Modeling the effects of toxins in metabolic networks

IEEE Engineering in Medicine and Biology Magazine

Volumn 26, Issue 2, 2007, Pages 37-46

  Tamaddoni Nezhad, Alireza ^a   Chaleil, Raphael ^a   Kakas, Antonis C ^b   Sternberg, Michael ^a   Nicholson, Jeremy ^a,c   Muggleton, Stephen ^a,c,d,e  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b UNIVERSITY OF CYPRUS   (Cyprus)

^c Imperial College ^*

^d Imperial College Computational Bioinformatics Centre   (United States)

^e American Association for Artificial Intelligence   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDRAZINE; PARACETAMOL; PROSTAGLANDIN; TOXIN;

BAYES THEOREM; CHEMICAL REACTION; CONFERENCE PAPER; ENZYME INHIBITION; EVALUATION; LEARNING; METABOLISM; METABOLITE; MODEL; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; REACTION ANALYSIS;

ANIMALS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; DOSE-RESPONSE RELATIONSHIP, DRUG; ENERGY METABOLISM; HUMANS; HYDRAZINES; LIVER; MODELS, BIOLOGICAL; PROTEOME; SIGNAL TRANSDUCTION;

EID: 33947622747     PISSN: 07395175     EISSN: None     Source Type: Journal    
DOI: 10.1109/MEMB.2007.335590     Document Type: Conference Paper

References (40)

