Consideration of metabolomics and transcriptomics data in the context of using avian embryos for toxicity testing

Haematological and metabolic profiles associated with age and sex in giant kokopu ( Galaxias argenteus ) (Gmelin 1789) broodstock

(2021) Ronald Lulijwa et al.   JOURNAL OF FISH BIOLOGY

MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights

(2021) Zhiqiang Pang et al.   NUCLEIC ACIDS RESEARCH

Integrative analysis of transcriptomics and metabolomics reveals the hepatotoxic mechanism of thiamethoxam on male Coturnix japonica

(2021) Yifan Pan et al.   ENVIRONMENTAL POLLUTION

EcoToxXplorer: Leveraging Design Thinking to Develop a Standardized Web‐Based Transcriptomics Analytics Platform for Diverse Users

(2021) Othman Soufan et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

(2020) Larry A. Cogburn et al.   BMC GENOMICS

MetaboAnalystR 3.0: Toward an Optimized Workflow for Global Metabolomics

(2020) Zhiqiang Pang et al.   Metabolites

Sex-dependent changes in the skin mucus metabolome of discus fish (Symphysodon haraldi) during biparental care

(2020) Bin Wen et al.   Journal of Proteomics

Inter-embryo gene expression variability recapitulates the hourglass pattern of evo-devo

(2020) Jialin Liu et al.   BMC BIOLOGY

Endocrine and physiological responses of hatchling American kestrels (Falco sparverius) following embryonic exposure to technical short-chain chlorinated paraffins (C10-13)

(2020) K.J. Fernie et al.   ENVIRONMENT INTERNATIONAL

EcoToxChip: A next-generation toxicogenomics tool for chemical prioritization and environmental management

(2019) Niladri Basu et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Early life exposure to triphenyl phosphate: Effects on thyroid function, growth, and resting metabolic rate of Japanese quail (Coturnix japonica) chicks

(2019) M.F. Guigueno et al.   ENVIRONMENTAL POLLUTION

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

(2019) Guangyan Zhou et al.   NUCLEIC ACIDS RESEARCH

An Early‐life Stage Alternative Testing Strategy for Assessing the Impacts of Environmental Chemicals in Birds

(2019) Amani Farhat et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

A comparative study of 3 alternative avian toxicity testing methods: Effects on hepatic gene expression in the chicken embryo

(2019) Krittika Mittal et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Assessment of the effects of early life exposure to triphenyl phosphate on fear, boldness, aggression, and activity in Japanese quail (Coturnix japonica) chicks

(2019) Ashley K. Hanas et al.   ENVIRONMENTAL POLLUTION

Effects on the hepatic transcriptome of chicken embryos in ovo exposed to phenobarbital

(2018) Jiahua Guo et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Potency of polycyclic aromatic hydrocarbons in chicken and Japanese quail embryos

(2018) Cynthia D. Franci et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Applicability of the fish embryo acute toxicity (FET) test (OECD 236) in the regulatory context of Registration, Evaluation, Authorisation, and Restriction of Chemicals (REACH)

(2018) Marta Sobanska et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Based serum metabolomics analysis reveals simultaneous interconnecting changes during chicken embryonic development

(2018) M. L. Peng et al.   JOURNAL OF ANIMAL PHYSIOLOGY AND ANIMAL NUTRITION

MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

(2018) Jasmine Chong et al.   NUCLEIC ACIDS RESEARCH

The induction of aryl hydrocarbon receptor (AHR) in immune organs of developing chicks by polycyclic aromatic hydrocarbons

(2018) A. R. Nisha et al.   TOXICOLOGY MECHANISMS AND METHODS

The induction of aryl hydrocarbon receptor (AHR) in immune organs of developing chicks by polycyclic aromatic hydrocarbons

(2018) A. R. Nisha et al.   TOXICOLOGY MECHANISMS AND METHODS

Embryotoxic effects of in-ovo triclosan injection to the yellow-legged gull

(2018) Cristina Daniela Possenti et al.   CHEMOSPHERE

Assessment of neuroanatomical and behavioural effects of in ovo methylmercury exposure in zebra finches ( Taeniopygia guttata )

(2017) Maria S. Yu et al.   NEUROTOXICOLOGY

Applying 'omics technologies in chemicals risk assessment: Report of an ECETOC workshop

(2017) Roland Buesen et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Why Batch Effects Matter in Omics Data, and How to Avoid Them

(2017) Wilson Wen Bin Goh et al.   TRENDS IN BIOTECHNOLOGY

Alternative approaches to vertebrate ecotoxicity tests in the 21st century: A review of developments over the last 2 decades and current status

(2016) Adam Lillicrap et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Deep sexual dimorphism in adult medaka fish liver highlighted by multi-omic approach

(2016) Qin Qiao et al.   Scientific Reports

Perspectives on the membrane fatty acid unsaturation/pacemaker hypotheses of metabolism and aging

(2015) Elisabeth A. Calhoon et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Omics for aquatic ecotoxicology: Control of extraneous variability to enhance the analysis of environmental effects

(2015) Denina B.D. Simmons et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Acute and chronic eggshell temperature manipulations during hatching term influence hatchability, broiler performance, and ascites incidence

(2015) A. Sozcu et al.   POULTRY SCIENCE

How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq

(2015) Luis Fernando García-Ortega et al.   PLoS One

Comprehensive Identification of Sexual Dimorphism-Associated Differentially Expressed Genes in Two-Way Factorial Designed RNA-Seq Data on Japanese Quail (Coturnix coturnix japonica)

(2015) Kelsey Caetano-Anolles et al.   PLoS One

RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature

(2014) Derrick J Coble et al.   BMC GENOMICS

The transcript catalogue of the short-lived fish Nothobranchius furzeri provides insights into age-dependent changes of mRNA levels

(2013) Andreas Petzold et al.   BMC GENOMICS

Ambient temperature and nutritional stress influence fatty acid composition of structural and fuel lipids in Japanese quail (Coturnix japonica) tissues

(2013) Miriam Ben-Hamo et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

What is metabolomics all about?

(2009) Ute Roessner et al.   BIOTECHNIQUES

Environmental metabolomics: a critical review and future perspectives

(2009) Jacob G. Bundy et al.   Metabolomics

Change in hepatic and plasma bile acid contents and its regulatory gene expression in the chicken embryo

(2008) Momoka Sato et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY