DNA Methylation Dynamics in Atlantic Salmon (Salmo salar) Challenged With High Temperature and Moderate Hypoxia

Epigenetic responses to temperature and climate

(2020) Beth McCaw et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Exposure of zebrafish to elevated temperature induces sex ratio shifts and alterations in the testicular epigenome of unexposed offspring

(2020) Alejandro Valdivieso et al.   ENVIRONMENTAL RESEARCH

Rearing environment affects the genetic architecture and plasticity of DNA methylation in Chinook salmon

(2020) Clare J. Venney et al.   HEREDITY

An Epigenetic Signature for Within-Generational Plasticity of a Reef Fish to Ocean Warming

(2020) Taewoo Ryu et al.   Frontiers in Marine Science

Epigenetic differences in the innate response after immune stimulation during zebrafish sex differentiation

(2020) J. Moraleda-Prados et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Footprints of global change in marine life: Inferring past environment based on DNA methylation and gene expression marks

(2020) Dafni Anastasiadi et al.   MOLECULAR ECOLOGY

Improved mitochondrial function in salmon (Salmo salar) following high temperature acclimation suggests that there are cracks in the proverbial ‘ceiling’

(2020) Lucie Gerber et al.   Scientific Reports

Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes

(2019) Raúl F. Pérez et al.   Journal of Translational Medicine

Fish response to hypoxia stress: growth, physiological, and immunological biomarkers

(2019) Mohsen Abdel-Tawwab et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

Differences in the fast muscle methylome provide insight into sex-specific epigenetic regulation of growth in Nile tilapia during early stages of domestication

(2019) Tomasz Podgorniak et al.   Epigenetics

Salmonid gene expression biomarkers indicative of physiological responses to changes in salinity and temperature, but not dissolved oxygen

(2019) Aimee Lee S. Houde et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Ten quick tips for effective dimensionality reduction

(2019) Lan Huong Nguyen et al.   PLoS Computational Biology

A clockwork fish: Age prediction using DNA methylation‐based biomarkers in the European seabass

(2019) Dafni Anastasiadi et al.   Molecular Ecology Resources

The impacts of increasing temperature and moderate hypoxia on the production characteristics, cardiac morphology and haematology of Atlantic Salmon (Salmo salar)

(2019) Anthony K. Gamperl et al.   AQUACULTURE

Immune genes, IL1β and Casp9, show sexual dimorphic methylation patterns in zebrafish gonads

(2019) M. Caballero-Huertas et al.   FISH & SHELLFISH IMMUNOLOGY

Marine Environmental Epigenetics

(2018) Jose M. Eirin-Lopez et al.   Annual Review of Marine Science

Epigenetics in teleost fish: From molecular mechanisms to physiological phenotypes

(2018) Carol Best et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Declining oxygen in the global ocean and coastal waters

(2018) Denise Breitburg et al.   SCIENCE

Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species

(2018) Dafni Anastasiadi et al.   Epigenetics & Chromatin

Longer and more frequent marine heatwaves over the past century

(2018) Eric C. J. Oliver et al.   Nature Communications

The epigenetic landscape of transgenerational acclimation to ocean warming

(2018) Taewoo Ryu et al.   Nature Climate Change

DNA methylation of the promoter region of bnip3 and bnip3l genes induced by metabolic programming

(2018) Vincent Veron et al.   BMC GENOMICS

Dynamic epimarks in sex-related genes predict gonad phenotype in seabass, a fish with mixed genetic and environmental sex determination

(2018) Dafni Anastasiadi et al.   Epigenetics

Marine heatwaves under global warming

(2018) Thomas L. Frölicher et al.   NATURE

Rapid coastal deoxygenation due to ocean circulation shift in the northwest Atlantic

(2018) Mariona Claret et al.   Nature Climate Change

Developing specific molecular biomarkers for thermal stress in salmonids

(2018) Arash Akbarzadeh et al.   BMC GENOMICS

Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon

(2018) Tamsyn M. Uren Webster et al.   Epigenetics

Age estimation in a long-lived seabird (Ardenna tenuirostris ) using DNA methylation-based biomarkers

