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Veselkov KA, Lindon JC, Ebbels TM, Crockford D, Volynkin VV, Holmes E, Davies DB, Nicholson JK. 2009. Recursive segment-wise peak alignment of biological  NMR spectra for improved metabolic biomarker recovery. Anal Chem 81: 56-66.
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Craig A, Cloarec O, Holmes E, Nicholson JK, Lindon JC. 2006. Scaling and normalization effects in NMR spectroscopic metabonomic data sets. Anal Chem 78: 2262-2267.
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Dieterle F, Ross A, Schlotterbeck G, Senn H. 2006. Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in NMR metabonomics. Anal Chem 78: 4281-4290.
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Savorani F, Rasmussen MA, Mikkelson MS, Engelsen SB. 2013. A primer to nutritional metabolomics by NMR spectroscopy and chemometrics. Food Res Int 54: 1131-1145.
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McNiven EM, German JB, Slupsky CM. 2011. Analytical metabolomics: nutritional opportunities for personalized health. J Nutr Biochem 22: 995-1002.
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Brennan L. 2013. Metabolomics in nutrition research: current status and perspectives. Biochem Soc Trans 41: 670-673
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Ismail NA, Posma JM, Frost G, Holmes E, Garcia-Perez I. 2013. The role of metabonomics as a tool for augmenting nutritional information in epidemiological studies. Electrophoresis 34: 2776-2786.
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Montoliu I, Genick U, Ledda M, Collino S, Martin FP, le Coutre J, Rezzi S. 2013. Current status on genome-metabolome- wide associations: an opportunity in nutrition research. Genes Nutr 8: 19-27.
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Jones DP, Park Y, Ziegler TR. 2012. Nutritional metabolomics: progress in addressing complexity in diet and health. Annu Rev Nutr 32: 183-202.
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Solanky KS, Bailey NJ, Beckwith-Hall BM, Davis A, Bingham S, Holmes E, Nicholson JK, Cassidy A. 2003. Application of biofluid nuclear magnetic resonancebased metabonomic techniques for the analysis of the biochemical effects of dietary isoflavones on human plasma profile. Anal Biochem 323: 197-204.
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Solanky KS, Bailey NJ, Beckwith-Hall BM, Bingham S, Davis A, Holmes E, Nicholson JK, Cassidy A. 2005. Biofluid NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J Nutr Biochem 16: 236-244.
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Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott P. 2008. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453: 396-400.
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Lenz EM, Bright J, Wilson ID, Hughes A, Morrisson J, Lindberg H, Lockton A. 2004. Metabonomics, dietary influences and cultural differences: a NMR-based study of urine samples obtained from healthy British and Swedish subjects. J Pharm Biomed Anal 36: 841-849.
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Pere-Trepat E, Ross AB, Martin FP, Rezzi S, Kochhar S, Hasselbalch AL, Kyvik KO, Sorensen TIA. 2010. Chemometric strategies to assess metabonomic imprinting of food habits in epidemiological studies. Chemom Intell Lab Syst 104: 95-100.
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Martin FP, Antille N, Rezzi S, Kochhar S. 2012. Everyday eating experiences of chocolate and non-chocolate snacks impact postprandial anxiety, energy and emotional states. Nutrients 4: 554-567.
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Dumas ME, Maibaum EC, Teague C, Ueshima H, Zhou B, Lindon JC, Nicholson JK, Stamler J, Elliott P, Chan Q, Holmes E. 2006. Assessment of analytical reproducibility of NMR spectroscopy based metabonomics for large-scale epidemiological research: the INTERMAP Study. Anal Chem 78: 2199-2208.
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Martin FP, Rezzi S, Pere-Trepat E, Kamlage B, Collino S, Leibold E, Kastler J, Rein D, Fay LB, Kochhar S. 2009. Metabolic effects of dark chocolate consumption on energy, gut microbiota, and stress-related metabolism in free-living subjects. J Proteome Res 8: 5568-5579.
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Martin FP, Montoliu I, Nagy K, Moco S, Collino S, Guy P, Redeuil K, Scherer M, Rezzi S, Kochhar S. 2012. Specific dietary preferences are linked to differing gut microbial metabolic activity in response to dark chocolate intake. J Proteome Res 11: 6252-6263.
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Newgard CB, An J, Bain JR, Muehlbauer MJ, Stevens RD, Lien LF, Haqq AM, Shah SH, Arlotto M, Slentz CA, Rochon J, Gallup D, Ilkayeva O, Wenner BR, Yancy WS Jr, Eisenson H, Musante G, Surwit RS, Millington DS, Butler MD, Svetkey LP. 2009. A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance. Cell Metab 9: 311-326.
