Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes

Evaluating Patient-Derived Colorectal Cancer Xenografts as Preclinical Models by Comparison with Patient Clinical Data

(2015) M. Nunes et al.   CANCER RESEARCH

Evaluating microRNA profiles reveals discriminative responses following genotoxic or non-genotoxic carcinogen exposure in primary mouse hepatocytes

(2015) Linda Rieswijk et al.   MUTAGENESIS

Multi-walled carbon nanotube-induced gene expression in vitro : Concordance with in vivo studies

(2015) Brandi N. Snyder-Talkington et al.   TOXICOLOGY

A transcriptomics-based hepatotoxicity comparison between the zebrafish embryo and established human and rodent in vitro and in vivo models using cyclosporine A, amiodarone and acetaminophen

(2015) Marja Driessen et al.   TOXICOLOGY LETTERS

Of text and gene – using text mining methods to uncover hidden knowledge in toxicogenomics

(2014) Mikyung Lee et al.   BMC Systems Biology

Colorectal Cancer Cell Lines Are Representative Models of the Main Molecular Subtypes of Primary Cancer

(2014) D. Mouradov et al.   CANCER RESEARCH

Classification of Hepatotoxicants Using HepG2 Cells: A Proof of Principle Study

(2014) Wim F. P. M. Van den Hof et al.   CHEMICAL RESEARCH IN TOXICOLOGY

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Open TG-GATEs: a large-scale toxicogenomics database

(2014) Yoshinobu Igarashi et al.   NUCLEIC ACIDS RESEARCH

ArrayExpress update—simplifying data submissions

(2014) Nikolay Kolesnikov et al.   NUCLEIC ACIDS RESEARCH

The Rat Genome Database 2015: genomic, phenotypic and environmental variations and disease

(2014) Mary Shimoyama et al.   NUCLEIC ACIDS RESEARCH

Common Handling Procedures Conducted in Preclinical Safety Studies Result in Minimal Hepatic Gene Expression Changes in Sprague-Dawley Rats

(2014) Yudong D. He et al.   PLoS One

Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in investigating mechanisms of hepatotoxicity, cell signaling and ADME

(2013) Patricio Godoy et al.   ARCHIVES OF TOXICOLOGY

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Improving the Human Hazard Characterization of Chemicals: A Tox21 Update

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

Rapid Measurement of Intracellular Unbound Drug Concentrations

(2013) André Mateus et al.   MOLECULAR PHARMACEUTICS

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

AlgiMatrix™ Based 3D Cell Culture System as an In-Vitro Tumor Model for Anticancer Studies

(2013) Chandraiah Godugu et al.   PLoS One

Pharmacokinetics explain in vivo/in vitro discrepancies of carcinogen-induced gene expression alterations in rat liver and cultivated hepatocytes

(2012) Markus Schug et al.   ARCHIVES OF TOXICOLOGY

Multi-cell type human liver microtissues for hepatotoxicity testing

(2012) S. Messner et al.   ARCHIVES OF TOXICOLOGY

Benzo[a]pyrene-induced transcriptomic responses in primary hepatocytes and in vivo liver: Toxicokinetics is essential for in vivo–in vitro comparisons

(2012) P. C. E. van Kesteren et al.   ARCHIVES OF TOXICOLOGY

Primary hepatocyte cultures for pharmaco-toxicological studies: at the busy crossroad of various anti-dedifferentiation strategies

(2012) J. Fraczek et al.   ARCHIVES OF TOXICOLOGY

Comparison of genotoxicant-modified transcriptomic responses in conventional and epigenetically stabilized primary rat hepatocytes with in vivo rat liver data

(2012) Tatyana Y. Doktorova et al.   ARCHIVES OF TOXICOLOGY

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data

(2012) Clare Pacini et al.   BIOINFORMATICS

A transcriptomics-based in vitro assay for predicting chemical genotoxicity in vivo

(2012) C. Magkoufopoulou et al.   CARCINOGENESIS

Applications of Connectivity Map in drug discovery and development

(2012) Xiaoyan A. Qu et al.   DRUG DISCOVERY TODAY

Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

(2012) I.-M. Wang et al.   Molecular Systems Biology

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

(2012) Andrea Califano et al.   NATURE GENETICS

Strategies for aggregating gene expression data: The collapseRows R function

(2011) Jeremy A Miller et al.   BMC BIOINFORMATICS

Boosting Signal-to-Noise in Complex Biology: Prior Knowledge Is Power

(2011) Trey Ideker et al.   CELL

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

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

Is My Network Module Preserved and Reproducible?

(2011) Peter Langfelder et al.   PLoS Computational Biology

Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

(2010) Qianqian Zhu et al.   BMC BIOINFORMATICS

Gene expression profiling in primary mouse hepatocytes discriminates true from false-positive genotoxic compounds

(2010) K. Mathijs et al.   MUTAGENESIS

Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways

(2010) Jeremy A. Miller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network analyses in systems pharmacology

(2009) S. I. Berger et al.   BIOINFORMATICS

Toxicology for the twenty-first century

(2009) Thomas Hartung   NATURE

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

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Are animal models predictive for humans?

(2009) Niall Shanks et al.   Philosophy Ethics and Humanities in Medicine