Design of human nutrigenomics studies

Design of Human Nutrigenomics Studies

Volumn , Issue , 2009, Pages 1-100

  Astley, S ^a   Penn, L ^b  

^a INSTITUTE OF FOOD RESEARCH   (United Kingdom)

^b NEWCASTLE UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84899163779     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.3920/978-90-8686-672-4     Document Type: Book

References (98)

1. Afman, L. and Muller, M., 2006. Nutrigenomics: from molecular nutrition to prevention of disease. Journal of the American Dietetic Association 106(4):569-576.
2. Aldred, S., Sozzi, T., Mudway, I., Grant, M.M., Neubert, H., Kelly, F.J. and Griffiths, H.R., 2006. Alpha tocopherol supplementation elevates plasma apolipoprotein A1 isoforms in normal healthy subjects. Proteomics 6: 1695-1703.
3. Arbones-Mainar, J.M., Ross, K., Rucklidge, G.J., Reid, M., Duncan, G., Arthur, J.R., Horgan, G.W., Navarro, M.A., Carnicer, R., Arnal, C., Osada, J. and De Roos, B., 2007. Extra virgin olive oils increase hepatic fat accumulation and hepatic antioxidant protein levels in APOE(-/-) mice. Journal of Proteome Research 6: 4041-4054.
4. Bedair, M. and Sumner, L.W., 2008. Current and emerging mass-spectrometry technologies for metabolomics. Trends in Analytical Chemistry 27(3):238-250.
5. Belshaw, N.J., Elliott, G.O., Foxall, R.J., Dainty, J.R., Pal, N., Coupe, A., Garg, D., Bradburn, D.M., Mathers, J.C. and Johnson, I.T., 2008. Profiling CpG island field methylation in both morphologically normal and neoplastic human colonic mucosa. British Journal of Cancer 99: 136-142.
6. Bergheanu, S.C., Reijmers, T., Zwinderman, A.H., Bobeldijk, I., Ramaker, R., Liem, A.-H., Van der Greef, J., Hankemeier, T. and Jukema, J.W., 2008. Lipidomic approach to evaluate rosuvastatin and atorvastatin at various dosages: investigating differential effects among statins. Current Medical Research and Opinion 24(9): 2477-2487.
7. Bergmann, M.M., Görman, U. and Mathers, J.C., 2008. Bioethical considerations for human nutrigenomics. Annual Review of Nutrition 28: 447-467.
8. Bernstein, B.E., Meissner, A. and Lander, E.S., 2007. The mammalian epigenome. Cell 128: 669-681.
9. Bestor, T.H., 2000 The DNA methyltransferases of mammals. Human Molecular Genetics 9: 2395-2402.
10. Bijlsma, S., Bobeldijk, I., Verheij, E.R., Ramaker, R., Kochhar, S., Macdonald, I.A., Van Ommen B. and Smilde, A.K., 2006. Large-scale human metabolomics studies: a strategy for data (pre-) processing and validation:Analytical Chemistry 78(2): 567-574.
11. Biron, D.G., Brun, C., Lefevre, T., Lebarbenchon, C., Loxdale, H.D., Chevenet, F., Brizard, J.P. and Thomas, F., 2006. The pitfalls of proteomics experiments without the correct use of bioinformatics tools. Proteomics 6: 5577-5596.
12. Bouwens, M., Afman, L.A. and Müller M., 2007. Fasting induces changes in peripheral blood mononuclear cell gene expression profiles related to increases in fatty acid beta-oxidation: functional role of peroxisome proliferator activated receptor alpha in human peripheral blood mononuclear cells. American Journal of Clinical Nutrition 86(5): 1515-1523.
13. Bouwens, M., Afman, L.A. and Müller, M., 2008. Activation of peroxisome proliferator-activated receptor alpha in human peripheral blood mononuclear cells reveals an individual gene expression profile response. BMC Genomics 9: 262.
14. Brena, R.M., Huang, T.H. and Plass, C., 2006. Toward a human epigenome. Nature Genetics 38: 1359-1360.
15. Carr, S., Aebersold, R., Baldwin, M., Burlingame, A., Clauser, K. and Nesvizhskii, A., 2004. The need for guidelines in publication of peptide and protein identification data: Working group on publication guidelines for peptide and protein identification data. Molecular and Cellular Proteomics 3: 531-533.
