Use of connectivity mapping to support read across: A deeper dive using data from 186 chemicals, 19 cell lines and 2 case studies

KN De Abrew, YK Shan, X Wang, JM Krailler… - Toxicology, 2019 - Elsevier
We previously demonstrated that the Connectivity Map (CMap)(Lamb et al., 2006) concept
can be successfully applied to a predictive toxicology paradigm to generate meaningful MoA …

Navigating transcriptomic connectivity mapping workflows to link chemicals with bioactivities

I Shah, J Bundy, B Chambers, LJ Everett… - Chemical research in …, 2022 - ACS Publications
Screening new compounds for potential bioactivities against cellular targets is vital for drug
discovery and chemical safety. Transcriptomics offers an efficient approach for assessing …

Grouping 34 chemicals based on mode of action using connectivity mapping

KN De Abrew, RM Kainkaryam, YK Shan… - Toxicological …, 2016 - academic.oup.com
Connectivity mapping is a method used in the pharmaceutical industry to find connections
between small molecules, disease states, and genes. The concept can be applied to a …

[HTML][HTML] Using read-across to build physiologically-based kinetic models: Part 1. Development of a KNIME workflow to assist analogue selection for PBK modelling

CV Thompson, SD Webb, JA Leedale… - Computational …, 2024 - Elsevier
Read-across refers to the process by which information from one (source) chemical is used
to infer information about another similar (target) chemical. This method can be used to fill …

[HTML][HTML] Fish connectivity mapping: linking chemical stressors by their mechanisms of action-driven transcriptomic profiles

RL Wang, AD Biales, N Garcia-Reyero, EJ Perkins… - BMC genomics, 2016 - Springer
Background A very large and rapidly growing collection of transcriptomic profiles in public
repositories is potentially of great value to developing data-driven bioinformatics …

Key read across framework components and biology based improvements

N Ball, J Madden, A Paini, M Mathea, AD Palmer… - … /Genetic Toxicology and …, 2020 - Elsevier
At the 2019 annual meeting of the European Environmental Mutagen and Genomics Society
a workshop session related to the use of read across concepts in toxicology was held. The …

Automated integration of structural, biological and metabolic similarities to improve read-across

D Gadaleta, AG Bakhtyari, GJ Lavado… - ALTEX-Alternatives to …, 2020 - altex.org
Read-across (RAX) is a popular data gap-filling technique that uses category and analogue
approaches to predict toxicological endpoints for a target. Despite its increasing relevance …

[HTML][HTML] t4 report: Supporting read-across using biological data

H Zhu, M Bouhifd, N Kleinstreuer, ED Kroese, Z Liu… - Altex, 2016 - ncbi.nlm.nih.gov
Read-across, ie filling toxicological data gaps by relating to similar chemicals, for which test
data are available, is usually done based on chemical similarity. Besides structure and …

Making big sense from big data in toxicology by read-across

T Hartung - ALTEX-Alternatives to animal experimentation, 2016 - altex.org
Modern information technologies have made big data available in safety sciences, ie,
extremely large data sets that may be analyzed only computationally to reveal patterns …

[HTML][HTML] Prospects and challenges of multi-omics data integration in toxicology

S Canzler, J Schor, W Busch, K Schubert… - Archives of …, 2020 - Springer
Exposure of cells or organisms to chemicals can trigger a series of effects at the regulatory
pathway level, which involve changes of levels, interactions, and feedback loops of …