Metabolomics: Current technologies and future trends

Proteomics

Volumn 6, Issue 17, 2006, Pages 4716-4723

  Hollywood, Katherine ^a   Brison, Daniel R ^b   Goodacre, Royston ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

^b ST MARY S HOSPITAL   (United Kingdom)

Author keywords

Chemometrics; Metabolomics

Indexed keywords

ANALYTIC METHOD; DATA BASE; DNA FOOTPRINTING; HUMAN; IN VITRO STUDY; INFORMATION SCIENCE; METABOLOMICS; MICROORGANISM; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; REVIEW; TRANSCRIPTOMICS;

BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; HUMANS; PROTEIN ARRAY ANALYSIS; PROTEINS; PROTEOMICS; SYSTEMS BIOLOGY;

ANIMALIA;

EID: 33748603444     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200600106     Document Type: Review

References (93)

1. Barabasi, A.-L., Oltvai, Z. N., Nat. Rev. Genet. 2004, 5, 101-113.
2. Fell, D. A., Understanding the Control of Metabolism, Portland Press, London 1996.
3. Hanash, S. M., Bobek, M. R., Rickman, D. S., Williams, T. et al., Proteomics 2002, 2, 69-75.
4. Eymann, C., Homuth, G., Scharf, C., Hecker, M., J. Bacteriol. 2002, 184, 2500-2520.
5. Jones, M. B., Krutzsch, H., Shu, H. J., Zhao, Y. M. et al., Proteomics 2002, 2, 76-84.
6. Aebersold, R., Mann, M., Nature 2003, 422, 198-207.
7. Fiehn, O., Plant Mol. Biol. 2002, 48, 155-171.
8. Goodacre, R., Vaidyanathan, S., Dunn, W. B., Harrigan, G. G., Kell, D. B., Trends Biotechnol. 2004, 22, 245-252.
9. Weckwerth, W., Morgenthal, K., Drug Discovery Today 2005, 10, 1551-1558.
10. Hall, R. D., New Phytologist 2006, 169, 453-468.
11. Raamsdonk, L. M., Teusink, B., Broadhurst, D., Zhang, N. S. et al., Nat. Biotechnol. 2001, 19, 45-50.
12. ter Kuile, B. H., Westerhoff, H. V., FEBS Lett. 2001, 500, 169-171.
13. Kell, D. B., Curr. Opin. Microbiol. 2004, 7, 296-307.
14. Westerhoff, H. V., Palsson, B. O., Nat. Biotechnol. 2004, 22, 1249-1252.
15. de la Fuente, A., Snoep, J. L., Westerhoff, H. V., Mendes, P., Eur. J. Biochem. 2002, 269, 4399-4408.
16. Tweeddale, H., Notley-McRobb, L., Ferenci, T., J. Bacteriol. 1998, 180, 5109-5116.
17. Viant, M. R., Pincetich, C. A., de Ropp, J. S., Tjeerdema, R. S., Metabolomics 2005, 1, 149-158.
18. Buchholz, A., Takors, R., Wandrey, C., Anal. Biochem. 2001, 295, 129-137.
19. Villas-Boas, S. G., Højer-Pedersen, J., Akesson, M., Smedsgaard, J., Nielsen, J., Yeast 2005, 22, 1155-1169.
20. Dunn, W. B., Ellis, D. I., Trends Anal. Chem. 2005, 24, 285-294.
21. Dunn, W. B., Bailey, N. J. C., Johnson, H. E., Analyst 2005, 130, 606-625.
22. Fiehn, O., Compar. Funct.I Genomics 2001, 2, 155-168.
23. Harrigan, G. G. and Goodacre, R., Metabolic Profiling: Its Role in Biomarker Discovery and Gene Function Analysis, Kl u wer Academic Publishers, Boston 2003, pp. 335.
24. Allen, J., Davey, H. M., Broadhurst, D., Heald, J. K. et al., Nat. Biotechnol. 2003, 21, 692-696.
25. Kaderbhai, N. N., Broadhurst, D. I., Ellis, D. I., Goodacre, R., Kell, D. B., Compar. Funct. Genomics 2003, 4, 376-391.
26. Allen, J., Davey, H. M., Broadhurst, D., Rowland, J. et al., Appl. Environm. Microbiol. 2004, 70, 6157-6165.
27. Kell, D. B., Brown, M., Davey, H. M., Dunn, W. B. et al., Nat. Rev. Microbiol. 2005, 3, 557-565.
