A Data Integration Multi-Omics Approach to Study Calorie Restriction-Induced Changes in Insulin Sensitivity

Affeldt, 2016, Spectral consensus strategy for accurate reconstruction of large biological networks., BMC Bioinformatics, 17, 10.1186/s12859-016-1308-y

Blaise, 2009, Statistical recoupling prior to significance testing in nuclear magnetic resonance based metabonomics., Anal. Chem., 81, 6242, 10.1021/ac9007754

Bouché, 2002, Five-week, low-glycemic index diet decreases total fat mass and improves plasma lipid profile in moderately overweight nondiabetic men., Diabetes Care, 25, 822, 10.2337/diacare.25.5.822

Capel, 2009, Macrophages and adipocytes in human obesity: adipose tissue gene expression and insulin sensitivity during calorie restriction and weight stabilization., Diabetes, 58, 1558, 10.2337/db09-0033

Chen, 2011, Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods., PLoS One, 6, 10.1371/journal.pone.0017238

Clément, 2004, Weight loss regulates inflammation-related genes in white adipose tissue of obese subjects., FASEB J., 18, 1657, 10.1096/fj.04-2204com

Cotillard, 2013, Dietary intervention impact on gut microbial gene richness., Nature, 500, 585, 10.1038/nature12480

Dao, 2015, Akkermansia muciniphilaand improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology., Gut, 65, 426, 10.1136/gutjnl-2014-308778

Dao, 2016, Losing weight for a better health: role for the gut microbiota., Clin. Nutr. Exp., 6, 39, 10.1016/j.yclnex.2015.12.001

Després, 2001, Treatment of obesity: need to focus on high risk abdominally obese patients., BMJ, 322, 716, 10.1136/bmj.322.7288.716

Dona, 2014, Precision high-throughput proton NMR spectroscopy of human urine, serum, and plasma for large-scale metabolic phenotyping., Anal. Chem., 86, 9887, 10.1021/ac5025039

Dona, 2016, A guide to the identification of metabolites in NMR-based metabonomics/metabolomics experiments., Comput. Struct. Biotechnol. J., 14, 135, 10.1016/j.csbj.2016.02.005

Dumas, 2006, Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice., Proc. Natl. Acad. Sci. U.S.A., 103, 12511, 10.1073/pnas.0601056103

Elliott, 2015, Urinary metabolic signatures of human adiposity., Sci. Transl. Med., 7, 10.1126/scitranslmed.aaa5680

Esposito Vinzi, 2010, Handbook of Partial Least Squares-Concepts., 10.1007/978-3-540-32827-8

Fetissov, 2017, Role of the gut microbiota in host appetite control: bacterial growth to animal feeding behaviour., Nat. Rev. Endocrinol., 13, 11, 10.1038/nrendo.2016.150

Forslund, 2015, Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota., Nature, 528, 262, 10.1038/nature15766

Gagnon-Bartsch, 2012, Using control genes to correct for unwanted variation in microarray data., Biostatistics, 13, 539, 10.1093/biostatistics/kxr034

Gao, 2009, Metabolite analysis of human fecal water by gas chromatography/mass spectrometry with ethyl chloroformate derivatization., Anal. Biochem., 393, 163, 10.1016/j.ab.2009.06.036

Genser, 2018, Increased jejunal permeability in human obesity is revealed by a lipid challenge and is linked to inflammation and type 2 diabetes., J. Pathol., 246, 217, 10.1002/path.5134

Geurts, 2014, Gut microbiota controls adipose tissue expansion, gut barrier and glucose metabolism: novel insights into molecular targets and interventions using prebiotics., Benef. Microbes, 5, 3, 10.3920/BM2012.0065

Hastie, 2009, The Elements of Statistical Learning - Data Mining, Inference., 10.1007/978-0-387-84858-7

Herman, 2010, Adipose tissue branched chain amino acid (BCAA) metabolism modulates circulating BCAA levels., J. Biol. Chem., 285, 11348, 10.1074/jbc.M109.075184

Herrgård, 2008, A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology., Nat. Biotechnol., 26, 1155, 10.1038/nbt1492

Karlsson, 2013, Gut metagenome in European women with normal, impaired and diabetic glucose control., Nature, 498, 99, 10.1038/nature12198

Khan, 2014, Microbial modulation of insulin sensitivity., Cell Metab., 20, 753, 10.1016/j.cmet.2014.07.006

Kidd, 2014, Unifying immunology with informatics and multiscale biology., Nat. Immunol., 15, 118, 10.1038/ni.2787

Kong, 2014, Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects., PLoS One, 9, 10.1371/journal.pone.0109434

Kong, 2013, Insulin resistance and inflammation predict kinetic body weight changes in response to dietary weight loss and maintenance in overweight and obese subjects by using a Bayesian network approach., Am. J. Clin. Nutr., 98, 1385, 10.3945/ajcn.113.058099

Kussmann, 2013, Perspective: a systems approach to diabetes research., Front. Genet., 4, 10.3389/fgene.2013.00205

Laferrère, 2011, Differential metabolic impact of gastric bypass surgery versus dietary intervention in obese diabetic subjects despite identical weight loss., Sci. Transl. Med., 3, 10.1126/scitranslmed.3002043

