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

Systems Toxicology: From Basic Research to Risk Assessment

(2014) Shana J. Sturla et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Distinctive Metabolite Profiles in In-Migrating Sockeye Salmon Suggest Sex-Linked Endocrine Perturbation

(2014) Jonathan P. Benskin et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Development of a Genomic DNA Reference Material Panel for Rett Syndrome (MECP2-Related Disorders) Genetic Testing

(2014) Lisa V. Kalman et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Measured and Modeled Toxicokinetics in Cultured Fish Cells and Application to In Vitro - In Vivo Toxicity Extrapolation

(2014) Julita Stadnicka-Michalak et al.   PLoS One

Maternal Experience with Predation Risk Influences Genome-Wide Embryonic Gene Expression in Threespined Sticklebacks (Gasterosteus aculeatus)

(2014) Brett C. Mommer et al.   PLoS One

Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio)

(2014) Rong-Lin Wang et al.   PLoS One

Development of a Standard Reference Material for Metabolomics Research

(2013) Karen W. Phinney et al.   ANALYTICAL CHEMISTRY

Impacts of 17α-ethynylestradiol exposure on metabolite profiles of zebrafish (Danio rerio) liver cells

(2013) Quincy Teng et al.   AQUATIC TOXICOLOGY

Recent developments in in vitro toxicology: perspectives of European research and Tox21

(2013) R. Marchan et al.   ARCHIVES OF TOXICOLOGY

EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments

(2013) Ning Leng et al.   BIOINFORMATICS

RNA-seq differential expression studies: more sequence or more replication?

(2013) Yuwen Liu et al.   BIOINFORMATICS

Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki

(2013) Kevin T Bilyk et al.   BMC GENOMICS

Environmental chemical stressors as epigenome modifiers: a new horizon in assessment of toxicological effects

(2013) Heqing Shen et al.   CHINESE SCIENCE BULLETIN

Robustness and sensitivity of weighting and aggregation in constructing composite indices

(2013) Melissa J. Dobbie et al.   ECOLOGICAL INDICATORS

Environmental estrogens in an urban aquatic ecosystem: I. Spatial and temporal occurrence of estrogenic activity in effluent-dominated systems

(2013) Dalma Martinovic-Weigelt et al.   ENVIRONMENT INTERNATIONAL

Improving the Human Hazard Characterization of Chemicals: A Tox21 Update

(2013) Raymond R. Tice et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

1-D and 2-D NMR-based metabolomics of earthworms exposed to endosulfan and endosulfan sulfate in soil

(2013) Jimmy Yuk et al.   ENVIRONMENTAL POLLUTION

Estrogen-like Effects in Male Goldfish Co-exposed to Fluoxetine and 17 Alpha-Ethinylestradiol

(2013) Helena C. Silva de Assis et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Gene Expression of Fathead Minnows (Pimephales promelas) Exposed to Two Types of Treated Municipal Wastewater Effluents

(2013) Doris. E. Vidal-Dorsch et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Guidelines for the design, analysis and interpretation of ‘omics’ data: focus on human endometrium

(2013) Signe Altmäe et al.   HUMAN REPRODUCTION UPDATE

The characterization and certification of a quantitative reference material forLegionelladetection and quantification by qPCR

(2013) M. Baume et al.   JOURNAL OF APPLIED MICROBIOLOGY

A survey of Canadian mechanical pulp and paper mill effluents: Insights concerning the potential to affect fish reproduction

(2013) Tibor G. Kovacs et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART A-TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING

The Plasma Proteome Identifies Expected and Novel Proteins Correlated with Micronutrient Status in Undernourished Nepalese Children

(2013) Robert N. Cole et al.   JOURNAL OF NUTRITION

Blood Plasma Reference Material: A Global Resource for Proteomic Research

(2013) Johan Malm et al.   JOURNAL OF PROTEOME RESEARCH

Functional decorations: post-translational modifications and heart disease delineated by targeted proteomics

(2013) Kiersten A Liddy et al.   Genome Medicine

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Systematic comparison of RNA-Seq normalization methods using measurement error models

(2012) Z. Sun et al.   BIOINFORMATICS

RNA-SeQC: RNA-seq metrics for quality control and process optimization

(2012) David S. DeLuca et al.   BIOINFORMATICS

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-Sequencing

(2012) José A Robles et al.   BMC GENOMICS

Application of a Label-free, Gel-free Quantitative Proteomics Method for Ecotoxicological Studies of Small Fish Species

(2012) K. J. Ralston-Hooper et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Proteomic Profiles of White Sucker (Catostomus commersonii) Sampled from within the Thunder Bay Area of Concern Reveal Up-Regulation of Proteins Associated with Tumor Formation and Exposure to Environmental Estrogens

(2012) Denina B. D. Simmons et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Interactive effects of inbreeding and endocrine disruption on reproduction in a model laboratory fish

(2012) Lisa K. Bickley et al.   Evolutionary Applications

Challenges for Biological Interpretation of Environmental Proteomics Data in Non-model Organisms

(2012) W. Wesley Dowd   INTEGRATIVE AND COMPARATIVE BIOLOGY

Exploring Androgen-Regulated Pathways in Teleost Fish Using Transcriptomics and Proteomics

(2012) Christopher J. Martyniuk et al.   INTEGRATIVE AND COMPARATIVE BIOLOGY

Salinity- and population-dependent genome regulatory response during osmotic acclimation in the killifish (Fundulus heteroclitus) gill

(2012) A. Whitehead et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

Hepatic Protein Expression Networks Associated with Masculinization in the Female Fathead Minnow (Pimephales promelas)

(2012) Christopher J. Martyniuk et al.   JOURNAL OF PROTEOME RESEARCH

Post-Translational Modification of Human Heat Shock Factors and Their Functions: A Recent Update by Proteomic Approach

(2012) Yan-Ming Xu et al.   JOURNAL OF PROTEOME RESEARCH

Linking proteome responses with physiological and biochemical effects in herbicide-exposed Chlamydomonas reinhardtii

(2012) Holger Nestler et al.   Journal of Proteomics

A critical evaluation of in vitro cell culture models for high-throughput drug screening and toxicity

(2012) Anna Astashkina et al.   PHARMACOLOGY & THERAPEUTICS

Setting an Optimal α That Minimizes Errors in Null Hypothesis Significance Tests

(2012) Joseph F. Mudge et al.   PLoS One

Applications for next-generation sequencing in fish ecotoxicogenomics

(2012) Alvine C. Mehinto et al.   Frontiers in Genetics

Normalization, testing, and false discovery rate estimation for RNA-sequencing data

(2011) J. Li et al.   BIOSTATISTICS

Conserved toxic responses across divergent phylogenetic lineages: a meta-analysis of the neurotoxic effects of RDX among multiple species using toxicogenomics

(2011) Natàlia Garcia-Reyero et al.   ECOTOXICOLOGY

Advancing the Omics in aquatic toxicology: SETAC North America 31st Annual Meeting

(2011) Nancy D. Denslow et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Metabolomics Reveals Target and Off-Target Toxicities of a Model Organophosphate Pesticide to Roach (Rutilus rutilus): Implications for Biomonitoring

(2011) Andrew D. Southam et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

(2011) Zhou Li et al.   JOURNAL OF PROTEOME RESEARCH

A Bayesian Mixture Model for Comparative Spectral Count Data in Shotgun Proteomics

(2011) James G. Booth et al.   MOLECULAR & CELLULAR PROTEOMICS

Web-based inference of biological patterns, functions and pathways from metabolomic data using MetaboAnalyst

(2011) Jianguo Xia et al.   Nature Protocols

Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry

(2011) Warwick B Dunn et al.   Nature Protocols

Less label, more free: Approaches in label-free quantitative mass spectrometry

(2011) Karlie A. Neilson et al.   PROTEOMICS

The speciation and physico-chemical forms of metals in surface waters and sediments

(2010) Jacek Namieśnik et al.   CHEMICAL SPECIATION AND BIOAVAILABILITY

Cell culture metabolomics: applications and future directions

(2010) Miroslava Čuperlović-Culf et al.   DRUG DISCOVERY TODAY

Mixtures of similarly acting compounds in Daphnia magna: From gene to metabolite and beyond

(2010) Tine Vandenbrouck et al.   ENVIRONMENT INTERNATIONAL

Systems biology: Leading the revolution in ecotoxicology

(2010) Natàlia Garcia-Reyero et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Presence of natural and anthropogenic organic contaminants and potential fish health impacts along two river gradients in Alberta, Canada

(2010) Ken M. Jeffries et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Some common misunderstandings in chemometrics

(2010) Karin Kjeldahl et al.   JOURNAL OF CHEMOMETRICS

Modification-specific proteomics in plant biology

(2010) A. Jimmy Ytterberg et al.   Journal of Proteomics

A practical approach to RT-qPCR—Publishing data that conform to the MIQE guidelines

(2010) Sean Taylor et al.   METHODS

Responses of white sucker (Catostomus commersoni) to 20 years of process and waste treatment changes at a bleached kraft pulp mill, and to mill shutdown

(2009) L.K. Bowron et al.   AQUATIC TOXICOLOGY

Genomic approaches in the identification of hypoxia biomarkers in model fish species

(2009) Ziping Zhang et al.   JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY

Statistical Design of Quantitative Mass Spectrometry-Based Proteomic Experiments

(2009) Ann L. Oberg et al.   JOURNAL OF PROTEOME RESEARCH

Spectral relative standard deviation: a practical benchmark in metabolomics

(2008) Helen M. Parsons et al.   ANALYST

Direct Effects, Compensation, and Recovery in Female Fathead Minnows Exposed to a Model Aromatase Inhibitor

(2008) Daniel L. Villeneuve et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Investigating Compensation and Recovery of Fathead Minnow (Pimephales promelas) Exposed to 17α-Ethynylestradiol with Metabolite Profiling

(2008) D. R. Ekman et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Profiling lipid metabolites yields unique information on sex- and time-dependent responses of fathead minnows (Pimephales promelas) exposed to 17α-ethynylestradiol

(2008) Drew R. Ekman et al.   Metabolomics

Bayesian Nonparametric Model for the Validation of Peptide Identification in Shotgun Proteomics

(2008) Jiyang Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY