This list contains references from the content that can be linked to their source. For a full set of references and notes please see the PDF or HTML where available.
1. DP Jones , Y Park & TR Ziegler (2012) Nutritional metabolomics: progress in addressing complexity in diet and health. Annu Rev Nutr 32, 183–202.
3. JW Lampe & JD Potter (2006) Genetic variation, diet and disease susceptibility. In Gene-Environment Interactions: Fundamentals of Ecogenetics, pp. 321–350 [ LG Costa and DL Eaton , editors]. Hoboken, NJ: John Wiley & Sons, Inc.
4. AD Bryan & KE Hutchison (2012) The role of genomics in health behavior change: challenges and opportunities. Public Health Genomics 15, 139–145.
5. C Gieger , L Geistlinger , E Altmaier (2008) Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum. PLoS Genet 4, e1000282.
6. K Suhre , H Wallaschofski , J Raffler (2011) A genome-wide association study of metabolic traits in human urine. Nat Genet 43, 565–569.
7. F Guarner & JR Malagelada (2003) Gut flora in health and disease. Lancet 361, 512–519.
8. J Qin , R Li , J Raes (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59–65.
9. SR Gill , M Pop , RT Deboy (2006) Metagenomic analysis of the human distal gut microbiome. Science 312, 1355–1359.
10. M Arumugam , J Raes , E Pelletier (2011) Enterotypes of the human gut microbiome. Nature 473, 174–180.
11. DR Donohoe & SJ Bultman (2012) Metaboloepigenetics: interrelationships between energy metabolism and epigenetic control of gene expression. J Cell Physiol 227, 3169–3177.
12. DR Donohoe , N Garge , XX Zhang (2011) The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 13, 517–526.
13. JM Ordovas & V Mooser (2006) Metagenomics: the role of the microbiome in cardiovascular diseases. Curr Opin Lipidol 17, 157–161.
14. JJ Qin , YR Li , ZM Cai (2012) A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 490, 55–60.
15. JR Marchesi , BE Dutilh , N Hall (2011) Towards the human colorectal cancer microbiome. PLoS One 6, e20447.
16. CS Plottel & MJ Blaser (2011) Microbiome and malignancy. Cell Host Microbe 10, 324–335.
17. BP Willing , J Dicksved , J Halfvarson (2010) A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. Gastroenterology 139, 1844–1854.
19. SL Navarro , J Chang , S Peterson (2009) Modulation of human serum glutathione S-transferase-A1/2 concentration by cruciferous vegetables in a controlled feeding study is influenced by GSTM1 and GSTT1 genotypes. Cancer Epidemiol Biomarkers Prev 18, 2974–2978.
20. AJ Cross , JM Major , R Sinha (2011) Urinary biomarkers of meat consumption. Cancer Epidemiol Biomarkers Prev 20, 1107–1111.
21. ML Neuhouser , Y Schwarz , C Wang (2012) A low-glycemic load diet reduces serum C-reactive protein and modestly increases adiponectin in overweight and obese adults. J Nutr 142, 369–374.
22. SL Navarro , Y Chen , L Li (2011) UGT1A6 and UGT2B15 polymorphisms and acetaminophen conjugation in response to a randomized, controlled diet of select fruits and vegetables. Drug Metab Dispos 39, 1650–1657.
23. WR Russell , SW Gratz , SH Duncan (2011) High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am J Clin Nutr 93, 1062–1072.
24. F Li , MA Hullar , Y Schwarz (2009) Human gut bacterial communities are altered by addition of cruciferous vegetables to a controlled fruit- and vegetable-free diet. J Nutr 139, 1685–1691.
25. KM Tuohy , S Kolida , AM Lustenberger (2001) The prebiotic effects of biscuits containing partially hydrolysed guar gum and fructo-oligosaccharides–a human volunteer study. Br J Nutr 86, 341–348.
