Computational toxicology at the European Commission's Joint Research Centre

Bibliography

• Nigsch F, Macalusi NJ, Mitchel JBO, Computational toxicology: an overview of the sources of data and of modelling methods. Expert Opin Drug Metab Toxicol 2009;5:1-14
   PubMed Web of Science ®Google Scholar
• Greene N. Computer systems for the prediction of toxicity: an update. Adv Drug Deliv Rev 2002;54:417-31
   PubMed Web of Science ®Google Scholar
• Cronin MTD, Livingstone DJ. Predicting chemical toxicity and fate. CRC Press, New York, USA; 2004
   Google Scholar
• National Toxicology Program. A National Toxicology Program for the 21st Century: a Roadmap for the Future. NTP, NIEHS, Research Triangle Park, NC, USA 2004. Available from: http://ntp.niehs.nih.gov/go/vision
   Google Scholar
• National Research Council. Toxicity testing in the 21st century: a vision and a strategy. National Academies Press, Washington, DC, USA; 2007
   Google Scholar
• Collins FS, Gray GM, Bucher JR. Transforming environmental health protection. Science 2008;319:906-7
   PubMed Web of Science ®Google Scholar
• Dix DJ, Houck KA, Martin MT, The ToxCast program for prioritizing toxicity testing of environmental chemicals. Toxicol Sci 2007;95:5-12
   PubMed Web of Science ®Google Scholar
• European Commission. Regulation (EC) No 1907/2006 of the European Parliament and of the Council of 18 December 2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH), establishing a European Chemicals Agency, amending Directive 1999/45/EC and repealing Council Regulation (EEC) No 793/93 and Commission Regulation (EC) No 1488/94 as well as Council Directive 76/769/EEC and Commission Directives 91/155/EEC, 93/67/EEC, 93/105/EC and 2000/21/EC. Official Journal of the European Union, L 396/1 of 30.12.2006. Office for Official Publications of the European Communities (OPOCE), Luxembourg; 2006
   Google Scholar
• European Commission. Directive 2006/121/EC of the European Parliament and of the Council of 18 December 2006 amending Council Directive 67/548/EEC on the approximation of laws, regulations and administrative provisions relating to the classification, packaging and labelling of dangerous substances in order to adapt it to Regulation (EC) No 1907/2006 concerning the Registration, Evaluation, Authorisation and Restriction of Chemicals (REACH) and establishing a European Chemicals Agency. Official Journal of the European Union, L 396/850 of 30.12.2006. Office for Official Publications of the European Communities (OPOCE), Luxembourg; 2006
   Google Scholar
• European Commission. Directive 98/8/EC of the European Parliament and of the Council of 16 February 1998 concerning the placing of biocidal products on the market. Official Journal of the European Union, L 132/1 of 24.04.1998. Office for Official Publications of the European Communities (OPOCE), Luxembourg; 1998
   Google Scholar
• European Commission. Council Directive 91/414/EEC of 15 July 1991 concerning the placing of plant protection products on the market. Official Journal of the European Union, L 230/1 of 19.08.1991. Office for Official Publications of the European Communities (OPOCE), Luxembourg; 1991
   Google Scholar
• European Commission. Directive 2000/60/EC of the European Parliament and of the Council of 23 October 2000 establishing a framework for the Community action in the field of water policy. Official Journal of the European Union, L 327/1 of 22.12.2000. Office for Official Publications of the European Communities (OPOCE), Luxembourg; 2000
   Google Scholar
• European Commission. Council Directive 76/768 of 27 July 1976 on the approximation of the laws of the Member States relating to cosmetic products. Official Journal of the European Union, L 262/169 of 27.09.1976. Office for Official Publications of the European Communities (OPOCE), Luxembourg; 1976
   Google Scholar
• Worth AP. The role of QSAR methodology in the regulatory assessment of chemicals. In: Puzyn T, Leszczynski J, Cronin MTD, editors, Recent advances in QSAR studies: methods and applications. Springer: Heidelberg, Germany; 2010. p. 367-82
   Google Scholar
• Organisation for Economic Co-operation and Development. Report on the Regulatory Uses and Applications in OECD Member Countries of (Quantitative) Structure–Activity Relationship [(Q)SAR] Models in the Assessment of New and Existing Chemicals. ENV/JM/MONO(2006)25, OECD, Paris, France 2007. Available from: http://www.oecd.org/
   Google Scholar
• Worth A, Patlewicz G, editors, A Compendium of Case Studies that helped to shape the REACH guidance on chemical categories and read across. European Commission report EUR 22481 EN, Office for Official Publications of the European Communities, Luxembourg; 2004. Available from: http://ecb.jrc.ec.europa.eu/qsar/publications/
   Google Scholar
