The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis

Ecotoxicogenomics: Microarray interlaboratory comparability

(2016) Doris E. Vidal-Dorsch et al.   CHEMOSPHERE

Inhibitory effect of progesterone during early embryonic development: Suppression of myocardial differentiation and calcium-related transcriptome by progesterone in mESCs

(2016) Hee Young Kang et al.   REPRODUCTIVE TOXICOLOGY

Stressor-induced proteome alterations in zebrafish: A meta-analysis of response patterns

(2015) Ksenia J. Groh et al.   AQUATIC TOXICOLOGY

Application of omics data in regulatory toxicology: report of an international BfR expert workshop

(2015) P. Marx-Stoelting et al.   ARCHIVES OF TOXICOLOGY

Systems Biology Approach Reveals a Calcium-Dependent Mechanism for Basal Toxicity in Daphnia magna

(2015) Philipp Antczak et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

High-throughput concentration-response analysis for omics datasets

(2015) Soňa Smetanová et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Calcium-dependentNr4a1expression in mouse Leydig cells requires distinct AP1/CRE and MEF2 elements

(2015) Houssein S Abdou et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

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

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

A transcriptomics-based hepatotoxicity comparison between the zebrafish embryo and established human and rodent in vitro and in vivo models using cyclosporine A, amiodarone and acetaminophen

(2015) Marja Driessen et al.   TOXICOLOGY LETTERS

Orphan nuclear receptor Nur77 affects cardiomyocyte calcium homeostasis and adverse cardiac remodelling

(2015) Lejla Medzikovic et al.   Scientific Reports

Network analysis reveals stage-specific changes in zebrafish embryo development using time course whole transcriptome profiling and prior biological knowledge

(2015) Yuji Zhang   BioData Mining

Molecular effects of the cyanobacterial toxin cyanopeptolin (CP1020) occurring in algal blooms: Global transcriptome analysis in zebrafish embryos

(2014) Susanne Faltermann et al.   AQUATIC TOXICOLOGY

Whole-genome expression profile in zebrafish embryos after chronic exposure to morphine: identification of new genes associated with neuronal function and mu opioid receptor expression

(2014) M Herrero-Turrión et al.   BMC GENOMICS

The toxicological application of transcriptomics and epigenomics in zebrafish and other teleosts

(2014) T. D. Williams et al.   Briefings in Functional Genomics

YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses

(2014) Kim-Anh Lê Cao et al.   GENOMICS

CEM-Designer: Design of custom expression microarrays in the post-ENCODE Era

(2014) Christian Arnold et al.   JOURNAL OF BIOTECHNOLOGY

Cell cycle population effects in perturbation studies

(2014) E. O'Duibhir et al.   Molecular Systems Biology

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

The InterPro protein families database: the classification resource after 15 years

(2014) Alex Mitchell et al.   NUCLEIC ACIDS RESEARCH

The Transcriptional Response to Oxidative Stress during Vertebrate Development: Effects of tert-Butylhydroquinone and 2,3,7,8-Tetrachlorodibenzo-p-Dioxin

(2014) Mark E. Hahn et al.   PLoS One

Crude Oil Impairs Cardiac Excitation-Contraction Coupling in Fish

(2014) F. Brette et al.   SCIENCE

Downregulation of Stanniocalcin 1 Is Responsible for Sorafenib-Induced Cardiotoxicity

(2014) Miko Kawabata et al.   TOXICOLOGICAL SCIENCES

Adverse Outcome Pathway Development II: Best Practices

(2014) Daniel L. Villeneuve et al.   TOXICOLOGICAL SCIENCES

Pentachlorophenol exposure causes Warburg-like effects in zebrafish embryos at gastrulation stage

(2014) Ting Xu et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Gene expression markers in the zebrafish embryo reflect a hepatotoxic response in animal models and humans

(2014) Marja Driessen et al.   TOXICOLOGY LETTERS

Effects of BDE-209 contaminated sediments on zebrafish development and potential implications to human health

(2013) Natàlia Garcia-Reyero et al.   ENVIRONMENT INTERNATIONAL

Transcriptome alterations in zebrafish embryos after exposure to environmental estrogens and anti-androgens can reveal endocrine disruption

(2013) Viktoria Schiller et al.   REPRODUCTIVE TOXICOLOGY

Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish

(2013) Katerine S. Saili et al.   REPRODUCTIVE TOXICOLOGY

Transcriptomic analysis in the developing zebrafish embryo after compound exposure: Individual gene expression and pathway regulation

