Main description:

This detailed volume explores key state-of-the-art computational applications that are crucial in Systems Toxicology. The recent technological developments in experimental biology and multi-omics measurements that enable Systems Biology and Systems Toxicology can only be fully leveraged by the application of a broad range of computational approaches ranging from data management to mathematical modeling. Taking this into account, chapters in this book cover data management and processing, data analysis, biological network building and analysis, as well as the application of computational methods to toxicological assessment.

Written for the Methods in Pharmacology and Toxicology series, Computational Systems Toxicology includes the kind of key practical advice that will aid readers in furthering our knowledge of toxic substances and reactions to them.

Contents:

1. The Adverse Outcome Pathway: A Conceptual Framework to Support Toxicity Testing in the 21st Century

Edward Perkins, Natalia Garcia-Reyero, Stephen Edwards, Clemens Wittwehr, Daniel Villeneuve, David Lyons, and Gerald Ankley

2. Metabolic Pathway Databases: A Word of Caution

Miranda D. Stobbe

3. Causal Biological Network Database: A Comprehensive Platform of Causal Biological Network Models Focused on the Pulmonary and Vascular Systems

Marja Talikka, Stephanie Boue, and Walter K. Schlage

4. Data Sources for Signature Discovery in Toxicology

Dragana Mitic Potkrajac, Branka Rakic, Gordana Apic, and Robert B. Russell

5. Data Management and Processing in Toxicoinformatics: From Chemical Databases to Automatic Extraction of Unstructured Resources

Juliane Fluck and Marc Zimmermann

6. Using a Crowdsourcing Approach for Network Verification

Natalia Boukharov and Jennifer S. Park

7. Toxicological Assessment Via Gene Network Analysis

Simona Iacobacci, Francesco Gregoretti, Gennaro Oliva, Roman Polishchuk, and Vincenzo Belcastro

8. Weaving Knowledge into Biological Pathways in a Collaborative Manner

Yukiko Matsuoka, Kazuhiro Fujita, Samik Ghosh, and Hiroaki Kitano

9. Pathway Analysis and Machine Learning as Tools in Systems Toxicology

Adi Laurentiu Tarca

10. Quantifying the Biological Impact of Active Substances Using Causal Network Models

Alain Sewer, Florian Martin, Walter K. Schlage, Julia Hoeng, and Manuel C. Peitsch

11. Analysis of Proteomic Data for Toxicological Applications

Bjoern Titz, Thomas Schneider, Ashraf Elamin, Florian Martin, Sophie Dijon, Nikolai V. Ivanov, Julia Hoeng, and Manuel C. Peitsch

12. Xenobiotic Metabolism Activation as a Biomarker of Cigarette Smoke Exposure Response

Anita R. Iskandar

13. High-Content Screening: Understanding and Managing Mechanistic Data to Better Predict Toxicity

Paul Walker, Tim Smith, Kerry Frost, Sarah Kelly, and Ignacio Gonzalez Suarez

14. A Systems Toxicology Approach to Investigating the Cardiovascular Effects of Cigarette Smoke and Environmental Pollutants in ApoE-Deficient Mice

Hector De Leon, Stephanie Boue, Manuel C. Peitsch, and Julia Hoeng

15. Computational Data Integration in Toxicogenomics

Simona Constantinescu, Shana J. Sturla, Giancarlo Marra, Bernd Wollscheid, and Niko Beerenwinkel

16. Aerosol Dosimetry Modeling Using Computational Fluid Dynamics

Markus Nordlund and Arkadiusz K. Kuczaj