Part 1. Toxicological/Pharmacological Endpoint Prediction

1. Methods for Building QSARs

James Devillers

2. Accessing and Using Chemical Databases

Nikolai Nikolov, Todor Pavlov, Jay R. Niemelä, and Ovanes Mekenyan

3. From QSAR to QSIIR: Searching for Enhanced Computational Toxicology Models

Hao Zhu

4. Mutagenicity, Carcinogenicity and Other Endpoints

Romualdo Benigni, Chiara Laura Battistelli, Cecilia Bossa, Mauro Colafranceschi, and Olga Tcheremenskaia

5. Classification Models for Safe Drug Molecules

A.K. Madan, Sanjay Bajaj, and Harish Dureja

6. QSAR and Metabolic Assessment Tools in the Assessment of Genotoxicity

Andrew P. Worth, Silvia Lapenna, and Rositsa Serafimova

Part II. Biological Network Modeling

7. Gene Expression Networks

Reuben Thomas and Christopher J. Portier

8. Construction of Cell Type-Specific Logic Models of Signaling Networks Using CellNetOptimizer

Melody K. Morris, Ioannis Melas, and Julio Saez-Rodriguez

9. Regulatory Networks

Gilles Bernot, Jean-Paul Comet, and Christine Risso- de Faverney

10. Computational Reconstruction of Metabolic Networks from KEGG

Tingting Zhou

Part III. Biomarkers

11. Biomarkers

Harmony Larson, Elena Chan, Sucha Sudarsanam, and Dale E. Johnson

12. Biomarkers: Environmental Public Health Indicators

Andrey I. Egorov, Dafina Dalbokova, and Michal Kryzanowski

Part IV. Modeling for Regulatory Purposes (Risk and Safety Assessment)

13. Modeling for Regulatory Purposes (Risk and Safety Assessment)

Hisham El-Masri

14. Developmental Toxicity Prediction

Raghuraman Venkatapathy and Nina Ching Y. Wang

15. Predictive Computational Toxicology to Support Drug Safety Assessment

Luis G. Valerio, Jr.

Part V. Integrated Modeling/Systems Toxicology Approaches

16. Developing a Practical Toxicogenomics Data Analysis System Utilizing Open-Source Software

Takehiro Hirai and Naoki Kiyosawa

17. Systems Toxicology from Genes to Organs

John Jack, John Wambaugh, and Imran Shah

18. Agent Based Models of Cellular Systems

Nicola Cannata, Flavio Corradini, Emanuela Merelli, and Luca Tesei

Part VI. Mathematical and Statistical Background

19. Linear Algebra

Kenneth Kuttler

20. Ordinary Differential Equations

Jiří Lebl

21. On the Development and Validation of QSAR Models

Paola Gramatica

22. Principal Components Analysis

Detlef Groth, Stefanie Hartmann, Sebastian Klie, and Joachim Selbig

23. Partial Least Square Methods: Partial Least Squares Correlation and Partial Least Square Regression

Hervé Abdi and Lynne J. Williams

24. Maximum Likelihood

Shuying Yang and Daniela De Angelis

25. Bayesian Inference

Frédéric Y. Bois