1Sutter, NB & Ostrander, EA (2004) Dog star rising: the canine genetic system. Nat Rev Genet 5, 900–910.
2Lindblad-Toh, K, Wade, CM, Mikkelsen, TS, et al. (2005) Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 438, 803–819.
3Yuzbasiyan-Gurkan, V, Blanton, SH, Cao, YY, et al. (1997) Linkage of a microsatellite marker to the canine copper toxicosis locus in Bedlington Terriers. Am J Vet Res 58, 23–27.
4Safra, N, Ling, GV, Schaible, RH, et al. (2005) Exclusion of urate oxidase as a candidate gene for hyperuricosuria in the Dalmatian dog using an interbreed backcross. J Hered 96, 750–754.
5Ko, KS, Backus, RC, Berg, JR, et al. (2007) Differences in taurine synthesis rate among dogs relate to differences in their maintenance energy requirement. J Nutr 137, 1171–1175.
6Cruz, F, Vila, C & Webster, MT (2008) The legacy of domestication: accumulation of deleterious mutations in the dog genome. Mol Biol Evol 25, 2331–2336.
7Swanson, KS, Schook, LB & Fahey, GC (2003) Nutritional genomics: implications for companion animals. J Nutr 133, 3033–3040.
8Weber, MP, Stambouli, F, Martin, LJ, et al. (2002) Influence of age and body size on gastrointestinal transit time of radiopaque markers in healthy dogs. Am J Vet Res 63, 677–682.
9Brown, WY, Vanselow, BA & Walkden-Brown, SW (2003) One dog's meat is another dog's poison – nutrition in the Dalmatian dog. Recent Adv Animal Nutr Aust 14, 123–131.
10German, JB, Roberts, MA & Watkins, SM (2003) Personal metabolomics as a next generation nutritional assessment. J Nutr 133, 4260–4266.
11Kaput, J, Ordovas, JM, Ferguson, L, et al. (2005) The case for strategic international alliances to harness nutritional genomics for public and personal health. Br J Nutr 94, 623–632.
12Meyer, H, Zentek, J, Habernoll, H, et al. (1999) Digestibility and compatibility of mixed diets and faecal consistency in different breeds of dog. J Vet Med A 46, 155–165.
13Stevenson, AE, Robertson, WG & Markwell, P (2003) Risk factor analysis and relative supersaturation as tools for identifying calcium oxalate stone-forming dogs. J Small Anim Pract 44, 491–496.
14Benyacoub, J, Czarnecki- Maulden, GL, Cavadini, C, et al. (2003) Supplementation of food with Enterococcus faecium (SF68) stimulates immune functions in young dogs. J Nutr 133, 1158–1162.
15Mata-Bilbao, MD, Andres-Lacueva, C, Roura, E, et al. (2007) Absorption and pharmacokinetics of grapefruit flavanones in Beagles. Br J Nutr 98, 86–92.
16Blaut, M & Clavel, T (2007) Metabolic diversity of the intestinal microbiota: implications for health and disease. J Nutr 137, 751S–755S.
17Wishart, DS, Tzur, D, Knox, C, et al. (2007) HMDB: The Human Metabolome Database. Nucleic Acids Res 35, D521–D526.
18Human Metabolome Database (2009) http://hmdb.ca (accessed April 2009).
19Viant, MR, Ludwig, C, Rhodes, S, et al. (2007) Validation of a urine metabolome fingerprint in dog for phenotypic classification. Metabolomics 3, 453–463.
20Saude, EJ & Sykes, BD (2007) Urine stability for metabolomic studies: effects of preparation and storage. Metabolomics 3, 19–27.
21Stella, C, Beckwith-Hall, B, Cloarec, O, et al. (2006) Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res 5, 2780–2788.
22Wilson, ID, Plumb, R, Granger, J, et al. (2005) HPLC-MS-based methods for the study of metabonomics. J Chromatogr B 817, 67–76.
