Non-linear modeling of 1H NMR metabonomic data using kernel-based orthogonal projections to latent structures optimized by simulated annealing

Analytica Chimica Acta

Volumn 705, Issue 1-2, 2011, Pages 72-80

  Fonville, Judith M ^a   Bylesjö, Max ^b   Coen, Muireann ^a   Nicholson, Jeremy K ^a   Holmes, Elaine ^a   Lindon, John C ^a   Rantalainen, Mattias ^c  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b Almac Sciences   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Classification; K OPLS; Kernel models; Kernel based orthogonal projections to latent structures; Metabonomics; Non linear; OPLS; Simulated annealing

Indexed keywords

K-OPLS; KERNEL MODELS; METABONOMICS; NON-LINEAR; OPLS; ORTHOGONAL PROJECTION;

CHLORINE COMPOUNDS; CLASSIFICATION (OF INFORMATION); COMPUTER SIMULATION; MERCURY COMPOUNDS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SEPARATION;

SIMULATED ANNEALING;

GALACTOSAMINE; MERCURIC CHLORIDE;

AFRICAN TRYPANOSOMIASIS; ANALYTICAL PARAMETERS; ARTICLE; AUTOMATION; COMPUTER PROGRAM; CONTROLLED STUDY; INTERMETHOD COMPARISON; KERNEL METHOD; LINEAR SYSTEM; MATHEMATICAL MODEL; METABOLOMICS; NONHUMAN; NONLINEAR SYSTEM; PERFORMANCE; PREDICTION; PRIORITY JOURNAL; PROTON NUCLEAR MAGNETIC RESONANCE; SIMULATION; TRYPANOSOMA BRUCEI;

COMPUTER SIMULATION; MAGNETIC RESONANCE SPECTROSCOPY; METABOLOMICS; MODELS, BIOLOGICAL; NONLINEAR DYNAMICS;

TRYPANOSOMA BRUCEI BRUCEI;

EID: 80053386488     PISSN: 00032670     EISSN: 18734324     Source Type: Journal    
DOI: 10.1016/j.aca.2011.04.016     Document Type: Article

References (66)