• Worth A, Bassan A, Fabjan E, The use of computational methods in the grouping and assessment of chemicals – preliminary investigations. European Commission report EUR 22941 EN, Office for Official Publications of the European Communities, Luxembourg; 2007. Available from: http://ecb.jrc.ec.europa.eu/qsar/publications/
   Google Scholar
• Pavan M, Worth A. A set of case studies to illustrate the applicability of DART (Decision Analysis by Ranking Techniques) in the ranking of chemicals. European Commission report EUR 23481 EN, Office for Official Publications of the European Communities, Luxembourg; 2008. Available from: http://ecb.jrc.ec.europa.eu/qsar/publications/
   Google Scholar
• Enoch SJ, Cronin MTD, Madden JC, Formation of Structural Categories to Allow for Read-Across for Teratogenicity. QSAR Comb Sci 2009;28:696-708
   Google Scholar
• Pavan M, Worth A. Publicly-accessible QSAR software tools developed by the Joint Research Centre. SAR QSAR Environ Res 2008;19:785-99
   PubMed Web of Science ®Google Scholar
• Tsakovska I, Worth A. The use of computational methods for the assessment of chemicals in REACH. BIO Automation 2009;13:151-62
   Google Scholar
• Jeliazkova N, Jaworska J, Worth AP. Open source tools for read across and category formation. In: Cronin MTD, Madden J, editors, In silico toxicology. Principles and applications, Royal Society of Chemistry: Cambridge, UK; 2010. In press
   Google Scholar
• JRC software tools. Available from: http://ecb.jrc.ec.europa.eu/qsar/
   Google Scholar
• Cramer GM, Ford RA, Hall RL. Estimation of toxic hazard–a decision tree approach. J Cosmet Toxicol 1978;16:255-76
   PubMedGoogle Scholar
• Patlewicz G, Jeliazkova N, Safford RJ, An evaluation of the implementation of the cramer classification scheme in the Toxtree software. SAR QSAR Environ Res 2008;19:495-524
   PubMed Web of Science ®Google Scholar
• Verhaar HJM, van Leeuwen CJ, Hermens JLM. Classifying environmental pollutants. 1. Structure-activity relationships for prediction of aquatic toxicity. Chemosphere 1992;25:471-91
   Web of Science ®Google Scholar
• Walker JD, Gerner I, Hulzebos E, The Skin Irritation Corrosion Rules Estimation Tool (SICRET). QSAR Comb Sci 2005;24:378-84
   Google Scholar
• Gerner I, Liebsch M, Spielmann H. Assessment of the eye irritating properties of chemicals by applying alternatives to the Draize rabbit eye test: the use of QSARs and in vitro tests for the classification of eye irritation. ATLA 2005;33:215-37
   Google Scholar
• Benigni R, Bossa C, Jeliazkova N, The Benigni/Bossa rulebase for mutagenicity and carcinogenicity – a module of Toxtree. European Commission report EUR 23241 EN, Office for Official Publications of the European Communities, Luxembourg; 2008
   Google Scholar
• Benigni R, Bossa C, Tcheremenskaia O, Development of structural alerts for the in vivo micronucleus assay in rodents. European Commission report EUR 23844 EN, Office for Official Publications of the European Communities, Luxembourg; 2009
   Google Scholar
• Benigni R, Bossa C, Worth A. Structural analysis and predictive value of the rodent in vivo micronucleus assay results. Mutagenesis 2010. In press
   Google Scholar
• Schultz TW, Yarbrough JW, Hunter RS, Verification of the structural alerts for michael acceptors. Chem Res Toxicol 2007;20:1359-63
   PubMed Web of Science ®Google Scholar
• Netzeva TI, Worth AP, Aldenberg T, Current status of methods for defining the applicability domain of (Quantitative) structure-activity relationships. The report and recommendations of ECVAM workshop 52. Altern Lab Anim 2005;33:155-73
   PubMed Web of Science ®Google Scholar
• Ellison CM, Enoch SJ, Cronin MT, Definition of the applicability domains of knowledge-based predictive toxicology expert systems by using a structural fragment-based approach. Altern Lab Anim 2009;37:533-45
   PubMed Web of Science ®Google Scholar
• Wu S, Blackburn K, Amburgey J, A framework for using structural, reactivity, metabolic and physicochemical similarity to evaluate the suitability of analogs for SAR-based toxicological assessments. Regul Toxicol Pharmacol 2010;56:67-81
   PubMed Web of Science ®Google Scholar
• Patlewicz G, Jeliazkova N, Gallegos Saliner A, Toxmatch – a new software tool to aid in the development and evaluation of chemically similar groups. SAR QSAR Environ Res 2008;19:397-412
   PubMed Web of Science ®Google Scholar
• Gallegos Saliner A, Poater A, Jeliazkova N, Toxmatch – A chemical classification and activity prediction tool based on similarity measures. Regul Toxicol Pharmacol 2008;52:77-84
   PubMed Web of Science ®Google Scholar
• Pavan M, Todeschini R. Multicriteria decision making methods. In: Walczak B, Taulér R, Brown S, editors, Comprehensive chemometrics, Elsevier: Amsterdam; 2009. p. 591-629
   Google Scholar
• Organisation for Economic Cooperation and Development, The report from the expert group on (quantitative) structure activity relationship ([Q]SARs) on the principles for the validation of (Q)SARs, Series on Testing and Assessment No 49, OECD report ENV/JM/MONO(2004)24, Paris; 2004