(2013) Sanne A.B. Hermsen et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Manipulation of the HIF–Vegf pathway rescues methyl tert-butyl ether (MTBE)-induced vascular lesions

(2013) Josephine A. Bonventre et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Structurally distinct polycyclic aromatic hydrocarbons induce differential transcriptional responses in developing zebrafish

(2013) Britton C. Goodale et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Zebrafish Expression Ontology of Gene Sets (ZEOGS): A Tool to Analyze Enrichment of Zebrafish Anatomical Terms in Large Gene Sets

(2013) Sergey V. Prykhozhij et al.   Zebrafish

Ethanol exposure disrupts extraembryonic microtubule cytoskeleton and embryonic blastomere cell adhesion, producing epiboly and gastrulation defects

(2013) S. Sarmah et al.   Biology Open

Triiodothyronine-induced changes in the zebrafish transcriptome during the eleutheroembryonic stage: Implications for bisphenol A developmental toxicity

(2012) Sergi Pelayo et al.   AQUATIC TOXICOLOGY

Studying the effects of genistein on gene expression of fish embryos as an alternative testing approach for endocrine disruption

(2012) Viktoria Schiller et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Global gene expression in larval zebrafish (Danio rerio) exposed to selective serotonin reuptake inhibitors (fluoxetine and sertraline) reveals unique expression profiles and potential biomarkers of exposure

(2012) June-Woo Park et al.   ENVIRONMENTAL POLLUTION

MicroRNAs control neurobehavioral development and function in zebrafish

(2012) Tamara L. Tal et al.   FASEB JOURNAL

ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

(2012) Douglas G. Howe et al.   NUCLEIC ACIDS RESEARCH

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

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

Transcriptional responses of zebrafish embryos exposed to potential sonic hedgehog pathway interfering compounds deviate from expression profiles of cyclopamine

(2012) Anita Büttner et al.   REPRODUCTIVE TOXICOLOGY

Concentration-Response Analysis of Differential Gene Expression in the Zebrafish Embryotoxicity Test Following Flusilazole Exposure

(2012) Sanne A. B. Hermsen et al.   TOXICOLOGICAL SCIENCES

DHODH modulates transcriptional elongation in the neural crest and melanoma

(2011) Richard Mark White et al.   NATURE

WikiPathways: building research communities on biological pathways

(2011) T. Kelder et al.   NUCLEIC ACIDS RESEARCH

Toxicogenomic and Phenotypic Analyses of Bisphenol-A Early-Life Exposure Toxicity in Zebrafish

(2011) Siew Hong Lam et al.   PLoS One

Transcriptional Response of Zebrafish Embryos Exposed to Neurotoxic Compounds Reveals a Muscle Activity Dependent hspb11 Expression

(2011) Nils Klüver et al.   PLoS One

Relative embryotoxicity of two classes of chemicals in a modified zebrafish embryotoxicity test and comparison with their in vivo potencies

(2011) Sanne A.B. Hermsen et al.   TOXICOLOGY IN VITRO

Hox genes and regional patterning of the vertebrate body plan

(2010) Moises Mallo et al.   DEVELOPMENTAL BIOLOGY

Adverse outcome pathways: A conceptual framework to support ecotoxicology research and risk assessment

(2010) Gerald T. Ankley et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Dynamic Zebrafish Interactome Reveals Transcriptional Mechanisms of Dioxin Toxicity

(2010) Andrey Alexeyenko et al.   PLoS One

Effects of the Protein Kinase Inhibitor PKC412 on Gene Expression and Link to Physiological Effects in Zebrafish Danio rerio Eleuthero-Embryos

(2010) Daniela M. Oggier et al.   TOXICOLOGICAL SCIENCES

The Evolution of Bioinformatics in Toxicology: Advancing Toxicogenomics

(2010) C. A. Afshari et al.   TOXICOLOGICAL SCIENCES

Minding the calcium store: Ryanodine receptor activation as a convergent mechanism of PCB toxicity

(2009) Isaac N. Pessah et al.   PHARMACOLOGY & THERAPEUTICS

The zebrafish embryo model in environmental risk assessment—applications beyond acute toxicity testing

(2008) Stefan Scholz et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

A snapshot of microarray-generated gene expression signatures associated with ovarian carcinoma

(2008) B. GYÖRFFY et al.   INTERNATIONAL JOURNAL OF GYNECOLOGICAL CANCER

The roles of the FGF signal in zebrafish embryos analyzed using constitutive activation and dominant-negative suppression of different FGF receptors

(2008) Satoshi Ota et al.   MECHANISMS OF DEVELOPMENT