Systems biology perspective for studying the gut microbiota in human physiology and liver diseases
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J. Nielsen | J. Borén | M. Uhlén | A. Mardinoğlu | O. Altay
[1] J. Nielsen,et al. Defining the human adipose tissue proteome to reveal metabolic alterations in obesity. , 2014, Journal of proteome research.
[2] Peter J. Turnbaugh,et al. The microbial pharmacists within us: a metagenomic view of xenobiotic metabolism , 2016, Nature Reviews Microbiology.
[3] Luke R. Thompson,et al. Best practices for analysing microbiomes , 2018, Nature Reviews Microbiology.
[4] Lanjuan Li,et al. Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma , 2018, Gut.
[5] William H. Bisson,et al. Gut microbiota and intestinal FXR mediate the clinical benefits of metformin , 2018, Nature Medicine.
[6] Lanjuan Li,et al. Disorganized Gut Microbiome Contributed to Liver Cirrhosis Progression: A Meta-Omics-Based Study , 2018, Front. Microbiol..
[7] Marju Orho-Melander,et al. The gut microbiome as a target for prevention and treatment of hyperglycaemia in type 2 diabetes: from current human evidence to future possibilities , 2017, Diabetologia.
[8] Lawrence A. David,et al. The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota , 2016, Hepatology.
[9] P. Gérard,et al. The links between the gut microbiome and non-alcoholic fatty liver disease (NAFLD) , 2019, Cellular and Molecular Life Sciences.
[10] Katherine H. Huang,et al. Structure, Function and Diversity of the Healthy Human Microbiome , 2012, Nature.
[11] Wei Jia,et al. Bile acid–microbiota crosstalk in gastrointestinal inflammation and carcinogenesis , 2018, Nature Reviews Gastroenterology & Hepatology.
[12] Jens Nielsen,et al. Personal model‐assisted identification of NAD+ and glutathione metabolism as intervention target in NAFLD , 2017, Molecular systems biology.
[13] Jens Nielsen,et al. An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans. , 2018, Cell metabolism.
[14] R. Schwabe,et al. The gut microbiome and liver cancer: mechanisms and clinical translation , 2017, Nature Reviews Gastroenterology &Hepatology.
[15] Eddy J. Bautista,et al. Integrative Personal Omics Profiles during Periods of Weight Gain and Loss. , 2018, Cell systems.
[16] J. Nielsen,et al. Systems biology in hepatology: approaches and applications , 2018, Nature Reviews Gastroenterology & Hepatology.
[17] P. Paci,et al. Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta‐omics‐based approach , 2017, Hepatology.
[18] Andmorgan R. Fisher,et al. Altered profile of human gut microbiome is associated with cirrhosis and its complications. , 2014, Journal of hepatology.
[19] Johannes Zimmermann,et al. BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities , 2017, PLoS Comput. Biol..
[20] Ines Thiele,et al. Anoxic Conditions Promote Species-Specific Mutualism between Gut Microbes In Silico , 2015, Applied and Environmental Microbiology.
[21] J. Bajaj. Alcohol, liver disease and the gut microbiota , 2019, Nature Reviews Gastroenterology & Hepatology.
[22] Justine W. Debelius,et al. The gut–liver axis and the intersection with the microbiome , 2018, Nature Reviews Gastroenterology & Hepatology.
[23] E. Ferrannini,et al. The diabetes pandemic and associated infections: suggestions for clinical microbiology , 2018, Reviews in medical microbiology : a journal of the Pathological Society of Great Britain and Ireland.
[24] S. Rabot,et al. Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice , 2012, Gut.
[25] Nicholas Chia,et al. MMinte: an application for predicting metabolic interactions among the microbial species in a community , 2016, BMC Bioinformatics.
[26] Caroline H. Johnson,et al. Metabolomics: beyond biomarkers and towards mechanisms , 2016, Nature Reviews Molecular Cell Biology.
[27] David Torrents,et al. Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug , 2017, Nature Medicine.
[28] M. Doebeli,et al. Calibration and analysis of genome-based models for microbial ecology , 2015, eLife.
[29] J. Raes,et al. Faecal Metaproteomic Analysis Reveals a Personalized and Stable Functional Microbiome and Limited Effects of a Probiotic Intervention in Adults , 2016, PloS one.
[30] Ali R. Zomorrodi,et al. d-OptCom: Dynamic multi-level and multi-objective metabolic modeling of microbial communities. , 2014, ACS synthetic biology.