23Gika, HG, Theodoridis, GA, Wingate, JE, et al. (2007) Within-day reproducibility of an HPLC-MS-based method for metabonomic analysis: application to human urine. J Proteome Res 6, 3291–3303.
24Zhang, Q, Wang, G, Du, Y, et al. (2007) GC/MS analysis of the rat urine for metabonomic research. J Chromatogr B 854, 20–25.
25Beckmann, M, Parker, D, Enot, DP, et al. (2008) High-throughput, nontargeted metabolite fingerprinting using nominal mass flow injection electrospray mass spectrometry. Nat Protoc 3, 486–504.
26Goodacre, R, Shann, B, Gilbert, RJ, et al. (2000) Detection of the dipicolinic acid biomarker in Bacillus spores using Curie-point pyrolysis mass spectrometry and Fourier transform infrared spectroscopy. Anal Chem 72, 119–127.
27Griffin, JL (2003) Metabonomics: NMR spectroscopy and pattern recognition analysis of body fluids and tissues for characterisation of xenobiotic toxicity and disease diagnosis. Curr Opin Chem Biol 7, 648–654.
28Wang, Y, Lawler, D, Larson, B, et al. (2007) Metabonomic investigations of aging and caloric restriction in a life-long dog study. J Proteome Res 6, 1846–1854.
29Cloarec, O, Dumas, M-E, Craig, A, et al. (2005) Statistical total correlation spectroscopy: an exploratory approach for latent biomarker identification from metabolic 1H NMR data sets. Anal Chem 77, 1282–1289.
30Walsh, MC, Brennan, L, Malthouse, JPG, et al. (2006) Effect of acute dietary standardization on the urinary, plasma, and salivary metabolomic profiles of healthy humans. Am J Clin Nutr 84, 531–539.
31Walsh, MC, Brennan, L, Pujos-Guillot, E, et al. (2007) Influence of acute phytochemical intake on human urinary metabolomic profiles. Am J Clin Nutr 86, 1687–1693.
32Allen, J, Davey, HM, Broadhurst, D, et al. (2003) High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 21, 692–696.
33Scholz, M, Gatzek, S, Sterling, A, et al. (2004) Metabolite fingerprinting: detecting biological features by independent component analysis. Bioinformatics 20, 2447–2454.
34Catchpole, GS, Beckmann, M, Enot, DP, et al. (2005) Hierarchical metabolomics demonstrates substantial compositional similarity between genetically modified and conventional potato crops. Proc Natl Acad Sci USA 102, 14458–14462.
35Enot, DP, Beckmann, M, Overy, D, et al. (2006) Predicting interpretability of metabolome models based on behavior, putative identity, and biological relevance of explanatory signals. Proc Natl Acad Sci USA 103, 14865–14870.
36Beckmann, M, Enot, DP, Overy, DP, et al. (2007) Representation, comparison, and interpretation of metabolome fingerprint data for total composition analysis and quality trait investigation in potato cultivars. J Agric Food Chem 55, 3444–3451.
37Overy, DP, Enot, DP, Tailliart, K, et al. (2008) Explanatory signal interpretation and metabolite identification strategies for nominal mass FIE-MS metabolite fingerprints. Nat Protoc 3, 471–485.
38Enot, DP, Lin, W, Beckmann, M, et al. (2008) Preprocessing, classification modeling and feature selection using flow injection electrospray mass spectrometry metabolite fingerprint data. Nat Protoc 3, 446–470.
39Thomaz, CE, Boardman, JP, Hill, DLG, et al. (2004) . In Medical Image Computing and Computer-Assisted Intervention – MICCAI, pp. 291–300. Berlin: Springer.
40Enot, DP & Draper, J (2007) Statistical measures for validating plant genotype similarity assessments following multivariate analysis of metabolome fingerprint data. Metabolomics 3, 349–355.
41Sing, T, Sander, O, Beerenwinkel, N, et al. (2005) ROCR: visualizing classifier performance in R. Bioinformatics 21, 3940–3941.
