Frontiers in Immunology

A validation of parentage-based tagging using hatchery steelhead in the Snake River basin

(2013) Craig A. Steele et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

(2013) Magdalena E. Potok et al.   CELL

Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos

(2013) Lan Jiang et al.   CELL

The EGFR signalling system in the liver: from hepatoprotection to hepatocarcinogenesis

(2013) Carmen Berasain et al.   JOURNAL OF GASTROENTEROLOGY

StAMPP: an R package for calculation of genetic differentiation and structure of mixed-ploidy level populations

(2013) Luke W. Pembleton et al.   Molecular Ecology Resources

The Positive Impact of the Early-Feeding of a Plant-Based Diet on Its Future Acceptance and Utilisation in Rainbow Trout

(2013) Inge Geurden et al.   PLoS One

Early Life History Variation in Hatchery- and Natural-Origin Spring Chinook Salmon in the Yakima River, Washington

(2013) Donald A. Larsen et al.   TRANSACTIONS OF THE AMERICAN FISHERIES SOCIETY

Sperm nuclear proteome and its epigenetic potential

(2013) J. Castillo et al.   Andrology

The sexually dimorphic on the Y-chromosome gene (sdY) is a conserved male-specific Y-chromosome sequence in many salmonids

(2012) Ayaka Yano et al.   Evolutionary Applications

Genome-wide association reveals genetic basis for the propensity to migrate in wild populations of rainbow and steelhead trout

(2012) Benjamin C. Hecht et al.   MOLECULAR ECOLOGY

Reversible switching between epigenetic states in honeybee behavioral subcastes

(2012) Brian R Herb et al.   NATURE NEUROSCIENCE

Epigenetics and the environment: emerging patterns and implications

(2012) Robert Feil et al.   NATURE REVIEWS GENETICS

PPARs: Fatty acid sensors controlling metabolism

(2012) Lars la Cour Poulsen et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Aging effects on DNA methylation modules in human brain and blood tissue

(2012) Steve Horvath et al.   GENOME BIOLOGY

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

(2012) Patrick Boyle et al.   GENOME BIOLOGY

Growth, osmoregulation and endocrine changes in wild Atlantic salmon smolts and post-smolts during marine migration

(2011) Sigurd O. Stefansson et al.   AQUACULTURE

PPARs are a unique set of fatty acid regulated transcription factors controlling both lipid metabolism and inflammation

(2011) Tamas Varga et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Sperm Methylation Profiles Reveal Features of Epigenetic Inheritance and Evolution in Primates

(2011) Antoine Molaro et al.   CELL

Development of natural growth regimes for hatchery-reared steelhead to reduce residualism, fitness loss, and negative ecological interactions

(2011) Barry A. Berejikian et al.   ENVIRONMENTAL BIOLOGY OF FISHES

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

DNA Methylation of the Gonadal Aromatase (cyp19a) Promoter Is Involved in Temperature-Dependent Sex Ratio Shifts in the European Sea Bass

(2011) Laia Navarro-Martín et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

No evidence for large differences in genomic methylation between wild and hatchery steelhead (Oncorhynchus mykiss)

(2010) Michael S. Blouin et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Environmental endocrinology of salmon smoltification

(2010) Björn Thrandur Björnsson et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Differential gene expression after total replacement of dietary fish meal and fish oil by plant products in rainbow trout (Oncorhynchus mykiss) liver

(2009) S. Panserat et al.   AQUACULTURE

FRANz: reconstruction of wild multi-generation pedigrees

(2009) M. Riester et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The Relationship of DNA Methylation with Age, Gender and Genotype in Twins and Healthy Controls

(2009) Marco P. Boks et al.   PLoS One

How well can captive breeding programs conserve biodiversity? A review of salmonids

(2008) Dylan J. Fraser   Evolutionary Applications

The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss

(2008) K. M. Nichols et al.   GENETICS

cDNA cloning and expression analysis of thyroid hormone receptor in the coho salmon Oncorhynchus kisutch during smoltification

(2007) Masafumi Harada et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Genetic adaptation to captivity in species conservation programs

(2007) RICHARD FRANKHAM   MOLECULAR ECOLOGY