[31] M. Uhlén,et al. Understanding the Representative Gut Microbiota Dysbiosis in Metformin-Treated Type 2 Diabetes Patients Using Genome-Scale Metabolic Modeling , 2018, Front. Physiol..
[32] S. Sarin,et al. Microbiome as a therapeutic target in alcohol-related liver disease. , 2019, Journal of hepatology.
[33] M. Simon,et al. Microbial Regulation of Glucose Metabolism and Insulin Resistance , 2017, Genes.
[34] E. Balskus,et al. Exploring and Understanding the Biochemical Diversity of the Human Microbiota. , 2016, Cell chemical biology.
[35] Xuan-xian Peng,et al. Functional metabolomics: from biomarker discovery to metabolome reprogramming , 2015, Protein & Cell.
[36] Beatriz García Jiménez,et al. FLYCOP: metabolic modeling-based analysis and engineering microbial communities , 2018, Bioinform..
[37] Eran Elinav,et al. Use of Metatranscriptomics in Microbiome Research , 2016, Bioinformatics and biology insights.
[38] J. Nielsen,et al. Predicting growth of the healthy infant using a genome scale metabolic model , 2017, npj Systems Biology and Applications.
[39] A. Gasbarrini,et al. Hepatocellular Carcinoma Is Associated With Gut Microbiota Profile and Inflammation in Nonalcoholic Fatty Liver Disease , 2018, Hepatology.
[40] K. Rioux,et al. Gut microbiota manipulation with prebiotics in patients with non-alcoholic fatty liver disease: a randomized controlled trial protocol , 2015, BMC Gastroenterology.
[41] J. Bajaj,et al. Microbiota, cirrhosis, and the emerging oral-gut-liver axis. , 2017, JCI insight.
[42] Cheng Zhang,et al. Applications of Genome-Scale Metabolic Models in Biotechnology and Systems Medicine , 2016, Front. Physiol..
[43] Peer Bork,et al. Extensive impact of non-antibiotic drugs on human gut bacteria , 2018, Nature.
[44] Nicholas Chia,et al. Microbiome at the Frontier of Personalized Medicine , 2017, Mayo Clinic proceedings.
[45] Jens Nielsen,et al. Systems Biology of Metabolism: A Driver for Developing Personalized and Precision Medicine. , 2017, Cell metabolism.
[46] Nichole Reisdorph,et al. Microbiome and metabolome data integration provides insight into health and disease. , 2017, Translational research : the journal of laboratory and clinical medicine.
[47] R. Gan,et al. Gut Microbiota’s Relationship with Liver Disease and Role in Hepatoprotection by Dietary Natural Products and Probiotics , 2018, Nutrients.
[48] W. Liao,et al. Influence of diet on the gut microbiome and implications for human health , 2017, Journal of Translational Medicine.
[49] D. Ciocan,et al. Characterization of intestinal microbiota in alcoholic patients with and without alcoholic hepatitis or chronic alcoholic pancreatitis , 2018, Scientific Reports.
[50] Wataru Iwasaki,et al. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond , 2016, Microbes and environments.
[51] M. Heikenwalder,et al. The Liver at the Nexus of Host-Microbial Interactions. , 2016, Cell host & microbe.
[52] John C. Earls,et al. A wellness study of 108 individuals using personal, dense, dynamic data clouds , 2017, Nature Biotechnology.
[53] Stephen T. C. Wong,et al. Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction , 2019, Bioinform..
[54] J. Nicholson,et al. Impact of the gut microbiota on inflammation, obesity, and metabolic disease , 2016, Genome Medicine.
[55] Jos Boekhorst,et al. A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets , 2013, BMC Genomics.
[56] L. Hood,et al. A personal view on systems medicine and the emergence of proactive P4 medicine: predictive, preventive, personalized and participatory. , 2012, New biotechnology.
[57] F. Bäckhed,et al. Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks , 2018, Proceedings of the National Academy of Sciences.
[58] W. Si,et al. Histopathological Features and Composition of Gut Microbiota in Rhesus Monkey of Alcoholic Liver Disease , 2019, Front. Microbiol..
[59] M. Marco,et al. Mice Fed a High-Fat Diet Supplemented with Resistant Starch Display Marked Shifts in the Liver Metabolome Concurrent with Altered Gut Bacteria. , 2016, The Journal of nutrition.
[60] Daniel Segrè,et al. Synthetic Ecology of Microbes: Mathematical Models and Applications. , 2016, Journal of molecular biology.
