Pre-Reading Spring 2015

Suggested Pre-Reading List for the Spring 2015 Meeting

Compiled by Thierry Hanser of Lhasa UK Ltd with contributions from the speakers listed below.  The Committee would like to extend their thanks to everyone for their input.

Combining an expert system with machine learning to rank metabolites.

Edward Rosser (Lhasa Limited)

  • Testa, B.; Balmat, A. L.; Long, A.; Judson, P. Predicting drug metabolism – an evaluation of the expert system METEOR. Biodivers. 2005, 2(7), 872-885.
  • Button, W. G; Judson, P. N.; Long, A.; Vessey, J. D. Using absolute and relative reasoning in the prediction of the potential metabolism of xenobiotics. Chem. Inf. Comput. Sci. 2003, 43(5), 1371-1377.

Using QSAR for metabolic network completion and metabolic engineering.

Jean-Loup Faulon (Institut of Systems & Synthetic Biology

  • Carbonell P, Parutto P, Herisson J, Pandit S.B, Faulon J.L. XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res. in press 2014, [PMID: 24792156].
  • Faulon J.L., Misra M., Martin S., Sale, K., Sapra R.. Genome Scale Enzyme-metabolites and Drug-Target interaction predictions using the signature molecular descriptor, Bioinformatics, 24, 225-233, 2008.
  • Fernández-Castané A, Fehér T, Carbonell P, Pauthenier C, Faulon J.L. Computer-aided design for metabolic engineering. J Biotechnol. in press 2014, [PMID: 24704607].


Drug Metabolism Prediction: Experiment and/or Computation?

Johannes Kirchmair (Center for Bioinformatics, University of Hamburg)

  • Johannes Kirchmair, Andreas H. Göller, Dieter Lang, Jens Kunze, Bernard Testa, Ian D. Wilson, Robert C. Glen & Gisbert Schneider. Predicting drug metabolism: experiment and/or computation? Nature Reviews Drug Discovery (2015) doi:10.1038/nrd4581 Published online 24 April 2015


Use of Read-Across in Filling Data Gap for Assessments.

Nora Aptula (Safety and Environmental Assurance Centre)

  • OECD (2007) Guidance document on grouping of chemicals, No 28.


  • ECHA (2010) Practical guide 10: How to avoid unnecessary testing on animals.



Identification of novel anti-convulsant drugs using a larval zebrafish model

Simon Hand (University of Sheffield)

  • Baxendale, C. J. Holdsworth, P. L. Meza Santoscoy, M. R. M. Harrison, J. Fox,C. A. Parkin, P. W. Ingham, and V. T. Cunliffe, Disease Models & Mechanisms, 2012, 01009, 1–12.
  • C. Baraban, M. R. Taylor, P. A. Castro, and H. Baier, Neuroscience, 2005, 131, 759–768


Towards an MIE atlas – Tools for toxicity prediction

Tim Allen (Centre for Molecular Informatics, Department of Chemistry, University of Cambridge)

  • T. Ankley, R.S. Bennett, R.J. Erickson, D.J. Hoff et al. (2007) Environ. Toxicol. Chem. 29; 730-741
  • E.H Allen, J.M. Goodman, S. Gutsell, P. Russell. (2014) Chem. Res. Toxicol. 27 (12); 2100-2112