Integrative Personal Omics Profiles during Periods of Weight Gain and Loss

Abubucker, 2012, Metabolic reconstruction for metagenomic data and its application to the human microbiome, PLoS Comput. Biol., 8, e1002358, 10.1371/journal.pcbi.1002358

Adams, 2011, Emerging perspectives on essential amino acid metabolism in obesity and the insulin-resistant state, Adv. Nutr., 2, 445, 10.3945/an.111.000737

Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170

Brown, 2011, Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes, PLoS One, 6, e25792, 10.1371/journal.pone.0025792

Cani, 2008, Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice, Diabetes, 57, 1470, 10.2337/db07-1403

Caporaso, 2010, QIIME allows analysis of high-throughput community sequencing data, Nat. Methods, 7, 335, 10.1038/nmeth.f.303

Chen, 2012, Personal omics profiling reveals dynamic molecular and medical phenotypes, Cell, 148, 1293, 10.1016/j.cell.2012.02.009

Chung, 2011, Increased risk of diabetes in patients with urinary calculi: a 5-year followup study, J. Urol., 186, 1888

Chung, 2016, Modulation of the human gut microbiota by dietary fibres occurs at the species level, BMC Biol., 14, 3, 10.1186/s12915-015-0224-3

Considine, 1996, Serum immunoreactive-leptin concentrations in normal-weight and obese humans, N. Engl. J. Med., 334, 292, 10.1056/NEJM199602013340503

Contrepois, 2015, Optimized analytical procedures for the untargeted metabolomic profiling of human urine and plasma by combining hydrophilic interaction (HILIC) and reverse-phase liquid chromatography (RPLC)-mass spectrometry, Mol. Cell. Proteomics, 14, 1684, 10.1074/mcp.M114.046508

Dao, 2016, Akkermansia muciniphila and improved metabolic health during a dietary intervention in obesity: relationship with gut microbiome richness and ecology, Gut, 65, 426, 10.1136/gutjnl-2014-308778

Daudon, 2006, Type 2 diabetes increases the risk for uric acid stones, J. Am. Soc. Nephrol., 17, 2026, 10.1681/ASN.2006030262

David, 2014, Diet rapidly and reproducibly alters the human gut microbiome, Nature, 505, 559, 10.1038/nature12820

Dela Cruz, 2009, Role of obesity in cardiomyopathy and pulmonary hypertension, Clin. Chest Med., 30, 509, 10.1016/j.ccm.2009.06.001

Dobin, 2012, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, 29, 15, 10.1093/bioinformatics/bts635

Duncan, 2002, Oxalobacter formigenes and its potential role in human health, Appl. Environ. Microbiol., 68, 3841, 10.1128/AEM.68.8.3841-3847.2002

Edgar, 2010, Search and clustering orders of magnitude faster than BLAST, Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461

Edgar, 2011, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194, 10.1093/bioinformatics/btr381

Engels, 2016, The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation, Front. Microbiol., 7, 713, 10.3389/fmicb.2016.00713

Everard, 2013, Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity, Proc. Natl. Acad. Sci. USA, 110, 9066, 10.1073/pnas.1219451110

Feng, 2015, Constitutive BDNF/TrkB signaling is required for normal cardiac contraction and relaxation, Proc. Natl. Acad. Sci. USA, 112, 1880, 10.1073/pnas.1417949112

Festa, 2000, Chronic subclinical inflammation as part of the insulin resistance syndrome: the Insulin Resistance Atherosclerosis Study (IRAS), Circulation, 102, 42, 10.1161/01.CIR.102.1.42

Finucane, 2011, National, regional, and global trends in body-mass index since 1980: systematic analysis of health examination surveys and epidemiological studies with 960 country-years and 9.1 million participants, Lancet, 377, 557, 10.1016/S0140-6736(10)62037-5

Flanagan, 2010, Role of carnitine in disease, Nutr. Metab. (Lond), 7, 30, 10.1186/1743-7075-7-30

Flegal, 2010, Prevalence and trends in obesity among US adults, 1999-2008, JAMA, 303, 235, 10.1001/jama.2009.2014

Fulgenzi, 2015, BDNF modulates heart contraction force and long-term homeostasis through truncated TrkB.T1 receptor activation, J. Cell Biol., 210, 1003, 10.1083/jcb.201502100

Futschik, 2005, Noise-robust soft clustering of gene expression time-course data, J. Bioinform. Comput. Biol., 3, 965, 10.1142/S0219720005001375

Greenfield, 1981, Assessment of insulin resistance with the insulin suppression test and the euglycemic clamp, Diabetes, 30, 387, 10.2337/diab.30.5.387

