The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome

Genomics pipelines and data integration: challenges and opportunities in the research setting

(2017) Jeremy Davis-Turak et al.   EXPERT REVIEW OF MOLECULAR DIAGNOSTICS

Bisphenol A Induces Fatty Liver by an Endocannabinoid-Mediated Positive Feedback Loop

(2016) Andrea Martella et al.   ENDOCRINOLOGY

Time- and Oil-Dependent Transcriptomic and Physiological Responses to Deepwater Horizon Oil in Mahi-Mahi (Coryphaena hippurus) Embryos and Larvae

(2016) Elvis Genbo Xu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Bisphenol A causes reproductive toxicity, decreasesdnmt1transcription, and reduces global DNA methylation in breeding zebrafish(Danio rerio)

(2016) L. V. Laing et al.   Epigenetics

Systems analysis of the prostate transcriptome in African–American men compared with European–American men

(2016) Gary Hardiman et al.   PHARMACOGENOMICS

Advancements in zebrafish applications for 21st century toxicology

(2016) Gloria R. Garcia et al.   PHARMACOLOGY & THERAPEUTICS

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure

(2016) Manon C. Bouwmeester et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Urea cycle regulation by mitochondrial sirtuin, SIRT5

(2016) Takashi Nakagawa et al.   Aging-US

BPA-Induced Deregulation Of Epigenetic Patterns: Effects On Female Zebrafish Reproduction

(2016) Stefania Santangeli et al.   Scientific Reports

HDACs Regulate miR-133a Expression in Pressure Overload Induced Cardiac Fibrosis

(2015) Ludivine Renaud et al.   Circulation-Heart Failure

Transgenerational inheritance of heart disorders caused by paternal bisphenol A exposure

(2015) Marta Lombó et al.   ENVIRONMENTAL POLLUTION

Effects of the environmental estrogenic contaminants bisphenol A and 17α-ethinyl estradiol on sexual development and adult behaviors in aquatic wildlife species

(2015) Ramji K. Bhandari et al.   GENERAL AND COMPARATIVE ENDOCRINOLOGY

Targeting the translation machinery in cancer

(2015) Mamatha Bhat et al.   NATURE REVIEWS DRUG DISCOVERY

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Low-dose exposure to bisphenol A and replacement bisphenol S induces precocious hypothalamic neurogenesis in embryonic zebrafish

(2015) Cassandra D. Kinch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dysregulation of microRNA biogenesis and gene silencing in cancer

(2015) Akiko Hata et al.   Science Signaling

Developmental bisphenol A (BPA) exposure leads to sex-specific modification of hepatic gene expression and epigenome at birth that may exacerbate high-fat diet-induced hepatic steatosis

(2015) Rita S. Strakovsky et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Dysregulation of microRNA biogenesis and gene silencing in cancer

(2015) Akiko Hata et al.   Science Signaling

Bisphenol A environmental exposure and the detrimental effects on human metabolic health: is it necessary to revise the risk assessment in vulnerable population?

(2015) R. Valentino et al.   JOURNAL OF ENDOCRINOLOGICAL INVESTIGATION

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

CAP-miRSeq: a comprehensive analysis pipeline for microRNA sequencing data

(2014) Zhifu Sun et al.   BMC GENOMICS

A developmental hepatotoxicity study of dietary bisphenol A in Sparus aurata juveniles

(2014) Francesca Maradonna et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Estrogen-related receptor γ is an in vivo receptor of bisphenol A

(2014) Marie Tohmé et al.   FASEB JOURNAL

Circulating microRNA signature in non-alcoholic fatty liver disease: from serum non-coding RNAs to liver histology and disease pathogenesis

(2014) Carlos J Pirola et al.   GUT

Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing

(2014) Michael E Baker et al.   JOURNAL OF MOLECULAR ENDOCRINOLOGY

Evidence that bisphenol A (BPA) can be accurately measured without contamination in human serum and urine, and that BPA causes numerous hazards from multiple routes of exposure

(2014) Frederick S. vom Saal et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

The role of hepatic lipids in hepatic insulin resistance and type 2 diabetes

(2014) Rachel J. Perry et al.   NATURE

Bisphenol A Increases Atherosclerosis in Pregnane X Receptor‐Humanized ApoE Deficient Mice

(2014) Yipeng Sui et al.   Journal of the American Heart Association

Urinary Bisphenol A and Obesity in US Children

(2013) Ruchi Bhandari et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Epigenetics: a new mechanism of regulation of heart failure?

(2013) Roberto Papait et al.   BASIC RESEARCH IN CARDIOLOGY

Genome-Wide Epigenetic Regulation of miRNAs in Cancer

(2013) C. Baer et al.   CANCER RESEARCH

SIRT5 Regulates the Mitochondrial Lysine Succinylome and Metabolic Networks

(2013) Matthew J. Rardin et al.   Cell Metabolism

Epidemiology and Natural History of Patients with NAFLD

(2013) Neeraj Bhala et al.   CURRENT PHARMACEUTICAL DESIGN

Non-Monotonic Dose Responses in Studies of Endocrine Disrupting Chemicals: Bisphenol a as a Case Study

(2013) Laura N. Vandenberg   Dose-Response

Developmental Programming: Gestational Bisphenol-A Treatment Alters Trajectory of Fetal Ovarian Gene Expression

(2013) Almudena Veiga-Lopez et al.   ENDOCRINOLOGY

Zebrafish as a model system to study toxicology

(2013) Yu-Jie Dai et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Steroid hormone synthesis in mitochondria

(2013) Walter L. Miller   MOLECULAR AND CELLULAR ENDOCRINOLOGY

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

Sorting out functions of sirtuins in cancer

(2013) M Roth et al.   ONCOGENE

Plastics Derived Endocrine Disruptors (BPA, DEHP and DBP) Induce Epigenetic Transgenerational Inheritance of Obesity, Reproductive Disease and Sperm Epimutations

(2013) Mohan Manikkam et al.   PLoS One

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

Estrogen Regulation of microRNAs, Target Genes, and microRNA Expression Associated with Vitellogenesis in the Zebrafish

(2013) Amit Cohen et al.   Zebrafish

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Early embryogenesis in zebrafish is affected by bisphenol A exposure

(2013) W. K. F. Tse et al.   Biology Open

Gavaging Adult Zebrafish

(2013) Chereen Collymore et al.   Jove-Journal of Visualized Experiments

Mitochondrial Dysfunction in Cancer

(2013) Michelle L. Boland et al.   Frontiers in Oncology

Differential Estrogenic Actions of Endocrine-Disrupting Chemicals Bisphenol A, Bisphenol AF, and Zearalenone through Estrogen Receptor α and β in Vitro

(2012) Yin Li et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Think Small: Zebrafish as a Model System of Human Pathology

(2012) J. R. Goldsmith et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Endocrine Disruptor Regulation of MicroRNA Expression in Breast Carcinoma Cells

(2012) Syreeta L. Tilghman et al.   PLoS One

Effects of short-term exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin on microRNA expression in zebrafish embryos

(2012) Matthew J. Jenny et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Overexpression of gankyrin induces liver steatosis in zebrafish (Danio rerio)

(2011) Guor Mour Her et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Epigenetic perspective on the developmental effects of bisphenol A

(2011) Marija Kundakovic et al.   BRAIN BEHAVIOR AND IMMUNITY

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

A Feedback Loop Between the Liver-Enriched Transcription Factor Network and Mir-122 Controls Hepatocyte Differentiation

(2011) Ilaria Laudadio et al.   GASTROENTEROLOGY

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs

(2011) David M Garcia et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

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

(2011) Siew Hong Lam et al.   PLoS One

Plastics and Health Risks

(2010) Rolf U. Halden   Annual Review of Public Health

A relationship between miRNA and gene expression in the mouse Sertoli cell line after exposure to bisphenol A

(2010) Hyunseok Cho et al.   BioChip Journal

Gankyrin promotes the proliferation of human pancreatic cancer

(2010) Yun Meng et al.   CANCER LETTERS

Evaluation of Hydrogen Peroxide as an Intraprocedural Hemostatic Agent in Manual Dermabrasion

(2010) Jonathan Weiss et al.   DERMATOLOGIC SURGERY

Urinary, Circulating, and Tissue Biomonitoring Studies Indicate Widespread Exposure to Bisphenol A

(2010) Laura N. Vandenberg et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Perinatal Exposure to Environmentally Relevant Levels of Bisphenol A Decreases Fertility and Fecundity in CD-1 Mice

(2010) Nicolas J. Cabaton et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Environmental causes of cancer: endocrine disruptors as carcinogens

(2010) Ana M. Soto et al.   Nature Reviews Endocrinology

Association of Urinary Bisphenol A Concentration with Heart Disease: Evidence from NHANES 2003/06

(2010) David Melzer et al.   PLoS One

Bisphenol A exposure leads to specific microRNA alterations in placental cells

(2010) Michele Avissar-Whiting et al.   REPRODUCTIVE TOXICOLOGY

In Utero Exposure to Diethylstilbestrol (DES) or Bisphenol-A (BPA) Increases EZH2 Expression in the Mammary Gland: An Epigenetic Mechanism Linking Endocrine Disruptors to Breast Cancer

(2010) Leo F. Doherty et al.   Hormones & Cancer

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

MicroRNA-29b induces global DNA hypomethylation and tumor suppressor gene reexpression in acute myeloid leukemia by targeting directly DNMT3A and 3B and indirectly DNMT1

(2009) R. Garzon et al.   BLOOD

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Epigenetic Silencing of the Tumor Suppressor MicroRNA Hsa-miR-124a Regulates CDK6 Expression and Confers a Poor Prognosis in Acute Lymphoblastic Leukemia

(2009) X. Agirre et al.   CANCER RESEARCH

DNA hypomethylation in the origin and pathogenesis of human diseases

(2009) Igor P. Pogribny et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Low Doses of Bisphenol A Promote Human Seminoma Cell Proliferation by Activating PKA and PKG via a Membrane G-Protein–Coupled Estrogen Receptor

(2009) Adil Bouskine et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

FACS-Assisted Microarray Profiling Implicates Novel Genes and Pathways in Zebrafish Gastrointestinal Tract Development

(2009) Carsten Stuckenholz et al.   GASTROENTEROLOGY

Occupational exposure to bisphenol-A (BPA) and the risk of Self-Reported Male Sexual Dysfunction

(2009) D. Li et al.   HUMAN REPRODUCTION

Glutathione Peroxidase-1 Regulates Mitochondrial Function to Modulate Redox-dependent Cellular Responses

(2009) Diane E. Handy et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A tissue-scale gradient of hydrogen peroxide mediates rapid wound detection in zebrafish

(2009) Philipp Niethammer et al.   NATURE

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Environmental Endocrine Disruptors Promote Adipogenesis in the 3T3-L1 Cell Line through Glucocorticoid Receptor Activation

(2009) Robert M. Sargis et al.   Obesity

Neonatal exposure of male rats to Bisphenol A impairs fertility and expression of sertoli cell junctional proteins in the testis

(2009) Smita Salian et al.   TOXICOLOGY

Genetic and Epigenetic Silencing of MicroRNA-203 Enhances ABL1 and BCR-ABL1 Oncogene Expression

(2008) María J. Bueno et al.   CANCER CELL

Transparent Adult Zebrafish as a Tool for In Vivo Transplantation Analysis

(2008) Richard Mark White et al.   Cell Stem Cell

Immunology and zebrafish: Spawning new models of human disease

(2008) Nathan D. Meeker et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Environmental epigenomics in human health and disease

(2008) Dana C. Dolinoy et al.   ENVIRONMENTAL AND MOLECULAR MUTAGENESIS

Bisphenol A at Environmentally Relevant Doses Inhibits Adiponectin Release from Human Adipose Tissue Explants and Adipocytes

(2008) Eric R. Hugo et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Distinct expression of three estrogen receptors in response to bisphenol A and nonylphenol in male Nile tilapias (Oreochromis niloticus)

(2008) Weiren Huang et al.   FISH PHYSIOLOGY AND BIOCHEMISTRY

MicroRNA-122, a tumor suppressor microRNA that regulates intrahepatic metastasis of hepatocellular carcinoma

(2008) Wei-Chih Tsai et al.   HEPATOLOGY

DNA methylomes, histone codes and miRNAs: Tying it all together

(2008) Sònia Guil et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Bisphenol A and Risk of Metabolic Disorders

(2008) Frederick S. vom Saal   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Association of Urinary Bisphenol A Concentration With Medical Disorders and Laboratory Abnormalities in Adults

(2008) Iain A. Lang   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Post-transcriptional Regulation of Human Pregnane X Receptor by Micro-RNA Affects the Expression of Cytochrome P450 3A4

(2008) Shingo Takagi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MicroRNA-221/222 Negatively Regulates Estrogen Receptorα and Is Associated with Tamoxifen Resistance in Breast Cancer

(2008) Jian-Jun Zhao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MiRNAs, epigenetics, and cancer

(2008) Arefeh Rouhi et al.   MAMMALIAN GENOME

Discovering microRNAs from deep sequencing data using miRDeep

(2008) Marc R Friedländer et al.   NATURE BIOTECHNOLOGY

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

A microRNA DNA methylation signature for human cancer metastasis

(2008) A. Lujambio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exposure of the U.S. Population to Bisphenol A and 4- tertiary -Octylphenol: 2003–2004

(2007) Antonia M. Calafat et al.   ENVIRONMENTAL HEALTH PERSPECTIVES