[61] Partho Sen,et al. Quantifying Diet-Induced Metabolic Changes of the Human Gut Microbiome. , 2015, Cell metabolism.
[62] A. Kurilshikov,et al. Environment dominates over host genetics in shaping human gut microbiota , 2018, Nature.
[63] Jens Nielsen,et al. The gut microbiota modulates host amino acid and glutathione metabolism in mice , 2015 .
[64] Timothy J. Hanly,et al. Dynamic flux balance modeling of microbial co‐cultures for efficient batch fermentation of glucose and xylose mixtures , 2011, Biotechnology and bioengineering.
[65] H. Tilg,et al. Liver-Microbiome Axis in Health and Disease. , 2018, Trends in immunology.
[66] Shibu Yooseph,et al. Gut Microbiome-Based Metagenomic Signature for Non-invasive Detection of Advanced Fibrosis in Human Nonalcoholic Fatty Liver Disease. , 2017, Cell metabolism.
[67] Junhua Li,et al. Impact of early events and lifestyle on the gut microbiota and metabolic phenotypes in young school-age children , 2019, Microbiome.
[68] K. Venema,et al. Gut microbial metabolites in obesity, NAFLD and T2DM , 2019, Nature Reviews Endocrinology.
[69] Alex H. Lang,et al. Metabolic resource allocation in individual microbes determines ecosystem interactions and spatial dynamics. , 2014, Cell reports.
[70] Oskar Hallatschek,et al. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts , 2018, bioRxiv.
[71] F. Bäckhed,et al. Diet–microbiota interactions as moderators of human metabolism , 2016, Nature.
[72] J. Schattenberg,et al. Insulin resistance alters hepatic ethanol metabolism: studies in mice and children with non-alcoholic fatty liver disease , 2015, Gut.
[73] F. Bruggeman,et al. Community Flux Balance Analysis for Microbial Consortia at Balanced Growth , 2013, PloS one.
[74] Barbara M. Bakker,et al. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism , 2013, Journal of Lipid Research.
[75] Intawat Nookaew,et al. Understanding the interactions between bacteria in the human gut through metabolic modeling , 2013, Scientific Reports.
[76] A. Goodman,et al. Mapping human microbiome drug metabolism by gut bacteria and their genes , 2019, Nature.
[77] K. Zengler,et al. Elucidation of complexity and prediction of interactions in microbial communities , 2017, Microbial biotechnology.
[78] J. Mohammadnejad,et al. A Systems Biology Approach to Understanding Alcoholic Liver Disease Molecular Mechanism: The Development of Static and Dynamic Models , 2017, Bulletin of Mathematical Biology.
[79] N. Lundbom,et al. Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome , 2018, Scientific Reports.
[80] Intawat Nookaew,et al. Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction , 2014, BMC Systems Biology.
[81] Dmitry S. Ischenko,et al. Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease , 2017, Microbiome.
[82] Costas D. Maranas,et al. SteadyCom: Predicting microbial abundances while ensuring community stability , 2017, PLoS Comput. Biol..
[83] Radhakrishnan Mahadevan,et al. Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments , 2011, The ISME Journal.
[84] T. Dinan,et al. Friends with social benefits: host-microbe interactions as a driver of brain evolution and development? , 2014, Front. Cell. Infect. Microbiol..
[85] Costas D. Maranas,et al. OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities , 2012, PLoS Comput. Biol..
[86] Microbiome Alteration in Type 2 Diabetes Mellitus Model of Zebrafish , 2019, Scientific Reports.
[87] W. Liu,et al. Abnormal fecal microbiota community and functions in patients with hepatitis B liver cirrhosis as revealed by a metagenomic approach , 2013, BMC Gastroenterology.
[88] Miguel Pignatelli,et al. Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota , 2011, PloS one.
[89] L. Henry,et al. Global epidemiology of nonalcoholic fatty liver disease—Meta‐analytic assessment of prevalence, incidence, and outcomes , 2016, Hepatology.
[90] H. Flint,et al. Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis. , 2015, FEMS microbiology letters.
[91] Yongzhong Zhao,et al. Gut microbiota derived metabolites in cardiovascular health and disease , 2018, Protein & Cell.
[92] C. Lynch,et al. Branched-chain amino acids in metabolic signalling and insulin resistance , 2014, Nature Reviews Endocrinology.
[93] Eran Segal,et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples , 2015, Science.
[94] Chongle Pan,et al. Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota , 2015, Proteomics.
[95] A. Heintz‐Buschart,et al. Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes , 2016, Nature Microbiology.