Haaskjold, 2015, Renal failure due to excessive intake of almonds in the absence of Oxalobacter formigenes, Am. J. Med., 128, e29, 10.1016/j.amjmed.2015.07.010

Harris, 1918, A biometric study of human basal metabolism, Proc. Natl. Acad. Sci. USA, 4, 370, 10.1073/pnas.4.12.370

Holmes, 2011, Understanding the role of gut microbiome-host metabolic signal disruption in health and disease, Trends Microbiol., 19, 349, 10.1016/j.tim.2011.05.006

Hood, 2015, Integrating big data and actionable health coaching to optimize wellness, BMC Med., 13, 4, 10.1186/s12916-014-0238-7

Huang da, 2009, Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Res., 37, 1, 10.1093/nar/gkn923

Huang da, 2009, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat. Protoc., 4, 44, 10.1038/nprot.2008.211

Integrative HMP (iHMP) Research Network Consortium, 2014, The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease, Cell Host Microbe, 16, 276, 10.1016/j.chom.2014.08.014

Janssen, 2017, Potential mediators linking gut bacteria to metabolic health: a critical view, J. Physiol., 595, 477, 10.1113/JP272476

Kahn, 2006, Mechanisms linking obesity to insulin resistance and type 2 diabetes, Nature, 444, 840, 10.1038/nature05482

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

Koeth, 2013, Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat. Med., 19, 576, 10.1038/nm.3145

Kumar, 2007, Mfuzz: a software package for soft clustering of microarray data, Bioinformation, 2, 5, 10.6026/97320630002005

Lam, 2012, Detecting and annotating genetic variations using the HugeSeq pipeline, Nat. Biotechnol., 30, 226, 10.1038/nbt.2134

Larsen, 2010, Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults, PLoS One, 5, e9085, 10.1371/journal.pone.0009085

Lecomte, 2015, Changes in gut microbiota in rats fed a high fat diet correlate with obesity-associated metabolic parameters, PLoS One, 10, e0126931, 10.1371/journal.pone.0126931

Lee, 2016, Integrated network analysis reveals an association between plasma mannose levels and insulin resistance, Cell Metab., 24, 172, 10.1016/j.cmet.2016.05.026

Ley, 2006, Microbial ecology: human gut microbes associated with obesity, Nature, 444, 1022, 10.1038/4441022a

Liao, 2014, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, 30, 923, 10.1093/bioinformatics/btt656

Mardi, 2005, Increased erythropoiesis and subclinical inflammation as part of the metabolic syndrome, Diabetes Res. Clin. Pract., 69, 249, 10.1016/j.diabres.2005.01.005

Matthews, 1985, Homeostasis model assessment: insulin resistance and beta-cell function from fasting plasma glucose and insulin concentrations in man, Diabetologia, 28, 412, 10.1007/BF00280883

McLaughlin, 2002, Differentiation between obesity and insulin resistance in the association with C-reactive protein, Circulation, 106, 2908, 10.1161/01.CIR.0000041046.32962.86

McLaughlin, 2007, Heterogeneity in the prevalence of risk factors for cardiovascular disease and type 2 diabetes mellitus in obese individuals: effect of differences in insulin sensitivity, Arch. Intern. Med., 167, 642, 10.1001/archinte.167.7.642

McLaughlin, 2014, Subcutaneous adipose cell size and distribution: relationship to insulin resistance and body fat, Obesity, 22, 673, 10.1002/oby.20209

McLaughlin, 2006, Plasma asymmetric dimethylarginine concentrations are elevated in obese insulin-resistant women and fall with weight loss, J. Clin. Endocrinol. Metab., 91, 1896, 10.1210/jc.2005-1441

McLaughlin, 2016, Adipose cell size and regional fat deposition as predictors of metabolic response to overfeeding in insulin-resistant and insulin-sensitive humans, Diabetes, 65, 1245, 10.2337/db15-1213

Nishimura, 2009, CD8+ effector T cells contribute to macrophage recruitment and adipose tissue inflammation in obesity, Nat. Med., 15, 914, 10.1038/nm.1964

Patten, 2013, Activity, distribution and function of indole-3-acetic acid biosynthetic pathways in bacteria, Crit. Rev. Microbiol., 39, 395, 10.3109/1040841X.2012.716819

Patwardhan, 2015, Achieving high-sensitivity for clinical applications using augmented exome sequencing, Genome Med., 7, 71, 10.1186/s13073-015-0197-4

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

Pei, 1994, Evaluation of octreotide to assess insulin-mediated glucose disposal by the insulin suppression test, Diabetologia, 37, 843, 10.1007/BF00404344