1. Trygg J., Holmes E., Lundstedt T. J. Proteome Res. 2007, 6:469-479.
2. Ebbels T.M.D., Cavill R. Prog. Nucl. Magn. Reson. Spectrosc. 2009, 55:361-374.
3. Madsen R., Lundstedt T., Trygg J. Anal. Chim. Acta 2010, 659:23-33.
4. Wold S., Ruhe A., Wold H., Dunn W.J. SIAM J. Sci. Stat. Comp. 1984, 5:735-743.
5. Trygg J., Wold S. J. Chemometr. 2002, 16:119-128.
6. Kemsley E.K., Tapp H.S. J. Chemometr. 2009, 23:263-264.
7. Ergon R. J. Chemometr. 2005, 19:1-4.
8. Stenlund H., Gorzsas A., Persson P., Sundberg B., Trygg J. Anal. Chem. 2008, 80:6898-6906.
9. Spegel P., Danielsson A.P.H., Bacos K., Nagorny C.L.F., Moritz T., Mulder H., Filipsson K. Metabolomics 2010, 6:56-66.
10. Bylesjo M., Rantalainen M., Cloarec O., Nicholson J.K., Holmes E., Trygg J. J. Chemometr. 2006, 20:341-351.
11. Wiklund S., Johansson E., Sjostrom L., Mellerowicz E.J., Edlund U., Shockcor J.P., Gottfries J., Moritz T., Trygg J. Anal. Chem. 2008, 80:115-122.
12. Fonville J.M., Richards S.E., Barton R.H., Boulange C.L., Ebbels T.M.D., Nicholson J.K., Holmes E., Dumas M.E. J. Chemometr. 2010, 24:636-649.
13. Fiehn O. Plant Mol. Biol. 2002, 48:155-171.
14. Nicholson J.K., Lindon J.C., Holmes E. Xenobiotica 1999, 29:1181-1189.
15. Fernie A.R., Trethewey R.N., Krotzky A.J., Willmitzer L. Nat. Rev. Mol. Cell Biol. 2004, 5:763-769.
16. Dunn W.B., Ellis D.I. TrAC - Trends Anal. Chem. 2005, 24:285-294.
17. Coen M., Holmes E., Lindon J.C., Nicholson J.K. Chem. Res. Toxicol. 2008, 21:9-27.
18. Robertson D.G. Toxicol. Sci. 2005, 85:809-822.
19. Kaddurah-Daouk R., Kristal B.S., Weinshilboum R.M. Annu. Rev. Pharmacol. Toxicol. 2008, 48:653-683.
20. Heinzmann S.S., Brown I.J., Chan Q., Bictash M., Dumas M.E., Kochhar S., Stamler J., Holmes E., Elliott P., Nicholson J.K. Am. J. Clin. Nutr. 2010, 92:436-443.
21. Makinen V.P., Soininen P., Forsblom C., Parkkonen M., Ingman P., Kaski K., Groop P.H., Ala-Korpela M. Mol. Syst. Biol. 2008, 4:167. FinnDiane Study Group.
22. Clayton T.A., Lindon J.C., Cloarec O., Antti H., Charuel C., Hanton G., Provost J.P., Le Net J.L., Baker D., Walley R.J., Everett J.R., Nicholson J.K. Nature 2006, 440:1073-1077.
23. Wishart D.S. Trends Food Sci. Technol. 2008, 19:482-493.
24. Holmes E., Loo R.L., Stamler J., Bictash M., Yap I.K.S., Chan Q., Ebbels T., De Iorio M., Brown I.J., Veselkov K.A., Daviglus M.L., Kesteloot H., Ueshima H., Zhao L.C., Nicholson J.K., Elliott P. Nature 2008, 453:396-400.
25. Wang Y.L., Utzinger J., Saric J., Li J.V., Burckhardt J., Dirnhofer S., Nicholson J.K., Singer B.H., Brun R., Holmes E. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:6127-6132.
26. Olszewski K.L., Morrisey J.M., Wilinski D., Burns J.M., Vaidya A.B., Rabinowitz J.D., Linas M. Cell Host Microbe 2009, 5:191-199.
27. Saric J., Li J.V., Utzinger J., Wang Y., Keiser J., Dirnhofer S., Beckonert O., Sharabiani M.T., Fonville J.M., Nicholson J.K., Holmes E. Mol. Syst. Biol. 2010, 6:396.
28. Oostendorp M., Engelke U.F.H., Willemsen M.A.A.P., Wevers R.A. Clin. Chem. 2006, 52:1395-1405.
29. Lindon J.C., Nicholson J.K., Holmes E., Antti H., Bollard M.E., Keun H., Beckonert O., Ebbels T.M., Reilly M.D., Robertson D., Stevens G.J., Luke P., Breau A.P., Cantor G.H., Bible R.H., Niederhauser U., Senn H., Schlotterbeck G., Sidelmann U.G., Laursen S.M., Tymiak A., Car B.D., Lehman-McKeeman L., Colet J.M., Loukaci A., Thomas C. Toxicol. Appl. Pharmacol. 2003, 187:137-146.
30. Muller K.R., Mika S., Ratsch G., Tsuda K., Scholkopf B. IEEE Trans. Neural Netw. 2001, 12:181-201.
31. Walczak B., Massart D.L. Anal. Chim. Acta 1996, 331:177-185.
32. Walczak B., Massart D.L. Anal. Chim. Acta 1996, 331:187-193.
33. Belousov A.I., Verzakov S.A., von Frese J. Chemometr. Intell. Lab. Syst. 2002, 64:15-25.
