Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects

Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies

(2019) Mohan S. Rao et al.   Frontiers in Genetics

The Power of Resolution: Contextualized Understanding of Biological Responses to Liver Injury Chemicals using High-throughput Transcriptomics and Benchmark Concentration Modeling

(2019) Sreenivasa C Ramaiahgari et al.   TOXICOLOGICAL SCIENCES

The next generation blueprint of computational toxicology at the U.S. Environmental Protection Agency

(2019) Russell S Thomas et al.   TOXICOLOGICAL SCIENCES

Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity

(2019) Heather L. Ciallella et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Impact of metal oxide nanoparticles on in vitro DNA amplification

(2019) Chun-Hui Gao et al.   PeerJ

An Overview of Machine Learning and Big Data for Drug Toxicity Evaluation

(2019) Andy H. Vo et al.   CHEMICAL RESEARCH IN TOXICOLOGY

INfORM: Inference of NetwOrk Response Modules

(2018) Veer Singh Marwah et al.   BIOINFORMATICS

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow

(2018) Jason R Phillips et al.   BIOINFORMATICS

Toxicogenomics: A 2020 Vision

(2018) Zhichao Liu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Generation and manipulation of hydrogel microcapsules by droplet-based microfluidics for mammalian cell culture

(2017) Haishui Huang et al.   LAB ON A CHIP

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Effective detection of variation in single-cell transcriptomes using MATQ-seq

(2017) Kuanwei Sheng et al.   NATURE METHODS

On the pivotal role of dose for particle toxicology and risk assessment: exposure is a poor surrogate for delivered dose

(2017) Otmar Schmid et al.   Particle and Fibre Toxicology

A generic Transcriptomics Reporting Framework (TRF) for ‘omics data processing and analysis

(2017) Timothy W. Gant et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

The challenge of the application of 'omics technologies in chemicals risk assessment: Background and outlook

(2017) Ursula G. Sauer et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Single-Cell RNA Sequencing: Unraveling the Brain One Cell at a Time

(2017) Dimitry Ofengeim et al.   TRENDS IN MOLECULAR MEDICINE

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling

(2017) Natasha M. Sanabria et al.   JOURNAL OF NANOBIOTECHNOLOGY

Role of omics techniques in the toxicity testing of nanoparticles

(2017) Eleonore Fröhlich   JOURNAL OF NANOBIOTECHNOLOGY

Microfluidic Platform for Cell Isolation and Manipulation Based on Cell Properties

(2017) Caffiyar Yousuff et al.   Micromachines

A Pipeline for High-Throughput Concentration Response Modeling of Gene Expression for Toxicogenomics

(2017) John S. House et al.   Frontiers in Genetics

Single-Cell mRNA Sequencing in Cancer Research: Integrating the Genomic Fingerprint

(2017) Sören Müller et al.   Frontiers in Genetics

Revising REACH guidance on information requirements and chemical safety assessment for engineered nanomaterials for aquatic ecotoxicity endpoints: recommendations from the EnvNano project

(2017) Steffen Foss Hansen et al.   Environmental Sciences Europe

A trichostatin A expression signature identified by TempO-Seq targeted whole transcriptome profiling

(2017) Joanne M. Yeakley et al.   PLoS One

Recommended approaches in the application of toxicogenomics to derive points of departure for chemical risk assessment

(2016) Reza Farmahin et al.   ARCHIVES OF TOXICOLOGY

Surface modification does not influence the genotoxic and inflammatory effects of TiO2nanoparticles after pulmonary exposure by instillation in mice

(2016) Håkan Wallin et al.   MUTAGENESIS

Multi-walled carbon nanotube physicochemical properties predict pulmonary inflammation and genotoxicity

(2016) Sarah S. Poulsen et al.   Nanotoxicology

CEBS: a comprehensive annotated database of toxicological data

(2016) Isabel A. Lea et al.   NUCLEIC ACIDS RESEARCH

Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors

(2016) Jennifer Yang et al.   NUCLEIC ACIDS RESEARCH

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

High-throughput, quantitative assessment of the effects of low-dose silica nanoparticles on lung cells: grasping complex toxicity with a great depth of field

(2015) Cédric Pisani et al.   BMC GENOMICS

Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water

(2015) Ivy Moffat et al.   CRITICAL REVIEWS IN TOXICOLOGY

Novel Transcription Factor Variants through RNA-Sequencing: The Importance of Being “Alternative”

(2015) Margherita Scarpato et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Practical approach to determine sample size for building logistic prediction models using high-throughput data

(2015) Dae-Soon Son et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Global transcriptomic analysis of model human cell lines exposed to surface-modified gold nanoparticles: the effect of surface chemistry

(2015) E. M. Grzincic et al.   Nanoscale

Extensive temporal transcriptome and microRNA analyses identify molecular mechanisms underlying mitochondrial dysfunction induced by multi-walled carbon nanotubes in human lung cells

(2015) Penny Nymark et al.   Nanotoxicology

Nano-risk Science: application of toxicogenomics in an adverse outcome pathway framework for risk assessment of multi-walled carbon nanotubes

(2015) Sarah Labib et al.   Particle and Fibre Toxicology

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

A Single Aspiration of Rod-like Carbon Nanotubes Induces Asbestos-like Pulmonary Inflammation Mediated in Part by the IL-1 Receptor

(2015) Elina M. Rydman et al.   TOXICOLOGICAL SCIENCES

MWCNTs of different physicochemical properties cause similar inflammatory responses, but differences in transcriptional and histological markers of fibrosis in mouse lungs

(2015) Sarah S. Poulsen et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Changes in Caco-2 cells transcriptome profiles upon exposure to gold nanoparticles

(2015) Edyta Bajak et al.   TOXICOLOGY LETTERS

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

Impact of Genomics Platform and Statistical Filtering on Transcriptional Benchmark Doses (BMD) and Multiple Approaches for Selection of Chemical Point of Departure (PoD)

(2015) A. Francina Webster et al.   PLoS One

High variability of genomic instability and gene expression profiling in different HeLa clones

(2015) Annalisa Frattini et al.   Scientific Reports

Multi-walled carbon nanotube length as a critical determinant of bioreactivity with primary human pulmonary alveolar cells

(2014) Sinbad Sweeney et al.   CARBON

A secretomics analysis reveals major differences in the macrophage responses towards different types of carbon nanotubes

(2014) Jaana Palomäki et al.   Nanotoxicology

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

(2014) Qiaonan Duan et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

Widespread Nanoparticle-Assay Interference: Implications for Nanotoxicity Testing

(2014) Kimberly J. Ong et al.   PLoS One

Gold Nanoparticle Interference Study during the Isolation, Quantification, Purity and Integrity Analysis of RNA

(2014) Natasha M. Sanabria et al.   PLoS One

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing

(2014) M.-C. W. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Understanding Interactions of Functionalized Nanoparticles with Proteins: A Case Study on Lactate Dehydrogenase

(2014) Oliver Stueker et al.   Small

mRNA and miRNA Regulatory Networks Reflective of Multi-Walled Carbon Nanotube-Induced Lung Inflammatory and Fibrotic Pathologies in Mice

(2014) Julian Dymacek et al.   TOXICOLOGICAL SCIENCES

Nanoparticles Inhibit DNA Replication by Binding to DNA: Modeling and Experimental Validation

(2013) Kungang Li et al.   ACS Nano

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

(2013) Yuwen Liu et al.   BIOINFORMATICS

Cellular Targets and Mechanisms in the Cytotoxic Action of Non-biodegradable Engineered Nanoparticles

(2013) Eleonore Fröhlich   CURRENT DRUG METABOLISM

Cellular uptake of nanoparticles as determined by particle properties, experimental conditions, and cell type

(2013) Katja Kettler et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Transcriptomic Analysis Reveals Novel Mechanistic Insight into Murine Biological Responses to Multi-Walled Carbon Nanotubes in Lungs and Cultured Lung Epithelial Cells

(2013) Sarah Søs Poulsen et al.   PLoS One

Case study on the utility of hepatic global gene expression profiling in the risk assessment of the carcinogen furan

(2013) Anna Francina Jackson et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Hepatic and Pulmonary Toxicogenomic Profiles in Mice Intratracheally Instilled With Carbon Black Nanoparticles Reveal Pulmonary Inflammation, Acute Phase Response, and Alterations in Lipid Homeostasis

(2012) Julie A. Bourdon et al.   TOXICOLOGICAL SCIENCES

Sample Size Calculations

(2011) Marlies Noordzij et al.   NEPHRON CLINICAL PRACTICE

Toxicity assessment of nanomaterials: methods and challenges

(2010) Alok Dhawan et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Power and sample size estimation in microarray studies

(2010) Wei-Jiun Lin et al.   BMC BIOINFORMATICS

Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

(2010) James H Bullard et al.   BMC BIOINFORMATICS

Toxicogenomics using yeast DNA microarrays

(2010) Daisuke Yasokawa et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Influence of nanoscale surface topography on protein adsorption and cellular response

(2010) Megan S. Lord et al.   Nano Today

A critical review of the biological mechanisms underlying thein vivoandin vitrotoxicity of carbon nanotubes: The contribution of physico-chemical characteristics

(2010) Helinor J. Johnston et al.   Nanotoxicology

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

(2010)   NATURE BIOTECHNOLOGY

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

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

Nanoscale and Fine Zinc Oxide Particles: Can in Vitro Assays Accurately Forecast Lung Hazards following Inhalation Exposures?

(2009) D. B. Warheit et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Effect of Nanoparticles on Protein Folding and Fibrillogenesis

(2009) Li Fei et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Importance of randomization in microarray experimental designs with Illumina platforms

(2009) Ricardo A. Verdugo et al.   NUCLEIC ACIDS RESEARCH

Toward a Public Toxicogenomics Capability for Supporting Predictive Toxicology: Survey of Current Resources and Chemical Indexing of Experiments in GEO and ArrayExpress

(2009) ClarLynda R. Williams-Devane et al.   TOXICOLOGICAL SCIENCES

Safety for people and environment

(2009) Heidi Foth   TOXICOLOGY LETTERS

Getting Started in Gene Expression Microarray Analysis

(2009) Donna K. Slonim et al.   PLoS Computational Biology

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Current in vitro methods in nanoparticle risk assessment: Limitations and challenges

(2008) Alexandra Kroll et al.   EUROPEAN JOURNAL OF PHARMACEUTICS AND BIOPHARMACEUTICS

Can in vitro assays substitute for in vivo studies in assessing the pulmonary hazards of fine and nanoscale materials?

(2008) Christie M. Sayes et al.   JOURNAL OF NANOPARTICLE RESEARCH

Protein-nanoparticle interactions

(2008) Iseult Lynch et al.   Nano Today

Carbon nanotubes introduced into the abdominal cavity of mice show asbestos-like pathogenicity in a pilot study

(2008) Craig A. Poland et al.   Nature Nanotechnology

Limitations and relative utility of screening assays to assess engineered nanoparticle toxicity in a human cell line

(2008) N.A. Monteiro-Riviere et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Single walled carbon nanotubes induce indirect cytotoxicity by medium depletion in A549 lung cells

(2008) A. Casey et al.   TOXICOLOGY LETTERS