26. K Faust & J Raes (2012) Microbial interactions: from networks to models. Nat Rev Microbiol 10, 538–550.
27. K Faust , JF Sathirapongsasuti , J Izard (2012) Microbial co-occurrence relationships in the human microbiome. PLoS Comput Biol 8, e1002606.
28. C Lozupone , K Faust , J Raes (2012) Identifying genomic and metabolic features that can underline early successional and opportunistic lifestyles of human gut symbionts. Genome Res 22, 1974–1984.
30. MD Niculescu , EA Pop , LM Fischer (2007) Dietary isoflavones differentially induce gene expression changes in lymphocytes from postmenopausal women who form equol as compared with those who do not. J Nutr Biochem 18, 380–390.
31. KS Solanky , NJ Bailey , BM Beckwith-Hall (2005) Biofluid 1H NMR-based metabonomic techniques in nutrition research - metabolic effects of dietary isoflavones in humans. J Nutr Biochem 16, 236–244.
32. HA Brauer , TE Libby , BL Mitchell (2011) Cruciferous vegetable supplementation in a controlled diet study alters the serum peptidome in a GSTM1-genotype dependent manner. Nutr J 10, 11.
33. S Rezzi , Z Ramadan , FP Martin (2007) Human metabolic phenotypes link directly to specific dietary preferences in healthy individuals. J Proteome Res 6, 4469–4477.
34. SS Heinzmann , CA Merrifield , S Rezzi (2012) Stability and robustness of human metabolic phenotypes in response to sequential food challenges. J Proteome Res 11, 643–655.
35. MY Hirai , M Yano , DB Goodenowe (2004) Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana. Proc Natl Acad Sci USA 101, 10205–10210.
36. MY Hirai , M Klein , Y Fujikawa (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem 280, 25590–25595.
37. KA Lê Cao , PG Martin , C Robert-Granié (2009) Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinformatics 10, 34.
38. SP Gygi , Y Rochon , BR Franza (1999) Correlation between protein and mRNA abundance in yeast. Mol Cell Biol 19, 1720–1730.
39. K Van Deun , AK Smilde , MJ van der Werf (2009) A structured overview of simultaneous component based data integration. BMC Bioinformatics 10, 246.
40. N Putluri , A Shojaie , VT Vasu (2011) Metabolomic profiling reveals a role for androgen in activating amino acid metabolism and methylation in prostate cancer cells. PLoS One 6, e21417.
41. N Putluri , A Shojaie , VT Vasu (2011) Metabolomic profiling reveals potential markers and bioprocesses altered in bladder cancer progression. Cancer Res 71, 7376–7386.
42. M Imielinski , S Cha , T Rejtar (2012) Integrated proteomic, transcriptomic, and biological network analysis of breast carcinoma reveals molecular features of tumorigenesis and clinical relapse. Mol Cell Proteomics 11, M111 014910.
43. LM Poisson , JM Taylor & D Ghosh (2011) Integrative set enrichment testing for multiple omics platforms. BMC Bioinformatics 12, 459.
44. A Jauhiainen , O Nerman , G Michailidis (2012) Transcriptional and metabolic data integration and modeling for identification of active pathways. Biostatistics 13, 748–761.
46. AD Coviello , R Haring , M Wellons (2012) A genome-wide association meta-analysis of circulating sex hormone-binding globulin reveals multiple Loci implicated in sex steroid hormone regulation. PLoS Genet 8, e1002805.
47. R Qayyum , BM Snively , E Ziv (2012) A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans. PLoS Genet 8, e1002491.
48. DR Nyholt , SK Low , CA Anderson (2012) Genome-wide association meta-analysis identifies new endometriosis risk loci. Nat Genet 44, 1355–1359.
49. RS Houlston , E Webb , P Broderick (2008) Meta-analysis of genome-wide association data identifies four new susceptibility loci for colorectal cancer. Nat Genet 40, 1426–1435.
50. E Zeggini , LJ Scott , R Saxena (2008) Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nat Genet 40, 638–645.
51. JD Cooper , DJ Smyth , AM Smiles (2008) Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci. Nat Genet 40, 1399–1401.