16. Caslake, M.J., Miles, E.A., Kofler, B.M., Lietz, G., Curtis, P., Armah, C.K., Kimber, A.C., Grew, J.P., Farrell, L., Stannard, J., Napper, F.L., Sala-Vila, A., West, A.L., Mathers, J.C., Packard, C., Williams, C.M., Calder, P.C. and Minihane, A.M., 2008. Effect of sex and genotype on cardiovascular biomarker response to fish oils: the FINGEN study. American Journal of Clinical Nutrition 88(3): 618-629.
17. Cebrian, A., Pharoah, P.D., Ahmed, S., Ropero, S., Fraga, M.F., Smith, P.L., Conroy, D., Luben, R., Perkins, B., Easton, D.F., Dunning, A.M., Esteller, M. and Ponder, B.A., 2006. Genetic variants in epigenetic genes and breast cancer risk. Carcinogenesis 27(8): 1661-1669.
18. Cobb, J.P., Mindrinos, M.N., Miller-Graziano, C., Calvano, S.E., Baker, H.V., Xiao, W., Laudanski, K., Brownstein, B.H., Elson, C.M., Hayden, D.L., Herndon, D.N., Lowry, S.F., Maier, R.V., Schoenfeld, D.A., Moldawer, L.L., Davis, R.W., Tompkins, R.G., Baker, H.V., Bankey, P., Billiar, T., Brownstein, B.H., Calvano, S.E., Camp, D., Chaudry, I., Cobb, J.P., Davis, R.W., Elson, C.M., Freeman, B., Gamelli, R., Gibran, N., Harbrecht, B., Hayden, D.L., Heagy, W., Heimbach, D., Herndon, D.N., Horton, J., Hunt, J., Laudanski, K., Lederer, J., Lowry, S.F., Maier, R.V., Mannick, J., McKinley, B., Miller-Graziano, C., Mindrinos, M.N., Minei, J., Moldawer, L.L., Moore, E., Moore, F., Munford, R., Nathens, A., O'keefe, G., Purdue, G., Rahme, L., Remick, D., Sailors, M., Schoenfeld, D.A., Shapiro, M., Silver, G., Smith, R., Stephanopoulos, G., Stormo, G., Tompkins, R.G., Toner, M., Warren, S., West, M., Wolfe, S., Xiao, W., Young, V. and Host Response to Injury Large-Scale Collaborative Research Program, 2005. Application of genomewide expression analysis to human health and disease. Proceedings of the National Academy of Sciences USA 102(13): 4801-4806.
19. Consortium WTCC, 2007. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447(7145):661-678.
20. Coulier, L., Wopereis, S., Hendriks, H., Radonjic, M. and Jellema, R., in press. Applied chemometrics in systems biology and nutritional metabolomics. Comprehensive Chemometrics: in press.
21. Crujeiras, A.B., Parra, D., Milagro, F.I., Goyenechea, E., Larrarte, E., Margareto, J. and Martínez, J.A., 2008. Differential expression of oxidative stress and inflammation related genes in peripheral blood mononuclear cells in response to a low-calorie diet: a nutrigenomics study. OMICS: A Journal of Integrative Biology 12(4): 251-261.
22. Curtis, R.K., Oresic, M. and Vidal-Puig, A., 2005. Pathways to the analysis of microarray data. Trends in Biotechnology 23(8): 429-435.
23. De Roos, B. and McArdle, H.J., 2008. Proteomics as a tool for the modelling of biological processes and biomarker development in nutrition research. British Journal of Nutrition 99: S66-S71.
24. De Roos, B., Duivenvoorden, I., Rucklidge, G., Reid, M., Ross, K., Lamers, R.J., Voshol, P.J., Havekes, L.M. and Teusink, B., 2005. Response of apolipoprotein E*3-Leiden transgenic mice to dietary fatty acids: combining liver proteomics with physiological data. FASEB J 19: 813-815.
25. De Roos, B., Duthie, S.J., Polley, A.C., Mulholland, F., Bouwman, F.G., Heim, C., Rucklidge, G.J., Johnson, I.T., Mariman, E.C., Daniel, H. and Elliott, R.M., 2008a. Proteomic methodological recommendations for studies involving human plasma, platelets, and peripheral blood mononuclear cells. Journal of Proteome Research 7: 2280-2290.