34. Boser B.E., Guyon I.M., Vapnik V.N. A training algorithm for optimal margin classifiers. Proceedings of the 5th Annual ACM Workshop on Computational Learning Theory 1992, 144-152.
35. Luts J., Ojeda F., Van de Plas R., De Moor B., Van Huffel S., Suykens J.A.K. Anal. Chim. Acta 2010, 665:129-145.
36. Rannar S., Lindgren F., Geladi P., Wold S. J. Chemometr. 1994, 8:111-125.
37. Rosipal R., Trejo L.J. J. Mach. Learn. Res. 2001, 2:97-123.
38. Saunders C., Gammerman A., Vovk V. Ridge regression learning algorithm in dual variables. Proceedings of the 15th International Conference on Machine Learning 1998, 515-521.
39. Rantalainen M., Bylesjo M., Cloarec O., Nicholson J.K., Holmes E., Trygg J. J. Chemometr. 2007, 21:376-385.
40. Bylesjo M., Rantalainen M., Nicholson J.K., Holmes E., Trygg J. BMC Bioinform. 2008, 9:106.
41. Jalali-Heravi M., Ebrahimi-Najafabadi H., Khodabandehloo A. QSAR Comb. Sci. 2009, 28:1432-1441.
42. Bertini I., Calalbro A., De Carli V., Luchinat C., Nepi S., Porfirio B., Renzi D., Saccenti E., Tenori L. J. Proteome Res. 2009, 8:170-177.
43. Kim K., Lee J.M., Lee I.B. Chemometr. Intell. Lab. Syst. 2005, 79:22-30.
44. Zhao C.H., Wang F.L., Mao Z.Z., Liu J.C. Investigation of nonlinear orthogonal signal correction algorithm and its effects on multivariate calibration. 10th International Conference on Control Automation Robotics & Vision 2008, 2049-2054.
45. Jia R.D., Mao Z.Z., Chang Y.Q., Zhang S.N. Chemometr. Intell. Lab. Syst. 2010, 100:91-98.
46. Kirkpatrick S., Gelatt C.D., Vecchi M.P. Science 1983, 220:671-680.
47. Corana A., Marchesi M., Martini C., Ridella S. ACM Trans. Math. Softw. 1987, 13:262-280.
48. Aizerman M.A., Braverman E.M., Rozonoer L.I. Automat. Rem. Contr. 1964, 25:821-837.
49. Shawe-Taylor J., Cristianini N. Kernel Methods for Pattern Analysis 2004, Cambridge University Press, Cambridge.
50. Pai P.F., Hong W.C. Energy Convers. Manage. 2005, 46:2669-2688.
51. Imbault F., Lebart K. A stochastic optimization approach for parameter tuning of Support Vector Machines. Proceedings of the 17th International Conference on Pattern Recognition 2004, 597-600.
52. Metropolis N., Rosenbluth A., Rosenbluth M., Teller A., Teller E. J. Chem. Phys. 1953, 21:1087-1092.
53. Bradley A.P. Pattern Recogn. 1997, 30:1145-1159.
54. Varma S., Simon R. BMC Bioinform. 2006, 7:91.
55. Filmoser P., Liebmann B., Varmuza K. J. Chemometr. 2009, 23:160-171.
56. Coen M., Hong Y.S., Clayton T.A., Rohde C.M., Pearce J.T., Reily M.D., Robertson D.G., Holmes E., Lindon J.C., Nicholson J.K. J. Proteome Res. 2007, 6:2711-2719.
57. Dieterle F., Ross A., Schlotterbeck G., Senn H. Anal. Chem. 2006, 78:4281-4290.
58. Evans W.E., Johnson J.A. Annu. Rev. Genomics Hum. Genet. 2001, 2:9-39.
59. Li H.K., Ni Y., Su M.M., Qiu Y.P., Zhou M.M., Qiu M.F., Zhao A.H., Zhao L.P., Jia W. J. Proteome Res. 2007, 6:1364-1370.
60. Winnike J.H., Li Z., Wright F.A., Macdonald J.M., O'Connell T.M., Watkins P.B. Clin. Pharmacol. Ther. 2010, 88:45-51.
61. Bollard M.E., Holmes E., Lindon J.C., Mitchell S.C., Branstetter D., Zhang W., Nicholson J.K. Anal. Biochem. 2001, 295:194-202.
62. Holmes E., Nicholls A.W., Lindon J.C., Connor S.C., Connelly J.C., Haselden J.N., Damment S.J.P., Spraul M., Neidig P., Nicholson J.K. Chem. Res. Toxicol. 2000, 13:471-478.
63. Kim K.B., Um S.Y., Chung M.W., Jung S.C., Oh J.S., Kim S.H., Na H.S., Lee B.M., Choi K.H. Toxicol. Appl. Pharmacol. 2010, 249:114-126.
64. Nicholson J.K., Connelly J., Lindon J.C., Holmes E. Nat. Rev. Drug Discov. 2002, 1:153-161.
65. Norinder U. Neurocomputing 2003, 55:337-346.
66. Huang C.L., Wang C.J. Expert Syst. Appl. 2006, 31:231-240.