28. Leese, H. J., Conaghan, J., Martin, K. L., Hardy, K., Bioessays 1993, 15, 259-264.
29. Houghton, F. D., Leese, H. J., Eur. J. Obstetrics Gynecol. Reprod. Biol. 2004, 115 Suppl 1, S92-S96.
30. Thomas, N., Goodacre, R., Timmins, É. M., Gaudoin, M., Fleming, R., Human Reprod. 2000, 15, 1667-1671.
31. Houghton, F. D., Hawkhead, J. A., Humpherson, P. G., Hogg, J. E. et al., Human Reprod. 2002, 17, 999-1005.
32. Brison, D. R., Houghton, F. D., Falconer, D., Roberts, S. A. et al., Human Reprod. 2004, 19, 2319-2324.
33. Nicholson, J. K., Holmes, E., Lindon, J. C., Wilson, I. D., Nat. Biotechnol. 2004, 22, 1268-1274.
34. Nicholson, J. K., Wilson, I. D., Nat. Rev. Drug Discov. 2003, 2, 668-676.
35. van Ommen, B., Stierum, R., Curr. Opin. Biotechnol. 2002, 13, 517-521.
36. German, J. B., Hammock, B. D., Watkins, S. M., Metabolomics 2005, 1, 3-9.
37. Forst, C. V., Drug Discov. Today 2006, 11, 220-227.
38. Allwood, J. W., Ellis, D. I., Heald, J. K., Goodacre, R., Mur, L. A., Plant J. 2006, 46, 351-368.
39. Jenkins, H., Hardy, N., Beckmann, M., Draper, J. et al., Nat. Biotechnol. 2004, 22, 1601-1606.
40. Lindon, J. C., Nicholson, J. K., Holmes, E., Keun, H. C. et al., Nat. Biotechnol. 2005, 23, 833-838.
41. Goodacre, R., Kell, D. B., Anal. Chem. 1996, 68, 271-280.
42. Goodacre, R., Timmins, E. M., Jones, A., Kell, D. B. et al., Anal. Chim. Acta 1997, 348, 511-532.
43. Fiehn, O., Kopka, J., Dörmann, P., Altmann, T. et al., Nat. Biotechnol. 2000, 18, 1157-1161.
44. Bino, R. J., Hall, R. D., Fiehn, O., Kopka, J. et al., Trends Plant Sci. 2004, 9, 418-425.
45. Kell, D. B., Sonnleitner, B., Trends Biotechnol. 1995, 13, 481-492.
46. Brown, M., Dunn, W. B., Ellis, D. I., Goodacre, R. et al., Metabolomics 2005, 1, 39-51.
47. Manly, B. F. J., Multivariate Statistical Methods: A Primer, Chapman & Hall, London 1994, p. 215.
48. Martens, H., Næs, T., Multivariate Calibration, John Wiley, Chichester 1989.
49. van der Greef, J., Curr. Opin. Chem. Biol. 2004, 8, 559-565.
50. Hastie, T., Tibshirani, R., Friedman, J., The elements of statistical learning: data mining, inference and prediction, Springer-Verlag, Berlin 2001.
51. Chatfield, C., Collins, A. J., Introduction to Multivariate Analysis, Chapman & Hall, London 1980.
52. Bishop, C. M., Neural Networks for Pattern Recognition, Clarendon Press, Oxford 1995.
53. Rumelhart, D. E., Hinton, G. E., Williams, R. J., in: Rumelhart, D. E., McClelland, J., (Eds.), Parallel Distributed Processing, Volume 1: Foundations, MIT Press, Cambridge, MA 1986.
54. Werbos, P. J., The Roots of Back-Propagation: from Ordered Derivatives to Neural Networks and Political Forecasting, John Wiley, Chichester 1994.
55. Broomhead, D. S., Lowe, D., Complex Syst. 1988, 2, 321-355.
56. Breiman, L., Friedman, J. H., Olshen, R. A., Stone, C. J., Classification and Regression Trees, Wadsworth, Inc., Pacific Grove, CA 1984.
57. Harrington, P. B., J. Chemometrics 1991, 5, 467-486.
58. Quinlan, J. R., C4.5: programs for machine learning, Morgan Kaufmann, San Mateo, CA 1993.
59. Bäck, T., Fogel, D. B., Michalewicz, Z., Handbook of Evolutionary Computation, IOPPublishing/Oxford University Press, Oxford 1997.
60. Holland, J. H., Adaption in natural and artifcial systems, MIT Press, Cambridge, MA 1992.