26. De Roos, B., Geelen, A., Ross, K., Rucklidge, G., Reid, M., Duncan, G., Caslake, M., Horgan, G. and Brouwer, I.A., 2008b. Identification of potential serum biomarkers of inflammation and lipid modulation that are altered by fish oil supplementation in healthy volunteers. Proteomics 8: 1965-1974.
27. Dragsted, L.O., Krath, B., Ravn-Haren, G., Vogel, U.B., Vinggaard, A.M., Bo Jensen, P., Loft, S., Rasmussen, S.E., Sandstrom, T.B. and Pedersen, A., 2006. Biological effects of fruit and vegetables. Proceedings of the Nutrition Society 65(1): 61-67.
28. Draisma, H.H., Reijmers, T.H., Bobeldijk-Pastorova, I., Meulman, J.J., Estourgie-Van Burk, G.F., Bartels, M., Ramaker, R., Van der Greef, J., Boomsma, D.I. and Hankemeier, T., 2008. Similarities and differences in lipidomics profiles among healthy monozygotic twin pairs. OMICS: A Journal of Integrative Biology 12(1): 17-31.
29. Dumas, M.E., Maibaum, E.C., Teague, C., Ueshima, H., Zhou, B., Lindon, J.C., Nicholson, J.K., Stamler, J., Elliott, P., Chan, Q. and Holmes, E., 2006. Assessment of analytical reproducibility of 1H NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study: Analytical Chemistry 78(7): 2199-2208.
30. Eady, J.J., Wortley, G.M., Wormstone, Y.M., Hughes, J.C., Astley, S.B., Foxall, R.J., Doleman, J.F. and Elliott, R.M., 2005. Variation in gene expression profiles of peripheral blood mononuclear cells from healthy volunteers. Physiological Genomics 22(3):402-411.
31. Eckhardt, F., Lewin, J., Cortese, R., Rakyan, V.K., Attwood, J., Burger, M., Burton, J., Cox, T.V., Davies, R., Down, T.A., Haefliger, C., Horton, R., Howe, K., Jackson, D.K., Kunde, J., Koenig, C., Liddle, J., Niblett, D., Otto, T., Pettett, R., Seemann, S., Thompson, C., West, T., Rogers, J., Olek, A., Berlin, K. and Beck, S., 2006. DNA methylation profiling of human chromosomes 6, 20 and 22. Nature Genetics 38: 1378-1385.
32. Fang, X and Zhang, W.W., 2008. Affinity separation and enrichment methods in proteomic analysis. Journal of Proteomics 71: 284-303.
33. Fraga, M.F., Ballestar, E., Paz, M.F., Ropero, S., Setien, F., Ballestar, M.L., Heine-Suner, D., Cigudosa, J.C., Urioste, M., Benitez, J., Boix-Chornet, M., Sanchez-Aguilera, A., Ling, C., Carlsson, E., Poulsen, P., Vaag, A., Stephan, Z., Spector, T.D., Wu, Y.Z., Plass, C. and Esteller, M., 2005. Epigenetic differences arise during the lifetime of monozygotic twins. Proceedings of the National Academy of Science USA 102: 10604-10609.
34. Friedman, D.B., Hill, S., Keller, J.W., Merchant, N.B., Levy, S.E., Coffey, R.J. and Caprioli, R.M., 2004. Proteome analysis of human colon cancer by two-dimensional difference gel electrophoresis and mass spectrometry. Proteomics 4(3): 793-811.
35. Friso, S., Choi, S.-W., Girelli, D., Mason, J.B., Dolnikowski, G.G., Bagley, P.J., Olivieri, O., Jacques, P.F., Rosenberg, I.H., Corrocher, R. and Selhub, J., 2002. A common mutation in the 5,10-methylenetetrahydrofolate reductase gene affects genomic DNA methylation through an interaction with folate status. Proceedings of the National Academy of Science USA 99: 5606-5611.
36. Fuchs, D., Piller, R., Linseisen, J., Daniel, H. and Wenzel, U., 2007a. The human peripheral blood mononuclear cell proteome responds to a dietary flaxseed-intervention and proteins identified suggest a protective effect in atherosclerosis. Proteomics 7: 3278-3288.
37. Fuchs, D., Vafeiadou, K., Hall, W.L., Daniel, H., Williams, C.M., Schroot, J.H. and Wenzel, U., 2007b. Proteomic biomarkers of peripheral blood mononuclear cells obtained from postmenopausal women undergoing an intervention with soy isoflavones. American Journal of Clinical Nutriton 86: 1369-1375.
