Divergent Carry-Over Effects of Hypoxia during the Early Development of Abalone

Long-read RNA sequencing of Pacific abalone Haliotis discus hannai reveals innate immune system responses to environmental stress

(2022) Yulong Sun et al.   FISH & SHELLFISH IMMUNOLOGY

Genome-Wide Identification of Long Non-coding RNAs in Crassostrea gigas and Their Association with Heat Stress

(2022) Kai Song   MARINE BIOTECHNOLOGY

Transcriptome profiling of the early developmental stages in the giant mussel Choromytilus chorus exposed to delousing drugs

(2022) Gustavo Núñez-Acuña et al.   Marine Genomics

Analysis of lncRNA and mRNA expression profiles in peripheral blood leukocytes of the half-smooth tongue sole (Cynoglossus semilaevis) treated with chitosan oligosaccharide

(2021) Shu Wei et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Context‐dependent carryover effects of hypoxia and warming in a coastal ecosystem engineer

(2021) Sarah C. Donelan et al.   ECOLOGICAL APPLICATIONS

Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

(2021) Sara Guirao‐Rico et al.   Molecular Ecology Resources

Integrated Analysis of Coding Genes and Non-coding RNAs Associated with Shell Color in the Pacific Oyster (Crassostrea gigas)

(2021) Zhuanzhuan Li et al.   MARINE BIOTECHNOLOGY

Oxidative stress induced by methomyl exposure reduces the quality of early embryo development in mice

(2021) Daohong He et al.   ZYGOTE

A beginner's guide to low‐coverage whole genome sequencing for population genomics

(2021) Runyang Nicolas Lou et al.   MOLECULAR ECOLOGY

Aquatic foods to nourish nations

(2021) Christopher D. Golden et al.   NATURE

Comparative Transcriptome Analysis of Heart Tissue in Response to Hypoxia in Silver Sillago (Sillago sihama)

(2021) Wanida Saetan et al.   Journal of Ocean University of China

Differential Expression of Long Non-Coding RNA (lncRNA) in Mediterranean Mussel (Mytilus galloprovincialis) Hemocytes under Immune Stimuli

(2021) Patricia Pereiro et al.   Genes

Distinct metabolic shifts occur during the transition between normoxia and hypoxia in the hybrid and its maternal abalone

(2021) Yawei Shen et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Prolonged exposure to hypoxia inhibits the growth of Pacific abalone by modulating innate immunity and oxidative status

(2020) Sang-Eun Nam et al.   AQUATIC TOXICOLOGY

The effects of constant and cyclical hypoxia on the survival, growth and metabolic physiology of incubating Atlantic salmon (Salmo salar)

(2020) Andrew T. Wood et al.   AQUACULTURE

Both maternal and embryonic exposure to mild hypoxia influence embryonic development of the intertidal gastropod Littorina littorea (Linnaeus, 1758)

(2020) James C. S. McCoy et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Evolved differences in energy metabolism and growth dictate the impacts of ocean acidification on abalone aquaculture

(2020) Daniel S. Swezey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combined effects of warming and hypoxia on early life stage Chinook salmon physiology and development

(2019) Annelise M Del Rio et al.   Conservation Physiology

Hypoxia Causes Transgenerational Impairment of Ovarian Development and Hatching Success in Fish

(2019) Keng Po Lai et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comparing Pool‐seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster ( Homarus americanus ) as a case study

(2019) Yann Dorant et al.   Ecology and Evolution

Recommendations for performance optimizations when using GATK3.8 and GATK4

(2019) Jacob R Heldenbrand et al.   BMC BIOINFORMATICS

Immunity-associated long non-coding RNA and expression in response to bacterial infection in large yellow croaker (Larimichthys crocea)

(2019) Xiaoxu Liu et al.   FISH & SHELLFISH IMMUNOLOGY

Regulation of gene expression by cis-acting long non-coding RNAs

(2019) Noa Gil et al.   NATURE REVIEWS GENETICS

A new indicator of hypoxia tolerance in abalone, developed based on heart rate fluctuations

(2019) Nan Chen et al.   AQUACULTURE

Limitations of cross‐ and multigenerational plasticity for marine invertebrates faced with global climate change

(2019) Maria Byrne et al.   GLOBAL CHANGE BIOLOGY

Stress across life stages: Impacts, responses and consequences for marine organisms

(2019) Jonathan Y.S. Leung et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Short- and long-term effects on growth and expression patterns in response to incubation temperatures in Senegalese sole

(2018) Carlos Carballo et al.   AQUACULTURE

OUP accepted manuscript

(2018)   BIOINFORMATICS

Metabolic response to hypoxia in European sea bass ( Dicentrarchus labrax ) displays developmental plasticity

(2018) Laura Cadiz et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

Temperature induced variation in gene expression of thyroid hormone receptors and deiodinases of European eel ( Anguilla anguilla ) larvae

(2018) S.N. Politis et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Moderate hypoxia but not warming conditions at larval stage induces adverse carry-over effects on hypoxia tolerance of European sea bass ( Dicentrarchus labrax ) juveniles

(2018) Laura Cadiz et al.   MARINE ENVIRONMENTAL RESEARCH

Declining oxygen in the global ocean and coastal waters

(2018) Denise Breitburg et al.   SCIENCE

Measuring Genetic Differentiation from Pool-seq Data

(2018) Valentin Hivert et al.   GENETICS

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Citrinin exposure affects oocyte maturation and embryo development by inducing oxidative stress-mediated apoptosis

(2017) Yu Wu et al.   Oncotarget

Identification of long non-coding RNAs in two anthozoan species and their possible implications for coral bleaching