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| 20 |
Suhre K, Meisinger C, Doring A, Altmaier E, Belcredi P, Gieger C, Chang D, Milburn MV, Gall WE, Weinberger KM, Mewes HW, Hrabe de Angelis M, Wichmann HE, Kronenberg F, Adamski J, Illig T. 2010. Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting. PLoS One 5: e13953.
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| 21 |
Tang WHW, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, Wu YW, Hazen SL. 2013. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 368: 1575-1584.
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| 22 |
Huffman KM, Shah SH, Stevens RD, Bain JR, Muehlbauer M, Slentz CA, Tanner CJ, Kuchibhatla M, Houmard JA, Newgard CB, Kraus WE. 2009. Relationships between circulating metabolic intermediates and insulin action in overweight to obese, inactive men and women. Diabetes Care 32: 1678-1683.
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| 23 |
Boulange CL, Claus SP, Chou CJ, Collino S, Montoliu I, Kochhar S, Holmes E, Rezzi S, Nicholson JK, Dumas ME, Martin FP. 2013. Early metabolic adaptation in C57BL/6 mice resistant to high fat diet induced weight gain involves an activation of mitochondrial oxidative pathways. J Proteome Res 12: 1956-1968.
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Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, DuGar B, Feldstein AE, Britt EB, Fu X, Chung YM, Wu Y, Schauer P, Smith JD, Allayee H, Tang WHW, DiDonato JA, Lusis AJ, Hazen SL. 2011. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 472: 57-63.
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Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT, Britt EB, Fu X, Wu Y, Li L, Smith JD, DiDonato JA, Chen J, Li H, Wu GD, Lewis JD, Warrier M, Brown JM, Krauss RM, Tang WHW, Bushman FD, Lusis AJ, Hazen SL. 2013. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 19: 576-585.
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| 26 |
Kim J, Choi JN, Choi JH, Cha YS, Muthaiya MJ, Lee CH. 2013. Effect of fermented soybean product (Cheonggukjang) intake on metabolic parameters in mice fed a high-fat diet. Mol Nutr Food Res 57: 1886-1891.
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An Y, Xu W, Li H, Lei H, Zhang L, Hao F, Duan Y, Yan X, Zhao Y, Wu J, Wang Y, Tang H. 2013. High-fat diet induces dynamic metabolic alterations in multiple biological matrices of rats. J Proteome Res 12: 3755-3768.
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| 28 |
Fardet A, Llorach R, Martin JF, Besson C, Lyan B, Pujos- Guillot E, Scalbert A. 2008. A liquid chromatography quadrupole time-of-flight (LC-QTOF)-based metabolomic approach reveals new metabolic effects of catechin in rats fed high-fat diets. J Proteome Res 7: 2388-2398.
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Martin FP, Sprenger N, Yap IK, Wang Y, Bibiloni R, Rochat F, Rezzi S, Cherbut C, Kochhar S, Lindon JC, Holmes E, Nicholson JK. 2009. Panorganismal gut microbiome- host metabolic crosstalk. J Proteome Res 8: 2090- 2105.
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Waldram A, Holmes E, Wang Y, Rantalainen M, Wilson ID, Tuohy KM, McCartney AL, Gibson GR, Nicholson JK. 2009. Top-down systems biology modeling of host metabotype- microbiome associations in obese rodents. J Proteome Res 8: 2361-2375.
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| 31 |
Wang Y, Utzinger J, Saric J, Li JV, Burckhardt J, Dirnhofer S, Nicholson JK, Singer BH, Brun R, Holmes E. 2008. Global metabolic responses of mice to Trypanosoma brucei brucei infection. Proc Natl Acad Sci USA 105: 6127-6132.
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| 32 |
Yap IK, Li JV, Saric J, Martin FP, Davies H, Wang Y, Wilson ID, Nicholson JK, Utzinger J, Marchesi JR, Holmes E. 2008. Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. J Proteome Res 7: 3718-3728.
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Oliver SG, Winson MK, Kell DB, Baganz F. 1998. Systematic functional analysis of the yeast genome. Trends Biotechnol 16: 373-378.
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Martin FP, Verdu EF, Wang Y, Dumas ME, Yap IK, Cloarec O, Bergonzelli GE, Corthesy-Theulaz I, Kochhar S, Holmes E, Lindon JC, Collins SM, Nicholson JK. 2006. Transgenomic metabolic interactions in a mouse disease model: interactions of Trichinella spiralis infection with dietary Lactobacillus paracasei supplementation. J Proteome Res 5: 2185- 2193.
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Hong YS, Hong KS, Park MH, Ahn YT, Lee JH, Huh CS, Lee J, Kim IK, Hwang GS, Kim JS. 2011. Metabonomic understanding of probiotic effects in humans with irritable bowel syndrome. J Clin Gastroenterol 45: 415-425.