38. Garcia, A., Watson, S.P., Dwek, R.A. and Zitzmann, N., 2005. Applying proteomics technology to platelet research. Mass Spectrometry Reviews 24:918-930.
39. Gerszten, R.E. and Wang, T.J., 2008. The search for new cardiovascular biomarkers. Nature 451: 949-52.
40. Gika, H.G., Theodoridis, G.A. and Wilson, I.D., 2008. Liquid chromatography and ultra-performance liquid chromatography-mass spectrometry fingerprinting of human urine. Sample stability under different handling and storage conditions for metabonomics studies. Journal of Chromatography A 1189: 314-322.
41. Hake, S.B., Xiao, A. and Allis, C.D., 2004. Linking the epigenetic 'language' of covalent histone modifications to cancer. British Journal of Cancer 90:761-769.
42. Horgan, G.W., 2007. Sample size and replication in 2D gel electrophoresis studies. Journal of Proteome Research 6(7): 2884-2887.
43. Hudgin, R.L., Pricer, W.E. Jr, Ashwell, G., Stockert, R.J. and Morell, A.G., 1974. Isolation and properties of a rabbit liver binding-protein specific for asialoglycoproteins. Journal of Biological Chemistry 249(17): 5536-5543.
44. Hunt, S.M., Thomas, M.R., Sebastian, L.T., Pedersen, S.K., Harcourt, R.L., Sloane, A.J. and Wilkins, M.R., 2005. Optimal replication and the importance of experimental design for gel-based quantitative proteomics. Journal of Proteome Research 4: 809-819.
45. Ilveskoski, E., Perola, M., Lehtimäki, T., Laippala, P., Savolainen, V., Pajarinen, J., Penttilä, A., Lalu, K.H., Männikkö, A., Liesto, K.K., Koivula, T. and Karhunen, P.J., 1999. Age-dependent association of apolipoprotein E genotype with coronary and aortic atherosclerosis in middle-aged men: an autopsy study. Circulation 100(6):608-613.
46. Irizarry, R.A., Warren, D., Spencer, F., Kim, I.F., Biswal, S., Frank, B.C., Gabrielson, E., Garcia, J.G., Geoghegan, J., Germino, G., Griffin, C., Hilmer, S.C., Hoffman, E., Jedlicka, A.E., Kawasaki, E., Martínez-Murillo, F., Morsberger, L., Lee, H., Petersen, D., Quackenbush, J., Scott, A., Wilson, M., Yang, Y., Ye, S.Q. and Yu, W., 2005. Multiple-laboratory comparison of microarray platforms. Nature Methods 2(5): 345-350.
47. Issaq, H.J., Abbott, E. and Veenstra, T.D., 2008. Utility of separation science in metabolomic studies. Journal of Separation Science 31: 1936-1947.
48. Jacob, R.A., Gretz, D.M., Taylor, P.C., James, S.J., Pogribny, I.P., Miller, B.J., Henning, S. M. and Swendseid, M.E., 1998. Moderate folate depletion increases plasma homocysteine and decreases lymphocyte DNA methylation in postmenopausal women. Journal of Nutrition 128: 1204-1212.
49. Jirtle, R.L. and Skinner, M.K., 2007. Environmental epigenomics and disease susceptibility. Nature Reviews Genetics 8: 253-262.
50. Joost, H.G., Gibney, M.J., Cashman, K.D., Görman, U., Hesketh, J.E., Muller, M., Van Ommen, B., Williams, C.M. and Mathers, J.C., 2007. Personalised nutrition: status and perspectives. British Journal of Nutrition 98: 26-31.
51. Kendziorski, C., Irizarry, R.A., Chen, K.-S., Haag, J.D. and Gould, M.N., 2005. On the utility of pooling biological samples in microarray experiments. Proceedings of the National Academy of Sciences USA 102(12): 4252-4257.
52. Klerk, M., Verhoef, P., Clarke, R., Blom, H.J., Kok, F.J. and Schouten, E.G., 2002. MTHFR 677C-->T polymorphism and risk of coronary heart disease: a meta-analysis. JAMA 288(16): 2023-2031.
53. Koek, M.M.; Muilwijk, B.; Van der Werf, M.J. and Hankemeier, T.H., 2006. Microbial metabolomics with gas chromatography/mass spectrometry. Analytical Chemistry 78: 1272-1281.