42Somorjai, RL, Dolenko, B & Baumgartner, R (2003) Class prediction and discovery using gene microarray and proteomics mass spectroscopy data: curses, caveats, cautions. Bioinformatics 19, 1484–1491.
43Berrar, D, Bradbury, I & Dubitzky, W (2006) Avoiding model selection bias in small-sample genomic datasets. Bioinformatics 22, 1245–1250.
44Stevenson, AE & Markwell, PJ (2001) Comparison of urine composition of healthy Labrador retrievers and miniature Schnauzers. Am J Vet Res 62, 1782–1786.
45Stevenson, AE, Hynds, WK & Markwell, PJ (2003) Effect of dietary moisture and sodium content on urine composition and calcium oxalate relative supersaturation in healthy miniature schnauzers and Labrador retrievers. Res Vet Sci 74, 145–151.
46Simpson, DP (1983) Citrate excretion – a window on renal metabolism. Am J Physiol 244, F223–F234.
47Hess, B, Michel, R, Takkinen, R, et al. (1994) Risk-factors for low urinary citrate in calcium nephrolithiasis – low vegetable fiber intake and low urine volume to be added to the list. Nephrol Dial Transplant 9, 642–649.
48Gonthier, MP, Cheynier, V, Donovan, JL, et al. (2003) Microbial aromatic acid metabolites formed in the gut account for a major fraction of the polyphenols excreted in urine of rats fed red wine polyphenols. J Nutr 133, 461–467.
49Deprez, S, Brezillon, C, Rabot, S, et al. (2000) Polymeric proanthocyanidins are catabolized by human colonic microflora into low-molecular-weight phenolic acids. J Nutr 130, 2733–2738.
50Gonthier, MP, Verny, MA, Besson, C, et al. (2003) Chlorogenic acid bioavailability largely depends on its metabolism by the gut microflora in rats. J Nutr 133, 1853–1859.
51Scalbert, A, Manach, C, Morand, C, et al. (2005) Dietary polyphenols and the prevention of diseases. Crit Rev Food Sci Nutr 45, 287–306.
52Fardet, A, Llorach, R, Orsoni, A, et al. (2008) Metabolomics provide new insight on the metabolism of dietary phytochemicals in rats. J Nutr 138, 1282–1287.
53Lafay, S, Gil-Izquierdo, A, Manach, C, et al. (2006) Chlorogenic acid is absorbed in its intact form in the stomach of rats. J Nutr 136, 1192–1197.
54Kim, K-H, Tsao, R, Yang, R, et al. (2006) Phenolic acid profiles and antioxidant activities of wheat bran extracts and the effect of hydrolysis conditions. Food Chem 95, 466–473.
55Nguyen, P, Dumon, H, Biourge, V, et al. (1998) Glycemic and insulinemic responses after ingestion of commercial foods in healthy dogs: influence of food composition. J Nutr 128, 2654S–2658S.
56Warmbier, HC, Schnickels, RA & Labuza, TP (1976) Effect of glycerol on nonenzymatic browning in a solid intermediate moisture model food system. J Food Sci 41, 528–531.
57Rastall, RA (2004) Bacteria in the gut: friends and foes and how to alter the balance. J Nutr 134, 2022S–2026S.
58Simpson, JM, Martineau, B, Jones, WE, et al. (2002) Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber. Microb Ecol 44, 186–197.
59Suchodolski, JS, Ruaux, CG, Steiner, JM, et al. (2004) Application of molecular fingerprinting for qualitative assessment of small-intestinal bacterial diversity in dogs. J Clin Microbiol 42, 4702–4708.
60Verdonk, J, Shim, SB, van Leeuwen, P, et al. (2005) Application of inulin-type fructans in animal feed and pet food. Br J Nutr 93, S125–S138.
61Strickling, JA, Harmon, DL, Dawson, KA, et al. (2000) Evaluation of oligosaccharide addition to dog diets: influences on nutrient digestion and microbial populations. Anim Feed Sci Technol 86, 205–219.