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Nicholson JK, Holmes E, Wilson ID. 2005. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3: 431-438.
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Nicholson JK, Lindon JC. 2008. Systems biology: Metabonomics. Nature 455: 1054-1056.
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Opinion. 2010. 2020 visions. Nature 463: 26-32.
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Nicholson JK, Lindon JC, Holmes E. 1999. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 29: 1181-1189.
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Saini A. 2012. Metabolomics. London's Olympic drug testing lab to become national phenome center. Science 337:513
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Nicholson JK, Holmes E, Kinross JM, Darzi AW, Takats Z, Lindon JC. 2012. Metabolic phenotyping in clinical and surgical environments. Nature 491: 384-392.
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| 42 |
Wang TJ, Larson MG, Vasan RS, Cheng S, Rhee EP, McCabe E, Lewis GD, Fox CS, Jacques PF, Fernandez C, O'Donnell CJ, Carr SA, Mootha VK, Florez JC, Souza A, Melander O, Clish CB, Gerszten RE. 2011. Metabolite profiles and the risk of developing diabetes. Nat Med 17: 448-453
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Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pettersson S. 2012. Host-gut microbiota metabolic interactions. Science 336: 1262-1267.
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Kinross J, Nicholson JK. 2012. Gut microbiota: Dietary and social modulation of gut microbiota in the elderly. Nat Rev Gastroenterol Hepatol 9: 563-564.
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| 45 |
Beckonert O, Coen M, Keun HC, Wang Y, Ebbels TM, Holmes E, Lindon JC, Nicholson JK. 2010. High-resolution magic-angle-spinning NMR spectroscopy for metabolic profiling of intact tissues. Nat Protoc 5: 1019-1032.
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| 46 |
Holmes E, Li JV, Marchesi JR, Nicholson JK. 2012. Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk. Cell Metab 16: 559-564.
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Beckonert O, Keun HC, Ebbels TM, Bundy J, Holmes E, Lindon JC, Nicholson JK. 2007. Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts. Nat Protoc 2: 2692-2703.
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| 48 |
Want EJ, Wilson ID, Gika H, Theodoridis G, Plumb RS, Shockcor J, Holmes E, Nicholson JK. 2010. Global metabolic profiling procedures for urine using UPLC-MS. Nat Protoc 5: 1005-1018.
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| 49 |
Dunn WB, Broadhurst D, Begley P, Zelena E, Francis- McIntyre S, Anderson N, Brown M, Knowles JD, Halsall A, Haselden JN, Nicholls AW, Wilson ID, Kell DB, Goodacre R. 2100. Procedures for large-scale metabolic profiling of serum and plasma using gas chromatography and liquid chromatography coupled to mass spectrometry. Nat Protoc 6: 1060-1083.
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Pearce JT, Athersuch TJ, Ebbels TM, Lindon JC, Nicholson JK, Keun HC. 2008. Robust algorithms for automated chemical shift calibration of 1D NMR spectra of blood serum. Anal Chem 80: 7158-7162.
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Savorani F, Tomasi G, Engelsen SB. 2010. icoshift: A versatile tool for the rapid alignment of 1D NMR spectra. J Magn Reson 202: 190-202.
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Cheng S, Rhee EP, Larson MG, Lewis GD, McCabe EL, Shen D, Palma MJ, Roberts LD, Dejam A, Souza AL, Deik AA, Magnusson M, Fox CS, O'Donnell CJ, Vasan RS, Melander O, Clish CB, Gerszten RE, Wang TJ. 2012. Metabolite profiling identifies pathways associated with metabolic risk in humans. Circulation 125: 2222-2231.
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| 53 |
Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM. 2009. Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature 457: 910-914.
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| 54 |
Hong YS, Coen M, Rhode CM, Reily MD, Robertson DG, Holmes E, Lindon JC, Nicholson JK. 2009. Chemical shift calibration of MAS NMR liver tissue spectra exemplified using a study of glycine protection of galactosamine toxicity. Magn Reson Chem 47: S47-S53.
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| 55 |
Rezzi S, Martin FP, Shanmuganayagam D, Colman RJ, Nicholson JK, Weindruch R. 2009. Metabolic shifts due to long-term caloric restriction revealed in nonhuman primates. Exp Gerontol 44: 356-362.
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| 56 |
Martin FP, Wang Y, Sprenger N, Holmes E, Lindon JC, Kochhar S, Nicholson JK. 2007. Effects of probiotic Lactobacillus paracasei treatment on the host gut tissue metabolic profiles probed via magic-angle-spinning NMR spectroscopy. J Proteome Res 6: 1471-1481.
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