54. Korshunova, Y., Maloney, R.K., Lakey, N., Citek, R.W., Bacher, B., Budiman, A., Ordway, J.M., McCombie, W.R., Leon, J., Jeddeloh, J.A. and McPherson, J.D., 2008. Massively parallel bisulphite pyrosequencing reveals the molecular complexity of breast cancer-associated cytosine-methylation patterns obtained from tissue and serum DNA. Genome Research 18: 19-29.
55. Lasky-Su, J., Lyon, H.N., Emilsson, V., Heid, I.M., Molony, C., Raby, B.A., Lazarus, R., Klanderman, B., Soto-Quiros, M.E., Avila, L., Silverman, E.K., Thorleifsson, G., Thorsteinsdottir, U., Kronenberg, F., Vollmert, C., Illig, T., Fox, C.S., Levy, D., Laird, N., Ding, X., McQueen, M.B., Butler, J., Ardlie, K., Papoutsakis, C., Dedoussis, G., O'Donnell, C.J., Wichmann, H.E., Celedón, J.C., Schadt, E., Hirschhorn, J., Weiss, S.T., Stefansson, K. and Lange, C., 2008. On the replication of genetic associations: timing can be everything! American Journal of Human Genetics 82(4): 849-858.
56. Macaulay, I.C., Carr, P., Gusnanto, A., Ouwehand, W.H., Fitzgerald, D. and Watkins, N.A., 2005. Platelet genomics and proteomics in human health and disease. Journal of Clinical Investigation 115: 3370-3377.
57. Martin, K.J., Graner, E., Li Y., Price, L.M., Kritzman, B.M., Fournier, M.V., Rhei, E. and Pardee, A.B., 2001. High-sensitivity array analysis of gene expression for the early detection of disseminated breast tumor cells in peripheral blood. Proceedings of the National Academy of Sciences USA 98(5): 2646-2651.
58. Mathers, J.C., 2006a. Candidate mechanisms for interactions between nutrients and genes. In: Choi, S.-W. and Friso, S. (eds.), Nutrient-gene interactions in cancer. Taylor & Francis Group, Boca Raton, 19-36pp.
59. Mathers, J.C., 2006b. Nutritional modulation of ageing: genomic and epigenetic approaches. Mechanisms of Ageing and Development 127: 584-589.
60. Mckay, J., Adriaens, M., Ford, D., Relton, C., Evelo, C. and Mathers, J.C., 2009. Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation - in press
61. Minihane, A.M., Khan, S., Leigh-Firbank, E.C., Talmud, P., Wright, J.W., Murphy, M.C., Griffin, B.A. and Williams, C.M., 2000. ApoE polymorphism and fish oil supplementation in subjects with an atherogenic lipoprotein phenotype. Arteriosclerosis, Thrombosis, and Vascular Biology 20(8):1990-1997.
62. Müller, M. and Kersten, S., 2003. Nutrigenomics: Goals and strategies. Nature Reviews Genetics 4: 315-322.
63. National Institutes of Health, 2008. NIH announces new initiative in epigenomics. NIH News: 22 January 2008.
64. Nijhout, H.F., Reed, M.C., Anderson, D.F., Mattingly, J.C., James, S.J. and Ulrich, C.M., 2006. Long-range allosteric interactions between the folate and methionine cycles stabilize DNA methylation reaction rate. Epigenetics 1: 81-87.
65. O'Neill, E.E., Brock, C.J., Von Kriegsheim, A.F., Pearce, A.C., Dwek, R.A., Watson, S.P. and Hebestreit, H.F., 2002. Towards complete analysis of the platelet proteome. Proteomics 2: 288-305.
66. Orchard, S., Hermjakob, H. and Apweiler, R., 2003. The proteomics standards initiative. Proteomics 3(7): 1374-1376.
67. Ordovas, J.M., 2002. Gene-diet interaction and plasma lipid responses to dietary intervention. Biochemical Society Transactions 30(2): 68-73.
68. Ordovas, J.M., Corella, D., Demissie, S., Cupples, L.A., Couture, P., Coltell, O., Wilson, P.W., Schaefer, E.J. and Tucker, K.L., 2002. Dietary fat intake determines the effect of a common polymorphism in the hepatic lipase gene promoter on high-density lipoprotein metabolism: evidence of a strong dose effect in this gene-nutrient interaction in the Framingham Study. Circulation 106(18): 2315-2321.