(2018) R. De Paoli-Iseppi et al.   Molecular Ecology Resources

Effects of an unprecedented summer heatwave on the growth performance, flesh colour and plasma biochemistry of marine cage-farmed Atlantic salmon (Salmo salar)

(2018) Nicholas M. Wade et al.   JOURNAL OF THERMAL BIOLOGY

The dietary replacement of marine ingredients by terrestrial animal and plant alternatives modulates the antiviral immune response of Atlantic salmon ( Salmo salar )

(2017) Albert Caballero-Solares et al.   FISH & SHELLFISH IMMUNOLOGY

Low salinity affects cellularity, DNA methylation, and mRNA expression of igf1 in the liver of half smooth tongue sole (Cynoglossus semilaevis)

(2017) Siping Li et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

The effect of thermal acclimation on aerobic scope and critical swimming speed in Atlantic salmon,Salmo salar

(2017) Malthe Hvas et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Dynamics and Context-Dependent Roles of DNA Methylation

(2017) Christina Ambrosi et al.   JOURNAL OF MOLECULAR BIOLOGY

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(2017) Alexandra Kuznetsova et al.   Journal of Statistical Software

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

DNA methylation and DNA methyltransferases

(2017) John R. Edwards et al.   Epigenetics & Chromatin

Epigenetics in aquaculture - the last frontier

(2017) Luana Granada et al.   Reviews in Aquaculture

Response of Atlantic salmon Salmo salar to temperature and dissolved oxygen extremes established using animal-borne environmental sensors

(2017) Kilian M. Stehfest et al.   Scientific Reports

Epigenetic considerations in aquaculture

(2017) Mackenzie R. Gavery et al.   PeerJ

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

Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish

(2017) Cunfang Zhang et al.   PLoS One

Small ocean temperature increases elicit stage-dependent changes in DNA methylation and gene expression in a fish, the European sea bass

(2017) Dafni Anastasiadi 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

What do we not know about mitochondrial potassium channels?

(2016) Michał Laskowski et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2016) Philip Ewels et al.   BIOINFORMATICS

Are fish in hot water? Effects of warming on oxidative stress metabolism in the commercial species Sparus aurata

(2016) Diana Madeira et al.   ECOLOGICAL INDICATORS

The Atlantic salmon genome provides insights into rediploidization

(2016) Sigbjørn Lien et al.   NATURE

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

Evolution of Plasticity: Mechanistic Link between Development and Reversible Acclimation

(2016) Julian E. Beaman et al.   TRENDS IN ECOLOGY & EVOLUTION

Biparental immune priming in the pipefish Syngnathus typhle

(2016) Anne Beemelmanns et al.   ZOOLOGY

Hypoxia causes transgenerational impairments in reproduction of fish

(2016) Simon Yuan Wang et al.   Nature Communications

The Impact of External Factors on the Epigenome:In Uteroand over Lifetime

(2016) Estela G. Toraño et al.   Biomed Research International

Variation of DNA Methylome of Zebrafish Cells under Cold Pressure

(2016) Bingshe Han et al.   PLoS One

IBS: an illustrator for the presentation and visualization of biological sequences: Fig. 1.

(2015) Wenzhong Liu et al.   BIOINFORMATICS

Atlantic salmon (Salmo salar) liver transcriptome response to diets containing Camelina sativa products

(2015) Xi Xue et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

The zebrafish miR-462/miR-731 cluster is induced under hypoxic stress via hypoxia-inducible factor 1α and functions in cellular adaptations

(2015) Chun-Xiao Huang et al.   FASEB JOURNAL

Nongenetic inheritance and transgenerational epigenetics

(2015) Moshe Szyf   TRENDS IN MOLECULAR MEDICINE

Epigenetic regulation by histone demethylases in hypoxia

(2015) Rebecca L Hancock et al.   Epigenomics

Molecular processes of transgenerational acclimation to a warming ocean

(2015) Heather D. Veilleux et al.   Nature Climate Change

A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B

(2014) Kazuyoshi Hosomichi et al.   BMC GENOMICS

Thermal plasticity of the miRNA transcriptome during Senegalese sole development

(2014) Catarina Campos et al.   BMC GENOMICS

Genomic patterns and context specific interpretation of DNA methylation

(2014) Tuncay Baubec et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Plastic and evolutionary responses to climate change in fish