61. Reeves, C. R., Genetic Algorithms - Principles and Perspectives: A Guide to GA Theory, Kluwer Academic Publishers, Dordrecht 2002.
62. Koza, J. R., Genetic Programming: On the Programming of Computers by Means of Natural Selection, MIT Press, Cambridge, MA 1992, p. 819.
63. Koza, J. R., Genetic Programming II: Automatic Discovery of Reusable Programs, MIT Press, Cambridge, MA 1994, p. 746.
64. Koza, J. R., Bennett, F. H., Keane, M. A., Andre, D., Genetic Programming III: Darwinian Invention and Problem Solving, Morgan Kaufmann, San Francisco 1999.
65. Koza, J. R., Keane, M. A., Streeter, M. J., Mydlowec, W. et al., Genetic Programming: Routine Human-Competitive Machine Intelligence, Kluwer, New York 2003.
66. Kell, D. B., Darby, R. M., Draper, J., Plant Physiol. 2001, 126, 943-951.
67. Rozen, S., Cudkowicz, M. E., Bogdanov, M., Matson, W. R. et al., Metabolomics 2005, 1, 101-108.
68. Kenny, L. C., Dunn, W. B., Ellis, D. I., Myers, J. et al., Metabolomics 2005, 1, 227-234.
69. Bijlsma, S., Bobeldijk, I., Verheij, E. R., Ramaker, R. et al., Anal. Chem. 2006, 78, 567-574.
70. Jeong, H., Tombor, B., Albert, R., Oltvai, Z. N., Barabási, A.-L., Nature 2000, 407, 651-654.
71. Wagner, A., Fell, D. A., Proc. Royal Soc. London B 2001, 268, 1803-1810.
72. Mendes, P., Brief Bioinform. 2002, 3, 134-45.
73. Weckwerth, W., Fiehn, O., Curr. Opin. Biotechnol. 2002, 13, 156-160.
74. Förster, J., Famili, I., Fu, P., Palsson, B. O., Nielsen, J., Genome Res. 2003, 13, 244-253.
75. Camacho, D., de la Fuente, A., Mendes, P., Metabolomics 2005, 1, 53-63.
76. Bederman, I. R., Reszko, A. E., Kasumov, T., David, F. et al., J. Biol. Chem. 2004, 279, 43207-43216.
77. Villas-Bôas, S. G., Mas, S., Åkesson, M., Smedsgaard, J., Nielsen, J., Mass Spectrom. Rev. 2005, 24, 616-646.
78. Satake, M., Dmochowska, B., Nishikawa, Y., Madaj, J. et al., Invest. Ophthalmol. Vis. Sci. 2003, 44, 2047-2058.
79. Welthagen, W., Shellie, R. A., Spranger, J. M., Ristow, M. et al., Metabolomics 2005, 1, 65-73.
80. Gamache, P. H., J. Am. Soc. Mass Spectrom. 2004, 15, 1717-1726.
81. Wilson, I. D., Plumb, R., Granger, J., Major, H. et al., J. Chromatogr. B 2005, 817, 67-76.
82. Tolstikov, V. V., Lommen, A., Nakanishi, K., Tanaka, N., Fiehn, O., Anal. Chem. 2003, 75, 6737-6740.
83. Soga, T., Ueno, Y., Naraoka, H., Ohashi, Y. et al., Anal. Chem. 2002, 74, 2233-2239.
84. Soga, T., Ohashi, Y., Ueno, Y., Naraoka, H. et al., J. Proteome Res. 2003, 2, 488-494.
85. Nicholson, J. K., Lindon, J. C., Holmes, E., Xenobiotica 1999, 29, 1181-1189.
86. Weifender, J. L., Ndjoko, K., Hostettmann, K., J. Chromatogr. A 2003, 1000, 437-455.
87. Harrigan, G. G., LaPlante, R. H., Cosma, G. N., Cockerell, G. et al., Toxicol. Lett. 2004, 146, 197-205.
88. Ellis, D. I., Goodacre, R., Analyst 2006, 131, 875-885.
89. Vaidyanathan, S., Kell, D. B., Goodacre, R., J. Am. Soc. Mass Spectrom. 2002, 13, 118-128.
90. Overy, S. A., Walker, H. J., Malone, S., Howard, T. P. et al., J. Exp. Botany 2005, 56, 287-296.
91. Vaidyanathan, S., Jones, D., Broadhurst, D. I., Ellis, J. et al., Metabolomics 2005, 1, 243-250.
92. Aharoni, A., Ric de Vos, C. H., Verhoeven, H. A., Maliepaard, C. A. et al., Omics 2003, 6, 217-234.
93. Boros, L. G., Metabolomics 2005, 1, 11-15.