69. Pearson, T.A. and Manolio, T.A., 2008. How to interpret a genome-wide association study. JAMA 299(11): 1335-1344.
70. Polley, A.C., Mulholland, F., Pin, C., Williams, E.A., Bradburn, D.M., Mills, S.J., Mathers, J.C. and Johnson I.T., 2006. Proteomic analysis reveals fieldwide changes in protein expression in the morphologically normal mucosa of patients with colorectal neoplasia. Cancer Research 66(13): 6553-6562.
71. Ptitsyn, A.A., Zvonic, S., Conrad, S.A., Scott, L.K., Mynatt, R.L. and Gimble, J.M., 2006. Circadian clocks are resounding in peripheral tissues. PLoS Computational Biology 2(3): e16. doi:10.1371/journal.pcbi.0020016
72. Radich, J.P., Mao, M., Stepaniants, S., Biery, M., Castle, J., Ward, T., Schimmack, G., Kobayashi, S., Carleton, M., Lampe, J. and Linsley, P.S., 2004. Individualspecific variation of gene expression in peripheral blood leukocytes. Genomics 83(6): 980-988.
73. Rakyan, V.K., Hildmann, T., Novik, K.L., Lewin, J., Tost, J., Cox, A.V., Andrews, T.D., Howe, K.L., Otto, T., Olek, A., Fischer, J., Gut, I. G., Berlin, K. and Beck, S., 2004. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biology 2(12): e405. doi:10.1371/journal.pbio.0020405
74. Reik, W., Dean, W. and Walter, J., 2001. Epigenetic reprogramming in mammalian development. Science 293: 1089-1093.
75. Sangster, T., Major, H., Plumb, R., Wilson, A.J. and Wilson, I.D., 2006. A pragmatic and readily implemented quality control strategy for HPLC-MS and GC-MS-based metabolomic analysis. Analyst 131: 1075-1078.
76. Saude, E.J. and Sykes, B.D., 2007. Urine stability for metabolomic studies:effects of preparation and storage. Metabolomics 3: 19-27.
77. Schnackenberg, L.K., Kaput, J. and Beger, R.D., 2008. Metabolomics: a tool for personalizing medicine? Biotechnology Advances 26(2): 169-176.
78. Shaham, O., Wei, R., Wang, T.J., Ricciardi, C., Lewis, G.D., Vasan, R.S., Carr, S.A., Thadhani, R., Gerszten, R.E. and Mootha, V.K., 2008. Metabolic profiling of the human response to a glucose challenge reveals distinct axes of insulin sensitivity. Molecular Systems Biology 4: 214.
79. Slupsky, C.M., Rankin, K.N., Wagner, J., Fu, H., Chang, D., Weljie, A.M., Saude, E.J., Lix, B., Adamko, D.J., Shah, S., Greiner, R., Sykes, B.D. and Marrie, T.J., 2007. Investigations of the effects of gender, diurnal variation, and age in human urinary metabolomic profiles. Analytical Chemistry 79(18): 6995-7004.
80. Smilde, A.K., Bro, R. and Geladi, P., 2004. Multi-way analysis: Applications in the chemical sciences. Wiley, West Sussex, UK, pp. 221-256.
81. Song, Y., Stampfer, M.J. and Liu, S., 2004. Meta-analysis: apolipoprotein E genotypes and risk for coronary heart disease. Annals of Internal Medicine 141(2): 137-147.
82. Stulík, J., Koupilova, K., Osterreicher, J., Knízek, J., Macela, A., Bures, J., Jandík, P., Langr, F., Dedic, K. and Jungblut, P.R., 1999. Protein abundance alterations in matched sets of macroscopically normal colon mucosa and colorectal carcinoma. Electrophoresis 20(18): 3638-3646.
83. Taylor, C.F., Paton, N.W., Lilley, K.S., Binz, P.A., Julian, R.K. Jr, Jones, A.R., Zhu, W., Apweiler, R., Aebersold, R., Deutsch, E.W., Dunn, M.J., Heck, A.J., Leitner, A., Macht, M., Mann, M., Martens, L., Neubert, T.A., Patterson, S.D., Ping, P., Seymour, S.L., Souda, P., Tsugita, A., Vandekerckhove, J., Vondriska, T.M., Whitelegge, J.P., Wilkins, M.R., Xenarios, I., Yates, J.R. 3rd and Hermjakob, H., 2007. The minimum information about a proteomics experiment (MIAPE). Nature Biotechnology 25(8): 887-893.