Le Chatelier, 2013, Richness of human gut microbiome correlates with metabolic markers., Nature, 500, 541, 10.1038/nature12506

Leek, 2010, Tackling the widespread and critical impact of batch effects in high-throughput data., Nat. Rev. Genet., 11, 733, 10.1038/nrg2825

Lemaire, 2011, Ubiquitin fold modifier 1 (UFM1) and its target UFBP1 protect pancreatic beta cells from ER stress-induced apoptosis., PLoS One, 6, 10.1371/journal.pone.0018517

Levy, 1998, Correct homeostasis model assessment (HOMA) evaluation uses the computer program., Diabetes Care, 21, 2191, 10.2337/diacare.21.12.2191

Mozaffarian, 2016, Dietary and policy priorities for cardiovascular disease, diabetes, and obesity: a comprehensive review., Circulation, 133, 187, 10.1161/CIRCULATIONAHA.115.018585

Munukka, 2014, Gut-adipose tissue axis in hepatic fat accumulation in humans., J. Hepatol., 61, 132, 10.1016/j.jhep.2014.02.020

Muoio, 2012, Muscle-specific deletion of carnitine acetyltransferase compromises glucose tolerance and metabolic flexibility., Cell Metab., 15, 764, 10.1016/j.cmet.2012.04.005

Mutch, 2006, Unraveling the genetics of human obesity., PLoS Genet, 2, 10.1371/journal.pgen.0020188

Newgard, 2009, A branched-chain amino acid-related metabolic signature that differentiates obese and lean humans and contributes to insulin resistance., Cell Metab., 9, 311, 10.1016/j.cmet.2009.02.002

Pallister, 2017, Hippurate as a metabolomic marker of gut microbiome diversity: modulation by diet and relationship to metabolic syndrome., Sci. Rep., 7, 10.1038/s41598-017-13722-4

Parker, 2014, Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction., Bioinforma. Oxf. Engl., 30, 2757, 10.1093/bioinformatics/btu375

Pedersen, 2016, Human gut microbes impact host serum metabolome and insulin sensitivity., Nature, 535, 376, 10.1038/nature18646

Piening, 2018, Integrative personal omics profiles during periods of weight gain and loss., Cell Syst., 6, e8, 10.1016/j.cels.2017.12.013

Plovier, 2017, A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice., Nat. Med., 23, 107, 10.1038/nm.4236

Prifti, 2008, FunNet: an integrative tool for exploring transcriptional interactions., Bioinforma. Oxf. Engl., 24, 2636, 10.1093/bioinformatics/btn492

Qin, 2012, A metagenome-wide association study of gut microbiota in type 2 diabetes., Nature, 490, 55, 10.1038/nature11450

Rizkalla, 2012, Differential effects of macronutrient content in 2 energy-restricted diets on cardiovascular risk factors and adipose tissue cell size in moderately obese individuals: a randomized controlled trial., Am. J. Clin. Nutr., 95, 49, 10.3945/ajcn.111.017277

Roberts, 2014, Towards metabolic biomarkers of insulin resistance and type 2 diabetes: progress from the metabolome., Lancet Diabetes Endocrinol., 2, 65, 10.1016/S2213-8587(13)70143-8

Ruggenenti, 2009, Ameliorating hypertension and insulin resistance in subjects at increased cardiovascular risk: effects of acetyl-L-carnitine therapy., Hypertens, 54, 567, 10.1161/HYPERTENSIONAHA.109.132522

Schooneman, 2016, Assessment of plasma acylcarnitines before and after weight loss in obese subjects., Arch. Biochem. Biophys., 606, 73, 10.1016/j.abb.2016.07.013

Schooneman, 2013, Acylcarnitines: reflecting or inflicting insulin resistance?, Diabetes, 62, 1, 10.2337/db12-0466

Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks., Genome Res., 13, 2498, 10.1101/gr.1239303

Smith, 2006, XCMS: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification., Anal. Chem., 78, 779, 10.1021/ac051437y

Sokol, 2008, Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients., Proc. Natl. Acad. Sci. U.S.A., 105, 16731, 10.1073/pnas.0804812105

Speakman, 2011, Caloric restriction., Mol. Aspects Med., 32, 159, 10.1016/j.mam.2011.07.001

Sumner, 2007, Proposed minimum reporting standards for chemical analysis chemical analysis working group (CAWG) metabolomics standards initiative (MSI)., Metabolomics, 3, 211, 10.1007/s11306-007-0082-2

Tremaroli, 2012, Functional interactions between the gut microbiota and host metabolism., Nature, 489, 242, 10.1038/nature11552

Viguerie, 2005, Transcriptomics applied to obesity and caloric restriction., Biochimie, 87, 117, 10.1016/j.biochi.2004.12.011

Wang, 2018, The gut-microglia connection: implications for central nervous system diseases., Front. Immunol., 9, 10.3389/fimmu.2018.02325

Wu, 2015, Linking microbiota to human diseases: a systems biology perspective., Trends Endocrinol. Metab., 26, 758, 10.1016/j.tem.2015.09.011

Xi, 2013, DDRGK1 regulates NF-κB activity by modulating IκBα stability., PLoS One, 8, 10.1371/journal.pone.0064231