   Google Scholar
• Franklin RB. In silico studies in ADME/Tox: caveat emptor. Curr Comput Aided Drug Des 2009;5:128-38
   Web of Science ®Google Scholar
• ECHA. Guidance on information requirements and chemical safety assessment. European Chemicals Agency, Helsinki, Finland 2008. Available from: http://guidance.echa.europa.eu/docs/guidance_document/information_requirements_en.htm
   Google Scholar
• European Commission. Directive 2008/105/EC of the European Parliament and of the Council on environmental quality standards in the field of water policy, amending and subsequently repealing Council Directives 82/176/EEC, 83/513/EEC, 84/156/EEC, 84/491/EEC, 86/280/EEC and amending Directive 2000/60/EC of the European Parliament and of the Council pp 14. 24/12/2008
   Google Scholar
• SCTEE, 2004. Opinion of the Scientific Committee on Toxicity, Ecotoxicity and the Environment on “The Setting of Environmental Quality Standards for the Priority Substances included in Annex X of Directive 2000/60/EC in Accordance with Article 16 thereof”. EC, Health and Consumer Protection DG. pp 32
   Google Scholar
• Daginnus K, Gottardo S, Mostrag-Szlichtyng A, A modelling approach for the prioritization of chemicals under the Water Framework Directive. European Commission report EUR 23241 EN, Office for Official Publications of the European Communities, Luxembourg; 2010
   Google Scholar
• Bassan A, Worth AP. The integrated use of models for the properties and effects of chemicals by means of a structured workflow. QSAR Comb Sci 2008;27:6-20
   Google Scholar
• van Leeuwen CJ, Patlewicz GY, Worth AP. Intelligent testing strategies. In: van Leeuwen CJ, Vermeire TG, editors, Risk assessment of chemicals. An introduction. 2nd edition. Springer: Heidelberg, Germany; 2007. p. 467-509
   Google Scholar
• Combes R, Grindon C, Cronin MTD, Proposed integrated decision-tree testing strategies for mutagenicity and carcinogenicity in relation to the EU REACH legislation. ATLA 2007;35:267-87
   Google Scholar
• Grindon C, Combes R, Cronin MTD, Integrated decision-tree testing strategies for skin corrosion and irritation with respect to the requirements of the EU REACH legislation. ATLA 2007;35:673-82
   Google Scholar
• Grindon C, Combes R, Cronin MTD, An integrated decision-tree testing strategy for skin sensitisation with respect to the requirements of the EU REACH legislation. ATLA 2007;35:683-97
   Google Scholar
• Combes R, Grindon C, Cronin MTD, Integrated decision-tree testing strategies for acute systemic toxicity and toxicokinetics with respect to the requirements of the EU REACH legislation. ATLA 2008;36:45-63
   Google Scholar
• Grindon C, Combes R, Cronin MTD, Integrated decision-tree testing strategies for developmental and reproductive toxicity with respect to the requirements of the EU REACH legislation. ATLA 2008;36:65-80
   Google Scholar
• Grindon C, Combes R, Cronin MTD, An integrated decision-tree testing strategy for eye irritation with respect to the requirements of the EU REACH legislation. ATLA 2008;36:81-92
   Google Scholar
• Grindon C, Combes R, Cronin MTD, An integrated decision-tree testing strategy for repeat dose toxicity with respect to the requirements of the EU REACH legislation. ATLA 2008;36:93-101
   Google Scholar
• Hewitt M, Ellison CM, Enoch SJ, Integrating (Q)SAR models, expert systems and read-across approaches for the prediction of developmental toxicity. Reprod Toxicol 2010, doi:10.1016/j.reprotox.2009.12.003
   Google Scholar
• DeJongh J, Forsby A, Houston JB, An integrated approach to the prediction of systemic toxicity using computer-based biokinetic models and biological in vitro test methods: overview of a prevalidation study based on the ECITTS Project. Toxicol in vitro 1999;13:549-54
   PubMed Web of Science ®Google Scholar
• Gubbels-van Hal WMLG, Blaauboer BJ, Barentsen HM, An alternative approach for the safety evaluation of new and existing chemicals, an exercise in integrated testing. Reg Toxicol Pharmacol 2005;42:284-95
   PubMed Web of Science ®Google Scholar
• Gülden M, Mörchel S, Seibert H. Factors influencing nominal effective concentrations of chemical compounds in vitro: cell concentration. Toxicol in vitro 2001;15:233-43
   PubMed Web of Science ®Google Scholar
• Gülden M, Seibert H. In vitro-in vivo extrapolation: estimation of human serum concentrations of chemicals equivalent cytotoxic concentrations in vitro. Toxicology 2003;189:211-22
   PubMed Web of Science ®Google Scholar
• Heringa MB, Schreurs RHMM, Busser F, Towards more useful in vitro toxicity data with measured free concentrations. Environ Sci Technol 2004;38:6263-70
   PubMed Web of Science ®Google Scholar
• Kramer NI. Measuring, modelling and increasing the free concentration of test chemicals in cell assays. PhD Thesis. Utrecht University; 2010
   Google Scholar