84. Thissen, U., Wopereis, S., Van den Berg, S.A., Bobeldijk, I., Kleemann, R., Kooistra, T., van Dijk, K.W., Van Ommen, B. and Smilde, A.K., 2009. Improving the analysis of designed studies by combining statistical modelling with study design information. BMC Bioinformatics 10: 52.
85. Valk, P.J., Verhaak, R.G., Beijen, M.A., Erpelinck, C.A., Barjesteh van Waalwijk van Doorn-Khosrovani, S., Boer, J.M., Beverloo, H.B., Moorhouse, M.J., Van der Spek, P.J., Löwenberg, B. and Delwel, R., 2004. Prognostically useful gene-expression profiles in acute myeloid leukemia. New England Journal of Medicine 350(16): 1617-1628.
86. Van der Greef, J., Hankemeier, T. and McBurney, R.N., 2006. Metabolomicsbased systems biology and personalized medicine: moving towards n = 1 clinical trials? Pharmacogenomics 7(7): 1087-1094.
87. Van der Greef, J., Martin, S., Juhasz, P., Adourian, A., Plasterer, T., Verheij, E.R. and McBurney, R.N., 2007. The art and practice of systems biology in medicine: Mapping patterns of relationships. Journal of Proteome Research 6: 1540-1559.
88. Van der Greef, J., Martin, S., Juhasz, P., Adourian, A., Plasterer, T., Verheij, E.R. and McBurney, R.N., 2007. The art and practice of systems biology in medicine: Mapping patterns of relationships. Journal of Proteome Research 6: 1540-1559.
89. Van Erk, M.J., Blom, W.A., Van Ommen, B. and Hendriks, H.F., 2006. High-protein and high-carbohydrate breakfasts differentially change the transcriptome of human blood cells. American Journal of Clinical Nutrition 84: 1233-1241.
90. Walsh, M.C., Brennan, L., Malthouse, J.P., Roche, H.M. and Gibney, M.J., 2006. Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans: American Journal of Clinical Nutrition 84(3): 531-539.
91. Wheelock, A.M. and Goto, S., 2006. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Reviews in Proteomics 3: 129-142.
92. Whitney, A.R., Diehn, M., Popper, S.J., Alizadeh, A.A., Boldrick, J.C., Relman, D.A. and Brown, P.O., 2003. Individuality and variation in gene expression patterns in human blood. Proceedings of the National Academy of Sciences USA 100(4): 1896-1901.
93. Wilkins, M.R., Appel, R.D., van Eyk, J.E., Chung, M.C., Görg, A., Hecker, M., Huber, L.A., Langen, H., Link, A.J., Paik, Y.K., Patterson, S.D., Pennington, S.R., Rabilloud, T., Simpson, R.J., Weiss, W. and Dunn, M.J., 2006. Guidelines for the next 10 years of proteomics. Proteomics 6: 4-8.
94. Wilson, A.S., Power, B.E. and Molloy, P.L., 2007 DNA hypomethylation and human diseases. Biochimica et Biophysica Acta 1775: 138-1362.
95. Wopereis, S., Rubingh, C.M., Van Erk, M.J., Verheij, E.R., van Vliet, T., Cnubben, N.H., Smilde, A.K., Van der Greef, J., Van Ommen, B. and Hendriks, H.F., 2009. Metabolic profiling of the response to an oral glucose tolerance test detects subtle metabolic changes. PLoS ONE 4(2):e4525 doi:10.1371/journal.pone.0004525.
96. Yang, A.S., Estecio, M.R., Doshi, K., Kondo, Y., Tajara, E.H. and Issa, J.P., 2004. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Research 32: e38.
97. Zdravkovic, S., Wienke, A., Pedersen, N.L., Marenberg, M.E., Yashin, A.I. and De Faire, U., 2002. Heritability of death from coronary heart disease:a 36-year follow-up of 20, 966 Swedish twins. Journal of Internal Medicine 252(3): 247-254.
98. Zvonic, S., Ptitsyn, A.A., Conrad, S.A., Scott, L.K., Floyd, Z.E., Kilroy, G., Wu, X., Goh, B.C., Mynatt, R.L. and Gimble, J.M., 2006. Characterization of peripheral circadian clocks in adipose tissues. Diabetes 55(4): 962-970.