52. P Wirapati , C Sotiriou , S Kunkel (2008) Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. Breast Cancer Res 10, R65.
53. DR Rhodes , J Yu , K Shanker (2004) Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci USA 101, 9309–9314.
55. SE Chiuve , TT Fung , EB Rimm (2012) Alternative dietary indices both strongly predict risk of chronic disease. J Nutr 142, 1009–1018.
56. S Hooda , BM Boler , MC Serao (2012) 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber. J Nutr 142, 1259–1265.
57. AB Ross , SJ Bruce , A Blondel-Lubrano (2011) A whole-grain cereal-rich diet increases plasma betaine, and tends to decrease total and LDL-cholesterol compared with a refined-grain diet in healthy subjects. Br J Nutr 105, 1492–1502.
58. A Costabile , A Klinder , F Fava (2008) Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br J Nutr 99, 110–120.
60. SC Smith , R Choy , SK Johnson (2006) Lupin kernel fiber consumption modifies fecal microbiota in healthy men as determined by rRNA gene fluorescent in situ hybridization. Eur J Nutr 45, 335–341.
61. SK Johnson , V Chua , RS Hall (2006) Lupin kernel fibre foods improve bowel function and beneficially modify some putative faecal risk factors for colon cancer in men. Br J Nutr 95, 372–378.
63. MO Weickert , AM Arafat , M Blaut (2011) Changes in dominant groups of the gut microbiota do not explain cereal-fiber induced improvement of whole-body insulin sensitivity. Nutr Metab (Lond) 8, 90.
64. SH Duncan , A Belenguer , G Holtrop (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 73, 1073–1078.
65. RE Ley , PJ Turnbaugh , S Klein (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444, 1022–1023.
66. FA van Dorsten , S Peters , G Gross (2012) Gut microbial metabolism of polyphenols from black tea and red wine/grape juice is source-specific and colon-region dependent. J Agric Food Chem 60, 11331–11342.
67. SS Heinzmann , IJ Brown , Q Chan (2010) Metabolic profiling strategy for discovery of nutritional biomarkers: proline betaine as a marker of citrus consumption. Am J Clin Nutr 92, 436–443.
69. S Tulipani , R Llorach , O Jauregui (2011) Metabolomics unveils urinary changes in subjects with metabolic syndrome following 12-week nut consumption. J Proteome Res 10, 5047–5058.
70. R Llorach , I Garrido , M Monagas (2010) Metabolomics study of human urinary metabolome modifications after intake of almond (Prunus dulcis (Mill.) D.A. Webb) skin polyphenols. J Proteome Res 9, 5859–5867.
71. FA Van Dorsten , CA Daykin , TP Mulder (2006) Metabonomics approach to determine metabolic differences between green tea and black tea consumption. J Agric Food Chem 54, 6929–6938.
72. LG Rasmussen , H Winning , F Savorani (2012) Assessment of the effect of high or low protein diet on the human urine metabolome as measured by NMR. Nutrients 4, 112–131.
73. AA Moazzami , JX Zhang , A Kamal-Eldin (2011) Nuclear magnetic resonance-based metabolomics enable detection of the effects of a whole grain rye and rye bran diet on the metabolic profile of plasma in prostate cancer patients. J Nutr 141, 2126–2132.
74. AM Zivkovic , MM Wiest , U Nguyen (2009) Assessing individual metabolic responsiveness to a lipid challenge using a targeted metabolomic approach. Metabolomics 5, 209–218.
75. R Llorach , M Urpi-Sarda , O Jauregui (2009) An LC-MS-based metabolomics approach for exploring urinary metabolome modifications after cocoa consumption. J Proteome Res 8, 5060–5068.
76. HC Bertram , C Hoppe , BO Petersen (2007) An NMR-based metabonomic investigation on effects of milk and meat protein diets given to 8-year-old boys. Br J Nutr 97, 758–763.
77. C Stella , B Beckwith-Hall , O Cloarec (2006) Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res 5, 2780–2788.