High-Throughput Transcriptomics Platform for Screening Environmental Chemicals

Deciphering the Molecular Mechanisms Sustaining the Estrogenic Activity of the Two Major Dietary Compounds Zearalenone and Apigenin in ER-Positive Breast Cancer Cell Lines

(2019) Sylvain Lecomte et al.   Nutrients

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

The NCATS BioPlanet – An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics

(2019) Ruili Huang et al.   Frontiers in Pharmacology

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Utility of In Vitro Bioactivity as a Lower Bound Estimate of In Vivo Adverse Effect Levels and in Risk-Based Prioritization

(2019) Katie Paul Friedman et al.   TOXICOLOGICAL SCIENCES

Comparison of base-line and chemical-induced transcriptomic responses in HepaRG and RPTEC/TERT1 cells using TempO-Seq

(2018) Alice Limonciel et al.   ARCHIVES OF TOXICOLOGY

Recommendation on test readiness criteria for new approach methods in toxicology: Exemplified for developmental neurotoxicity

(2018) Anna Bal-Price   ALTEX-Alternatives to Animal Experimentation

BMDExpress 2: enhanced transcriptomic dose-response analysis workflow

(2018) Jason R Phillips et al.   BIOINFORMATICS

Multi-dimensional in vitro bioactivity profiling for grouping of glycol ethers

(2018) Fabian A. Grimm et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

Transcriptomics in toxicology

(2017) Pius Joseph   FOOD AND CHEMICAL TOXICOLOGY

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

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

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

ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology

(2016) Ann M. Richard et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Grouping 34 Chemicals Based on Mode of Action Using Connectivity Mapping

(2016) K. Nadira De Abrew et al.   TOXICOLOGICAL SCIENCES

Analysis of the Effects of Cell Stress and Cytotoxicity onIn VitroAssay Activity Across a Diverse Chemical and Assay Space

(2016) Richard Judson et al.   TOXICOLOGICAL SCIENCES

Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

(2016) Natalia Ryan et al.   TOXICOLOGICAL SCIENCES

Transcriptomic Effects of Estrogen Starvation and Induction in the MCF7 Cells. The Meta-analysis of Microarray Results

(2015) Anna Stanislawska-Sachadyn et al.   CURRENT PHARMACEUTICAL BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanisms

(2014) Nicole C Kleinstreuer et al.   NATURE BIOTECHNOLOGY

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

Transcriptomic profiling of rat liver samples in a comprehensive study design by RNA-Seq

(2014) Binsheng Gong et al.   Scientific Data

Profiling 976 ToxCast Chemicals across 331 Enzymatic and Receptor Signaling Assays

(2013) Nisha S. Sipes et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Beyond modules and hubs: the potential of gene coexpression networks for investigating molecular mechanisms of complex brain disorders

(2013) C. Gaiteri et al.   GENES BRAIN AND BEHAVIOR

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Gene batteries and synexpression groups applied in a multivariate statistical approach to dose–response analysis of toxicogenomic data

(2013) C. Parfett et al.   REGULATORY TOXICOLOGY AND PHARMACOLOGY

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

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

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Estimating Toxicity-Related Biological Pathway Altering Doses for High-Throughput Chemical Risk Assessment

(2011) Richard S. Judson et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Adaptation of High-Throughput Screening in Drug Discovery—Toxicological Screening Tests

(2011) Paweł Szymański et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Use of transcriptomics in understanding mechanisms of drug-induced toxicity

(2010) Yuxia Cui et al.   PHARMACOGENOMICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

In Vitro Screening of Environmental Chemicals for Targeted Testing Prioritization: The ToxCast Project

(2009) Richard S. Judson et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1

(2009) David A. Barbie et al.   NATURE

Use of toxicogenomics to understand mechanisms of drug-induced hepatotoxicity during drug discovery and development

(2008) Eric A.G. Blomme et al.   TOXICOLOGY LETTERS