1. P.A. Flach and A.C. Kakas, Eds., Abductive and Inductive Reasoning, Pure and Applied Logic. Norwell, MA: Kluwer, 2000.
2. A. Yamamoto, "Which hypotheses can be found with inverse entailment?" in Proc. 7th Int. Workshop Inductive Logic Programming, Berlin, 1997, pp. 296-308.
3. K. Ito and A. Yamamoto, "Finding hypotheses from examples by computing the least generalization of bottom clauses," in Proc. Discovery Science '98, Berlin, vol. 1532, LNAI, Springer-Verlag, pp. 303-314.
4. K. Inoue, "Induction, abduction and consequence-finding," in Proc. Int. Workshop Inductive Logic Programming, vol. 2157, LNAI, Springer-Verlag, 2001, pp. 65-79.
5. S.H. Muggleton and C.H. Bryant, "Theory completion using inverse entailment," in Proc. 10th Int. Workshop Inductive Logic Programming, Berlin, vol. 1866, LNAI, Springer-Verlag, 2000, pp. 130-146.
6. S. Moyle, "Using theory completion to learn a robot navigation control program," in Proc. 12th Int. Conf. Inductive Logic Programming, vol. 2583, LNAI, Springer-Verlag, 2002, pp. 182-197.
7. O. Ray, K. Broda, and A. Russo, "Hybrid abductive inductive learning: A generalisation of Progol," in Proc. 13th Int. Conf. Inductive Logic Programming, 2835, LNAI, Springer-Verlag, 2003, pp. 311-328.
8. B. Zupan, I. Bratko, J. Demsar, P. Juvan, J.A Halter, A. Kuspa, and G. Shaulsky, "GenePath: A system for automated construction of genetic networks from mutant data," Bioinformatics, vol. 19, no. 3, pp. 383-389, 2003.
9. R.D. King, K.E. Whelan, F.M. Jones, P.K.G. Reiser, C.H. Bryant, S.H. Muggleton, D.B. Kell, and S.G. Oliver, "Functional genomic hypothesis generation and experimentation by a robot scientist," Nature, vol. 427, pp. 247-252, 2004.
10. MetaLog [Online]. Available: http://www.doc.ic.ac.uk/bioinformatics/ metalog/.
11. H. Ogata, S. Goto, K. Sato, W. Fujibuchi, H. Bono, and M. Kanehisa, "KEGG: Kyoto encyclopedia of genes and genomes," Nucleic Acids Res., vol. 27, no. 1, pp. 29-34, 1999.
12. A. Tamaddoni-Nezhad, A. Kakas, S.H. Muggleton, and F. Pazos, "Modelling inhibition in metabolic pathways through abduction and induction," in Proc. 14th Int. Conf. Inductive Logic Programming, vol. 3195, LNAI, Springer-Verlag, 2004, pp. 305-322.
13. A. Tamadonni-Nezhad, R. Chaleil, A.Kakas, and S.H. Muggleton, "Application of abductive ILP to learning metabolic network inhibition from temporal data," Machine Learning., vol. 64, pp. 209-230, 2006.
14. J.C. Lindon, J.K. Nicholson, E. Holmes, et al., "Contemporary issues in toxicology. The role of metabonomics in toxicology and its evaluation by the COMET project," Tox. Appl. Pharm., vol. 187, pp. 137-146, 2003.
15. E. Ravasz, A.L. Somera, D.A. Mongru, Z.N. Oltvai, and A.L. Barabasi, "Hierarchical organization of modularity in metabolic networks," Science, vol. 297, no. 5586, pp. 1551-1555, 2002.
16. E. Alm and A.P. Arkin, "Biological networks," Curr. Opin. Struct. Biol., vol. 13, no. 2, pp. 193-202, 2003.
17. B. Alberts, D. Bray, J. Lewis, M. Raff, K Roberts, and J.D. Watson, Molecular Biology of the Cell, 3rd ed. New York: Garland, 1994.
18. J.A. Papin, N.D. Price, S.J. Wiback, D.A. Fell, and B.O. Palsson, "Metabolic pathways in the post-genome era," Trends Biochem. Sci., vol. 28, no. 5, pp. 250-258, May 2003.
19. R. Alves, R.A. Chaleil, and M.J. Sternberg, "Evolution of enzymes in metabolism: A network perspective," Mol. Biol., vol. 320, no. 4, pp. 751-770, 2002.
20. T.A. Swierkosz, L. Jordan, M. McBride, K. McGough, J. Devlin, and R.M. Botting, "Actions of paracetamol on cyclooxygenases in tissue and cell homogenates of mouse and rabbit," Med. Sci. Monit., vol. 8, no. 12, pp. 496-503, Dec. 2002.
21. H.J. Zimmerman and W.C. Maddrey, "Acetaminophen (paracetamol) hepatotoxicity with regular intake of alcohol: analysis of instances of therapeutic misadventure," Hepatology, vol. 22, no. 3, pp. 767-773, Sept. 1995.
22. K. Popper, The Logic of Scientific Discovery. New York: Basic Books, 1959.
23. C.G. Hempel, Aspects of Scientific Explanation and Other Essays in the Philosophy of Science. New York: Free Press, 1965.
24. C.S. Peirce, Essays in the Philosophy of Science. Liberal Arts Press, 1957.
25. J.R. Josephson and S.G. Josephson, Eds., Abductive Inference: Computation, Philosophy, Technology. Cambridge, UK: Cambridge Univ. Press, 1994.
26. L. Magnani, Abduction, Reason and Science. Norwell, MA: Kluwer, 2001.
27. P. Flach and A.C. Kakas, "Abductive and inductive reasoning: Background and issues," in Abductive and Inductive Reasoning, Pure and Applied Logic, P.A. Flach and A.C. Kakas, Eds. Norwell, MA: Kluwer, 2000.
28. S. Moyle and S.H. Muggleton, "Learning programs in the event calculus," in Proc. 7th Inductive Logic Programming Workshop, vol. 1297, LNAI, Springer-Verlag, 1997, pp. 205-212.
29. BRENDA Webpage [Online]. Available: http://www.brenda.uni-koeln.de/.
30. A.C. Kakas, R.A. Kowalski, and F. Toni, "Abductive logic programming," J. Logic Computat., vol. 2, no. 6, pp. 719-770, 1993.
31. A.C. Kakas and M. Denecker, "Abduction in logic programming," in Computational Logic: Logic Programming and Beyond. Part I, A.C. Kakas and F. Sadri, Eds., 2002, pp. 402-436.
32. D.J. Crockford, H.C. Keun, L.M. Smith, E. Holmes, and J.K. Nicholson, "Curve-fitting method for direct quantitation of compounds in complex biological mixtures using 1h NMR: Application in metabonomic toxicology studies," Anal. Chem., vol. 77, no. 14, pp. 4556-4562, 2005.
33. K.L. Clark, "Negation as failure," in Readings in Nonmonotonic Reasoning, M.L. Ginsberg, Ed. Los Altos, CA: Kaufmann, 1987, pp. 311-325.
34. A.W. Nicholls, E. Holmes, J.C. Lindon, R.D. Farrant, J.N. Haselden, S.J.P. Damment, C.J. Waterfield, and J.K. Nicholson, "Metabonomic investigations into hydrazine toxicity in the rat," Chem. Res. Toxicol., vol. 14, no. 8, pp. 975-987, 2001.
35. I. Papatheodorou, A. Kakas, and M. Sergot, "Inference of gene relations from microarray data by abduction," Dept. Computing, Imperial College London, London, UK, Tech. Rep. 2005/3, 2005.
36. B.R. Wellner, "An abductive-inductive learning framework for logic-based agents," master's thesis, Imperial College of Science Technology and Medicine, London, UK, 1999.
37. N. Friedman, M. Linial, I. Nachman, and D. Pe'er, "Using Bayesian networks to analyze expression data," J. Comp. Bio., vol. 7, no. 3-4, pp. 601-620, 2000.
38. S. Imoto, T. Goto, and S. Miyano, "Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression," in Proc. Pacific Symp. Biocomputing, 2002, pp. 175-186.
39. A. Tamaddoni-Nezhad, S. Muggleton, and J. Bang, "A Bayesian model for metabolic pathways," in Proc. Int. Joint Conf. Artificial Intelligence Workshop Learning Statistical Models from Relational Data, Acapulco, Mexico, 2003, pp. 50-57, 2003.
40. S.H. Muggleton, A. Tamaddoni-Nezhad, and H. Watanabe, "Induction of enzyme classes from biological databases," in Proc. 13th Int. Conf. Inductive Logic Programming, vol. 2835, LNAI, Springer-Verlag, 2003, pp. 269-280.