(2017) Chen Huang et al.   Scientific Reports

Exposure to an acute hypoxic stimulus during early life affects the expression of glucose metabolism-related genes at first-feeding in trout

(2017) Jingwei Liu et al.   Scientific Reports

Transcriptomic analysis of maternally provisioned cues for phenotypic plasticity in the annual killifish, Austrofundulus limnaeus

(2017) Amie L. Romney et al.   EvoDevo

Hatchery Conditions do not Negatively Impact Respiratory Response of Early Life-Stage Development in Australian Hybrid Abalone

(2016) Katharina Alter et al.   JOURNAL OF SHELLFISH RESEARCH

Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

(2016) Stefan Dennenmoser et al.   MOLECULAR ECOLOGY

Unique features of long non-coding RNA biogenesis and function

(2016) Jeffrey J. Quinn et al.   NATURE REVIEWS GENETICS

Hypoxia causes transgenerational impairments in reproduction of fish

(2016) Simon Yuan Wang et al.   Nature Communications

Acute and sub-lethal exposure to copper oxide nanoparticles causes oxidative stress and teratogenicity in zebrafish embryos

(2015) Santhanamari Ganesan et al.   JOURNAL OF APPLIED TOXICOLOGY

Growth and survival in a changing environment: Combined effects of moderate hypoxia and low pH on juvenile bivalve Macoma balthica

(2015) Anna Jansson et al.   JOURNAL OF SEA RESEARCH

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Developmental Critical Windows and Sensitive Periods as Three-Dimensional Constructs in Time and Space

(2015) Warren W. Burggren et al.   PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY

Adaptive developmental plasticity: what is it, how can we recognize it and when can it evolve?

(2015) Daniel Nettle et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Emerging roles of long non-coding RNA in root developmental plasticity and regulation of phosphate homeostasis

(2015) Jeremie Bazin et al.   Frontiers in Plant Science

Three-Year Breeding Cycle of Rainbow Trout (Oncorhynchus mykiss) Fed a Plant-Based Diet, Totally Free of Marine Resources: Consequences for Reproduction, Fatty Acid Composition and Progeny Survival

(2015) Viviana Lazzarotto et al.   PLoS One

Hypoxia turns genotypic female medaka fish into phenotypic males

(2014) Catis Hin Ying Cheung et al.   ECOTOXICOLOGY

The biology of developmental plasticity and the Predictive Adaptive Response hypothesis

(2014) Patrick Bateson et al.   JOURNAL OF PHYSIOLOGY-LONDON

Assessment of oxidative damage to DNA, transcriptional expression of key genes, lipid peroxidation and histopathological changes in carp Cyprinus carpio L. following exposure to chronic hypoxic and subsequent recovery in normoxic conditions

(2014) Sanaa A. Mustafa et al.   MUTAGENESIS

A Comprehensive View of the Epigenetic Landscape. Part II: Histone Post-translational Modification, Nucleosome Level, and Chromatin Regulation by ncRNAs

(2014) Anna Sadakierska-Chudy et al.   NEUROTOXICITY RESEARCH

Can environmental conditions experienced in early life influence future generations?

(2014) T. Burton et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Hypoxia-inducible factor-1 mediates adaptive developmental plasticity of hypoxia tolerance in zebrafish, Danio rerio

(2014) C. E. Robertson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Biological carryover effects: linking common concepts and mechanisms in ecology and evolution

(2014) Constance M. O'Connor et al.   Ecosphere

Incubation temperature induces changes in muscle cellularity and gene expression in Senegalese sole (Solea senegalensis)

(2013) Catarina Campos et al.   GENE

Latent effects of hypoxia on the gastropod Crepidula onyx

(2013) A Li et al.   MARINE ECOLOGY PROGRESS SERIES

Fantastically plastic: fish larvae equipped for a new world

(2013) Karin Pittman et al.   Reviews in Aquaculture

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Variation in rates of early development in Haliotis asinina generate competent larvae of different ages

(2012) Daniel J Jackson et al.   Frontiers in Zoology

The genetic differentiation at quantitative trait loci under local adaptation

(2012) VALÉRIE LE CORRE et al.   MOLECULAR ECOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish

(2012) G. R. Scott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Responses of threespine stickleback (Gasterosteus aculeatus, L) transcriptome to hypoxia

(2011) L. Leveelahti et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

Oxidative stress in zebrafish embryos induced by short-term exposure to bisphenol A, nonylphenol, and their mixture

(2011) Minghong Wu et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Developmental trajectories, critical windows and phenotypic alteration during cardio-respiratory development

(2011) Warren W. Burggren et al.   RESPIRATORY PHYSIOLOGY & NEUROBIOLOGY

Acclimation to predicted ocean warming through developmental plasticity in a tropical reef fish

(2010) JENNIFER M. DONELSON et al.   GLOBAL CHANGE BIOLOGY

Carry-over effects as drivers of fitness differences in animals

(2010) Xavier A. Harrison et al.   JOURNAL OF ANIMAL ECOLOGY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

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

Effects of ocean acidification on the early life history of a tropical marine fish

(2009) P. L. Munday et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A global view of genomic information – moving beyond the gene and the master regulator

(2009) John S. Mattick et al.   TRENDS IN GENETICS

Defending against hypoxia: Behavioural, physiological and biochemical strategies of hypoxia survival in nearshore marine sculpins

(2008) M. Mandic et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Spreading Dead Zones and Consequences for Marine Ecosystems

(2008) R. J. Diaz et al.   SCIENCE

Early growth conditions, phenotypic development and environmental change

(2007) P. Monaghan   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES