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

Editor’s Highlight: Comparative Dose-Response Analysis of Liver and Kidney Transcriptomic Effects of Trichloroethylene and Tetrachloroethylene in B6C3F1 Mouse

(2017) Yi-Hui Zhou et al.   TOXICOLOGICAL SCIENCES

In vitro cardiotoxicity assessment of environmental chemicals using an organotypic human induced pluripotent stem cell-derived model

(2017) Oksana Sirenko et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

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

tcpl: the ToxCast pipeline for high-throughput screening data

(2016) Dayne L. Filer et al.   BIOINFORMATICS

A chemical–biological similarity-based grouping of complex substances as a prototype approach for evaluating chemical alternatives

(2016) Fabian A. Grimm et al.   GREEN CHEMISTRY

High-Content Assay Multiplexing for Toxicity Screening in Induced Pluripotent Stem Cell-Derived Cardiomyocytes and Hepatocytes

(2015) Fabian Alexander Grimm et al.   ASSAY AND DRUG DEVELOPMENT TECHNOLOGIES

Hypothesis testing at the extremes: fast and robust association for high-throughput data

(2015) Y.-H. Zhou et al.   BIOSTATISTICS

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

A novel transcriptomics based in vitro method to compare and predict hepatotoxicity based on mode of action

(2015) K. Nadira De Abrew et al.   TOXICOLOGY

Dose-Response Analysis Using R

(2015) Christian Ritz et al.   PLoS One

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

(2014) S. Anders et al.   BIOINFORMATICS

Standardizing Benchmark Dose Calculations to Improve Science-Based Decisions in Human Health Assessments

(2014) Jessica A. Wignall et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

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

RNA-Seq optimization with eQTL gold standards

(2013) Shannon E Ellis et al.   BMC GENOMICS

Temporal Concordance Between Apical and Transcriptional Points of Departure for Chemical Risk Assessment

(2013) Russell S. Thomas et al.   TOXICOLOGICAL SCIENCES

Assessment of beating parameters in human induced pluripotent stem cells enables quantitative in vitro screening for cardiotoxicity

(2013) Oksana Sirenko et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Predicting Drug-Induced Hepatotoxicity Using QSAR and Toxicogenomics Approaches

(2011) Yen Low et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Discovery and Preclinical Validation of Drug Indications Using Compendia of Public Gene Expression Data

(2011) M. Sirota et al.   Science Translational Medicine

Ruffus: a lightweight Python library for computational pipelines

(2010) Leo Goodstadt   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Application of Transcriptional Benchmark Dose Values in Quantitative Cancer and Noncancer Risk Assessment

(2010) Russell S. Thomas et al.   TOXICOLOGICAL SCIENCES

The Japanese toxicogenomics project: Application of toxicogenomics

(2009) Takeki Uehara et al.   MOLECULAR NUTRITION & FOOD RESEARCH

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Drug Target Identification Using Side-Effect Similarity

(2008) M. Campillos et al.   SCIENCE

A toxicogenomics approach for early assessment of potential non-genotoxic hepatocarcinogenicity of chemicals in rats

(2008) Takeki Uehara et al.   TOXICOLOGY