[HTML][HTML] Network and pathway analysis of toxicogenomics data

G Barel, R Herwig - Frontiers in Genetics, 2018 - frontiersin.org
Toxicogenomics is the study of the molecular effects of chemical, biological and physical
agents in biological systems, with the aim of elucidating toxicological mechanisms, building …

Emerging bioinformatics methods and resources in drug toxicology

K Audouze, O Taboureau - In Silico Methods for Predicting Drug Toxicity, 2022 - Springer
Assessing the drug safety at an early stage of a drug discovery program is a critical issue.
With the recent advances in molecular biology and genomic, massive amounts of generated …

Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data

B Alexander-Dann, LL Pruteanu, E Oerton… - Molecular omics, 2018 - pubs.rsc.org
The toxicogenomics field aims to understand and predict toxicity by using 'omics' data in
order to study systems-level responses to compound treatments. In recent years there has …

Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity

JJ Sutherland, YW Webster, JA Willy… - The …, 2018 - nature.com
Despite investment in toxicogenomics, nonclinical safety studies are still used to predict
clinical liabilities for new drug candidates. Network-based approaches for genomic analysis …

Network-based analysis of transcriptional profiles from chemical perturbations experiments

F Mulas, A Li, DH Sherr, S Monti - BMC bioinformatics, 2017 - Springer
Background Methods for inference and comparison of biological networks are emerging as
powerful tools for the identification of groups of tightly connected genes whose activity may …

[HTML][HTML] Mining toxicogenomic data for dose-responsive pathways: implications in advancing next-generation risk assessment

AR Barutcu, MB Black, A Nong - Frontiers in Toxicology, 2023 - ncbi.nlm.nih.gov
Introduction: While targeted investigation of key toxicity pathways has been instrumental for
biomarker discovery, unbiased and holistic analysis of transcriptomic data provides a …

A system-based approach to interpret dose-and time-dependent microarray data: quantitative integration of gene ontology analysis for risk assessment

X Yu, WC Griffith, K Hanspers, JF Dillman III… - Toxicological …, 2006 - academic.oup.com
Although microarray technology has emerged as a powerful tool to explore expression
levels of thousands of genes or even complete genomes after exposure to toxicants, the …

Inferring drug-disease associations from integration of chemical, genomic and phenotype data using network propagation

YF Huang, HY Yeh, VW Soo - BMC medical genomics, 2013 - Springer
Background During the last few years, the knowledge of drug, disease phenotype and
protein has been rapidly accumulated and more and more scientists have been drawn the …

Practical application of toxicogenomics for profiling toxicant-induced biological perturbations

N Kiyosawa, S Manabe, T Yamoto… - International journal of …, 2010 - mdpi.com
A systems-level understanding of molecular perturbations is crucial for evaluating chemical-
induced toxicity risks appropriately, and for this purpose comprehensive gene expression …

Computational network analysis for drug toxicity prediction

C Hardt, C Bauer, J Schuchhardt, R Herwig - Computational cell biology …, 2018 - Springer
The computational prediction of compound effects from molecular data is an important task
in hazard and risk assessment and pivotal for judging the safety of any drug, chemical or …