(2014) Lisa G. Crozier et al.   Evolutionary Applications

Evaluation of the impact of camelina oil-containing diets on the expression of genes involved in the innate anti-viral immune response in Atlantic cod (Gadus morhua)

(2014) Marije Booman et al.   FISH & SHELLFISH IMMUNOLOGY

Epigenetic estimation of age in humpback whales

(2014) Andrea M. Polanowski et al.   Molecular Ecology Resources

Identification and Expression Profiling of MicroRNAs in the Brain, Liver and Gonads of Marine Medaka (Oryzias melastigma) and in Response to Hypoxia

(2014) Karen Lau et al.   PLoS One

Physiological plasticity increases resilience of ectothermic animals to climate change

(2014) Frank Seebacher et al.   Nature Climate Change

Genomics of CpG Methylation in Developing and Developed Zebrafish

(2014) David M. McGaughey et al.   G3-Genes Genomes Genetics

DNA Methylation Biomarkers: Cancer and Beyond

(2014) Thomas Mikeska et al.   Genes

Family-specific differences in growth rate and hepatic gene expression in juvenile triploid growth hormone (GH) transgenic Atlantic salmon (Salmo salar)

(2013) Qingheng Xu et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

An ExPosition of multivariate analysis with the singular value decomposition in R

(2013) Derek Beaton et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Epigenetic Modifications During Sex Change Repress Gonadotropin Stimulation ofCyp19a1ain a Teleost Ricefield Eel (Monopterus albus)

(2013) Yang Zhang et al.   ENDOCRINOLOGY

Temperature affects methylation of themyogeninputative promoter, its expression and muscle cellularity in Senegalese sole larvae

(2013) Catarina Campos et al.   Epigenetics

Epigenetic memory of environmental organisms: A reflection of lifetime stressor exposures

(2013) Leda Mirbahai et al.   MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS

Reintroducing domesticated wild mice to sociality induces adaptive transgenerational effects on MUP expression

(2013) A. C. Nelson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic regulation of the ribosomal cistron seasonally modulates enrichment of H2A.Z and H2A.Zub in response to different environmental inputs in carp (Cyprinus carpio)

(2013) Nicolas Simonet et al.   Epigenetics & Chromatin

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

DNA methylation age of human tissues and cell types

(2013) Steve Horvath   GENOME BIOLOGY

The effect of intermittent hypoxia on growth, appetite and some aspects of the immune response of Atlantic salmon (Salmo salar)

(2012) Kimberly Burt et al.   AQUACULTURE RESEARCH

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers

(2012) S. Seisenberger et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Environmental conditions and occurrence of hypoxia within production cages of Atlantic salmon on the south coast of Newfoundland

(2011) Kim Burt et al.   AQUACULTURE RESEARCH

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Timing is everything

(2011) Christopher Faulk et al.   Epigenetics

Epigenetics and environment: a complex relationship

(2010) Oscar Aguilera et al.   JOURNAL OF APPLIED PHYSIOLOGY

The physiology of climate change: how potentials for acclimatization and genetic adaptation will determine 'winners' and 'losers'

(2010) G. N. Somero   JOURNAL OF EXPERIMENTAL BIOLOGY

Gene expression analysis for the identification of selection and local adaptation in fishes

(2010) P. F. Larsen et al.   JOURNAL OF FISH BIOLOGY

Environmentally induced phenotypes and DNA methylation: how to deal with unpredictable conditions until the next generation and after

(2010) BERNARD ANGERS et al.   MOLECULAR ECOLOGY

MacroH2A subtypes contribute antagonistically to the transcriptional regulation of the ribosomal cistron during seasonal acclimatization of the carp fish

(2010) Ingrid Araya et al.   Epigenetics & Chromatin

Improving Bioscience Research Reporting: The ARRIVE Guidelines for Reporting Animal Research

(2010) Carol Kilkenny et al.   PLOS BIOLOGY

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Epigenetic responses to environmental change and their evolutionary implications

(2009) B. M. Turner   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Persistent epigenetic differences associated with prenatal exposure to famine in humans

(2008) B. T. Heijmans et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlative gene expression and DNA methylation profiling in lung development nominate new biomarkers in lung cancer

(2007) Rene Cortese et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY