Transcriptional analysis of endocrine disruption using zebrafish and massively parallel sequencing

Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood

(2014) Kenneth G Frey et al.   BMC GENOMICS

The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light

(2014) Zohar Ben-Moshe et al.   NUCLEIC ACIDS RESEARCH

Biodegradation of Endocrine Disruptors in Solid-Liquid Two-Phase Partitioning Systems by Enrichment Cultures

(2013) Richard Villemur et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular Mechanisms of Toxicity of Silver Nanoparticles in Zebrafish Embryos

(2013) Ronny van Aerle et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

The new sequencer on the block: comparison of Life Technology’s Proton sequencer to an Illumina HiSeq for whole-exome sequencing

(2013) Joseph F. Boland et al.   HUMAN GENETICS

The Effects of Nanomaterials as Endocrine Disruptors

(2013) Ivo Iavicoli et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Contaminants and impoSEX: transcriptomics of contaminant-induced sex change

(2013) Robert W. Chapman et al.   MOLECULAR ECOLOGY

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Genomics: Zebrafish earns its stripes

(2013) Alexander F. Schier   NATURE

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

(2013) Kerstin Howe et al.   NATURE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s

(2013) D. R. Nelson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Low Concentrations of Silver Nanoparticles in Biosolids Cause Adverse Ecosystem Responses under Realistic Field Scenario

(2013) Benjamin P. Colman et al.   PLoS One

Rapid 16S rRNA Next-Generation Sequencing of Polymicrobial Clinical Samples for Diagnosis of Complex Bacterial Infections

(2013) Stephen J. Salipante et al.   PLoS One

Genome-Wide Identification of Molecular Pathways and Biomarkers in Response to Arsenic Exposure in Zebrafish Liver

(2013) Hongyan Xu et al.   PLoS One

Molecular Analysis of Endocrine Disruption in Hornyhead Turbot at Wastewater Outfalls in Southern California Using a Second Generation Multi-Species Microarray

(2013) Michael E. Baker et al.   PLoS One

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

What are the physiological estrogens?

(2013) Michael E. Baker   STEROIDS

The mineralocorticoid signaling pathway throughout development: Expression, regulation and pathophysiological implications

(2012) Laetitia Martinerie et al.   BIOCHIMIE

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

The Ubiquitous Mineralocorticoid Receptor: Clinical Implications

(2012) Urseline A. Hawkins et al.   CURRENT HYPERTENSION REPORTS

Going beyond five bases in DNA sequencing

(2012) Jonas Korlach et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Progress in Ion Torrent semiconductor chip based sequencing

(2012) Barry Merriman et al.   ELECTROPHORESIS

Biosensor Zebrafish Provide New Insights into Potential Health Effects of Environmental Estrogens

(2012) Okhyun Lee et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

Rapid Development of Microsatellite Markers for the Endangered Fish Schizothorax biddulphi (Günther) Using Next Generation Sequencing and Cross-Species Amplification

(2012) Wei Luo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptomics andin vivotests reveal novel mechanisms underlying endocrine disruption in an ecological sentinel,Nucella lapillus

(2012) Sonia Pascoal et al.   MOLECULAR ECOLOGY

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

3D Models of MBP, a Biologically Active Metabolite of Bisphenol A, in Human Estrogen Receptor α and Estrogen Receptor β

(2012) Michael E. Baker et al.   PLoS One

Brain on stress: How the social environment gets under the skin

(2012) B. S. McEwen   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Steroid biosynthesis and prostate cancer

(2012) Nima Sharifi et al.   STEROIDS

Insights from the structure of estrogen receptor into the evolution of estrogens: Implications for endocrine disruption

(2011) Michael E. Baker   BIOCHEMICAL PHARMACOLOGY

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Identification and correction of systematic error in high-throughput sequence data

(2011) Frazer Meacham et al.   BMC BIOINFORMATICS

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

(2011) Bonnie A Fraser et al.   BMC GENOMICS

Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites

(2011) Aaron W. Aday et al.   DEVELOPMENTAL BIOLOGY

Visualization of Estrogen Receptor Transcriptional Activation in Zebrafish

(2011) Daniel A. Gorelick et al.   ENDOCRINOLOGY

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

(2011) Håvard Aanes et al.   GENOME RESEARCH

Sequencing technologies and genome sequencing

(2011) Chandra Shekhar Pareek et al.   JOURNAL OF APPLIED GENETICS

Disruption of androgen receptor signaling in males by environmental chemicals

(2011) Doug C. Luccio-Camelo et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

Bisphenol A: An endocrine disruptor with widespread exposure and multiple effects

(2011) Beverly S. Rubin   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Performance comparison of whole-genome sequencing platforms

(2011) Hugo Y K Lam et al.   NATURE BIOTECHNOLOGY

Origins of theE. coliStrain Causing an Outbreak of Hemolytic–Uremic Syndrome in Germany

(2011) David A. Rasko et al.   NEW ENGLAND JOURNAL OF MEDICINE

Comparison of Sequence Reads Obtained from Three Next-Generation Sequencing Platforms

(2011) Shingo Suzuki et al.   PLoS One

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Structural Overview of the Nuclear Receptor Superfamily: Insights into Physiology and Therapeutics

(2010) Pengxiang Huang et al.   Annual Review of Physiology

Does Breast Cancer Start in the Womb?

(2010) Ana M. Soto et al.   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

RNA deep sequencing of the Atlantic cod transcriptome

(2010) Steinar D. Johansen et al.   Comparative Biochemistry and Physiology D-Genomics & Proteomics

What are nuclear receptor ligands?

(2010) Frances M. Sladek   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Nuclear hormone receptors in chordates

(2010) Stéphanie Bertrand et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

The gene regulatory networks controlled by estrogens

(2010) Hui Gao et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Evolution of promiscuous nuclear hormone receptors: LXR, FXR, VDR, PXR, and CAR

(2010) Matthew D. Krasowski et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

De novo assembly and analysis of RNA-seq data

(2010) Gordon Robertson et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

The Origin of the Haitian Cholera Outbreak Strain

(2010) Chen-Shan Chin et al.   NEW ENGLAND JOURNAL OF MEDICINE

ZFIN: enhancements and updates to the zebrafish model organism database

(2010) Y. Bradford et al.   NUCLEIC ACIDS RESEARCH

Advances in pharmacogenomics technologies

(2010) C Ramana Bhasker et al.   PHARMACOGENOMICS

Serum bisphenol A pharmacokinetics and prostate neoplastic responses following oral and subcutaneous exposures in neonatal Sprague–Dawley rats

(2010) Gail S. Prins et al.   REPRODUCTIVE TOXICOLOGY

Spatial and Temporal Variations of Groundwater Arsenic in South and Southeast Asia

(2010) S. Fendorf et al.   SCIENCE

ERβ: recent understanding of estrogen signaling

(2010) Nobuhiro Sugiyama et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Massively Parallel Sequencing: The Next Big Thing in Genetic Medicine

(2009) Tracy Tucker et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Generation of a fluorescent transgenic zebrafish for detection of environmental estrogens

(2009) Hao Chen et al.   AQUATIC TOXICOLOGY

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

(2009) Likun Wang et al.   BIOINFORMATICS

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

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

Parallel DNA pyrosequencing unveils new zebrafish microRNAs

(2009) Ana R Soares et al.   BMC GENOMICS

Next-Generation Sequencing: From Basic Research to Diagnostics

(2009) K. V. Voelkerding et al.   CLINICAL CHEMISTRY

Bisphenol-A and the Great Divide: A Review of Controversies in the Field of Endocrine Disruption

(2009) Laura N. Vandenberg et al.   ENDOCRINE REVIEWS

Endocrine-Disrupting Chemicals: An Endocrine Society Scientific Statement

(2009) Evanthia Diamanti-Kandarakis et al.   ENDOCRINE REVIEWS

Sexual Reprogramming and Estrogenic Sensitization in Wild Fish Exposed to Ethinylestradiol

(2009) Anke Lange et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

PHARMACEUTICAL METABOLITES IN THE ENVIRONMENT: ANALYTICAL CHALLENGES AND ECOLOGICAL RISKS

(2009) Mary D. Celiz et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Reconsidering the Roles of the Mineralocorticoid Receptor

(2009) John W. Funder   HYPERTENSION

Interpreting endocrine disruption from an integrative biology perspective

(2009) Ana M. Soto et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Role of nutrition and environmental endocrine disrupting chemicals during the perinatal period on the aetiology of obesity☆

(2009) Jerrold J. Heindel et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Deep sequencing of the zebrafish transcriptome response to mycobacterium infection

(2009) Zoltán Hegedűs et al.   MOLECULAR IMMUNOLOGY

Transcriptome sequencing to detect gene fusions in cancer

(2009) Christopher A. Maher et al.   NATURE

A small-cell lung cancer genome with complex signatures of tobacco exposure

(2009) Erin D. Pleasance et al.   NATURE

How to map billions of short reads onto genomes

(2009) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

A critical analysis of the biological impacts of plasticizers on wildlife

(2009) J. Oehlmann et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Independent elaboration of steroid hormone signaling pathways in metazoans

(2009) G. V. Markov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exposure and effects assessment of persistent organohalogen contaminants in arctic wildlife and fish

(2009) Robert J. Letcher et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Glucocorticoid and mineralocorticoid action: Why should we consider influences by environmental chemicals?

(2008) Alex Odermatt et al.   BIOCHEMICAL PHARMACOLOGY

Zebrafish (Danio rerio) as a model organism for investigating endocrine disruption

(2008) Helmut Segner   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY

Analysis of Endocrine Disruption in Southern California Coastal Fish Using an Aquatic Multispecies Microarray

(2008) Michael E. Baker et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

A critical evaluation of the environmental risk assessment for plasticizers in the freshwater environment in Europe, with special emphasis on bisphenol A and endocrine disruption

(2008) Jörg Oehlmann et al.   ENVIRONMENTAL RESEARCH

Reproductive Disruption in Fish Downstream from an Estrogenic Wastewater Effluent

(2008) Alan M. Vajda et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Fetal and postnatal environmental exposures and reproductive health effects in the male: recent findings

(2008) Shanna H. Swan   FERTILITY AND STERILITY

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Keeping Up With the Next Generation

(2008) John R. ten Bosch et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

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

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

Ultra-high-throughput sequencing, microarray-based genomic selection and pharmacogenomics

(2007) Gary Hardiman   PHARMACOGENOMICS