Transcriptomics in toxicogenomics, part III: data modelling for risk assessment

A Serra, M Fratello, L Cattelani, I Liampa, G Melagraki… - Nanomaterials, 2020 - mdpi.com
Transcriptomics data are relevant to address a number of challenges in Toxicogenomics
(TGx). After careful planning of exposure conditions and data preprocessing, the TGx data …

Transcriptomics in toxicogenomics, part II: preprocessing and differential expression analysis for high quality data

A Federico, A Serra, MK Ha, P Kohonen, JS Choi… - Nanomaterials, 2020 - mdpi.com
Preprocessing of transcriptomics data plays a pivotal role in the development of
toxicogenomics-driven tools for chemical toxicity assessment. The generation and …

Transcriptomics in toxicogenomics, part I: experimental design, technologies, publicly available data, and regulatory aspects

PAS Kinaret, A Serra, A Federico, P Kohonen… - Nanomaterials, 2020 - mdpi.com
The starting point of successful hazard assessment is the generation of unbiased and
trustworthy data. Conventional toxicity testing deals with extensive observations of …

Manually curated transcriptomics data collection for toxicogenomic assessment of engineered nanomaterials

LA Saarimäki, A Federico, I Lynch, AG Papadiamantis… - Scientific data, 2021 - nature.com
Toxicogenomics (TGx) approaches are increasingly applied to gain insight into the possible
toxicity mechanisms of engineered nanomaterials (ENMs). Omics data can be valuable to …

[HTML][HTML] Nextcast: a software suite to analyse and model toxicogenomics data

A Serra, LA Saarimäki, A Pavel, G Del Giudice… - Computational and …, 2022 - Elsevier
The recent advancements in toxicogenomics have led to the availability of large omics data
sets, representing the starting point for studying the exposure mechanism of action and …

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 …

Toxicogenomics–what added value do these approaches provide for carcinogen risk assessment?

S Schmitz-Spanke - Environmental research, 2019 - Elsevier
It is still a major challenge to protect humans at workplaces and in the environment. To cope
with this task, it is a prerequisite to obtain detailed information on the extent of chemical …

Toxicogenomics: a 2020 vision

Z Liu, R Huang, R Roberts, W Tong - Trends in pharmacological sciences, 2019 - cell.com
Toxicogenomics (TGx) has contributed significantly to toxicology and now has great
potential to support moves towards animal-free approaches in regulatory decision making …

Machine learning-based biomarkers identification from toxicogenomics–Bridging to regulatory relevant phenotypic endpoints

SM Rahman, J Lan, D Kaeli, J Dy… - Journal of hazardous …, 2022 - Elsevier
One of the major challenges in realization and implementations of the Tox21 vision is the
urgent need to establish quantitative link between in-vitro assay molecular endpoint and in …

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 …