Pesu, 2008, T-cell-expressed proprotein convertase furin is essential for maintenance of peripheral immune tolerance, Nature, 455, 246, 10.1038/nature07210

Poretsky, 2014, Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics, PLoS One, 9, e93827, 10.1371/journal.pone.0093827

Price, 2017, A wellness study of 108 individuals using personal, dense, dynamic data clouds, Nat. Biotechnol., 35, 747, 10.1038/nbt.3870

Rego, 2017, High frequency actionable pathogenic exome mutations in an average-risk cohort, bioRxiv

Ridaura, 2013, Gut microbiota from twins discordant for obesity modulate metabolism in mice, Science, 341, 1241214, 10.1126/science.1241214

Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616

Roopchand, 2015, Dietary polyphenols promote growth of the gut bacterium Akkermansia muciniphila and attenuate high-fat diet-induced metabolic syndrome, Diabetes, 64, 2847, 10.2337/db14-1916

Rosas-Vargas, 2011, Brain-derived neurotrophic factor, food intake regulation, and obesity, Arch. Med. Res., 42, 482, 10.1016/j.arcmed.2011.09.005

Schmieder, 2011, Quality control and preprocessing of metagenomic datasets, Bioinformatics, 27, 863, 10.1093/bioinformatics/btr026

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

Segata, 2012, Metagenomic microbial community profiling using unique clade-specific marker genes, Nat. Methods, 9, 811, 10.1038/nmeth.2066

Serino, 2012, Metabolic adaptation to a high-fat diet is associated with a change in the gut microbiota, Gut, 61, 543, 10.1136/gutjnl-2011-301012

Shah, 2011, Comparing bacterial communities inferred from 16S rRNA gene sequencing and shotgun metagenomics, Pac. Symp. Biocomput., 2011, 165

Shen, 1970, Comparison of impedance to insulin-mediated glucose uptake in normal subjects and in subjects with latent diabetes, J. Clin. Invest., 49, 2151, 10.1172/JCI106433

Tiwari, 2014, The role of obesity in cardiomyopathy and nephropathy, Curr. Pharm. Des., 20, 1409, 10.2174/13816128113199990562

Truong, 2015, MetaPhlAn2 for enhanced metagenomic taxonomic profiling, Nat. Methods, 12, 902, 10.1038/nmeth.3589

Turnbaugh, 2009, A core gut microbiome in obese and lean twins, Nature, 457, 480, 10.1038/nature07540

Turnbaugh, 2006, An obesity-associated gut microbiome with increased capacity for energy harvest, Nature, 444, 1027, 10.1038/nature05414

Ussher, 2013, Gut microbiota metabolism of L-carnitine and cardiovascular risk, Atherosclerosis, 231, 456, 10.1016/j.atherosclerosis.2013.10.013

van Etten, 2002, Impaired NO-dependent vasodilation in patients with type II (non-insulin-dependent) diabetes mellitus is restored by acute administration of folate, Diabetologia, 45, 1004, 10.1007/s00125-002-0862-1

Vatanen, 2016, Variation in microbiome LPS immunogenicity contributes to autoimmunity in humans, Cell, 165, 842, 10.1016/j.cell.2016.04.007

Wang, 2007, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl. Environ. Microbiol., 73, 5261, 10.1128/AEM.00062-07

Wang, 2013, Circulating prolactin associates with diabetes and impaired glucose regulation: a population-based study, Diabetes Care, 36, 1974, 10.2337/dc12-1893

Wang, 2009, RNA-Seq: a revolutionary tool for transcriptomics, Nat. Rev. Genet., 10, 57, 10.1038/nrg2484

Wikoff, 2009, Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites, Proc. Natl. Acad. Sci. USA, 106, 3698, 10.1073/pnas.0812874106

Williams, 2016, Systems proteomics of liver mitochondria function, Science, 352, aad0189, 10.1126/science.aad0189

Xia, 2016, Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis, Curr. Protoc. Bioinformatics, 55, 14 10 11, 10.1002/cpbi.11

Yeni-Komshian, 2000, Relationship between several surrogate estimates of insulin resistance and quantification of insulin-mediated glucose disposal in 490 healthy nondiabetic volunteers, Diabetes Care, 23, 171, 10.2337/diacare.23.2.171

Yoon, 2016, The emerging role of branched-chain amino acids in insulin resistance and metabolism, Nutrients, 8, 10.3390/nu8070405

Zhang, 2005, A general framework for weighted gene co-expression network analysis, Stat. Appl. Genet. Mol. Biol., 4, Article17, 10.2202/1544-6115.1128