Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome
Tóm tắt
Từ khóa
Tài liệu tham khảo
2012, Structure, Function and Diversity of the Human Microbiome in an Adult Reference Population. Nature.
B Stecher, 2008, The role of microbiota in infectious disease., Trends Microbiol, 16, 107, 10.1016/j.tim.2007.12.008
JL Round, 2009, The gut microbiota shapes intestinal immune responses during health and disease., Nat Rev Immunol, 9, 313, 10.1038/nri2515
WS Garrett, 2010, Homeostasis and inflammation in the intestine., Cell, 140, 859, 10.1016/j.cell.2010.01.023
PJ Turnbaugh, 2009, A core gut microbiome in obese and lean twins., Nature, 457, 480, 10.1038/nature07540
H Li, 2008, Mapping short DNA sequencing reads and calling variants using mapping quality scores., Genome Res, 18, 1851, 10.1101/gr.078212.108
J Ravel, 2011, Vaginal microbiome of reproductive-age women., Proc Natl Acad Sci U S A, 108, 4680, 10.1073/pnas.1002611107
EA Grice, 2010, Longitudinal shift in diabetic wound microbiota correlates with prolonged skin defense response., Proc Natl Acad Sci U S A, 107, 14799, 10.1073/pnas.1004204107
2012, A framework for human microbiome research. Nature.
EK Costello, 2009, Bacterial community variation in human body habitats across space and time., Science, 326, 1694, 10.1126/science.1177486
J Qin, 2010, A human gut microbial gene catalogue established by metagenomic sequencing., Nature, 464, 59, 10.1038/nature08821
VM Markowitz, 2008, IMG/M: a data management and analysis system for metagenomes., Nucleic Acids Res, 36, D534, 10.1093/nar/gkm869
F Meyer, 2008, The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes., BMC Bioinformatics, 9, 386, 10.1186/1471-2105-9-386
S Mitra, 2011, Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG., BMC Bioinformatics, 12, S21, 10.1186/1471-2105-12-S1-S21
SR Gill, 2006, Metagenomic analysis of the human distal gut microbiome., Science, 312, 1355, 10.1126/science.1124234
TA Gianoulis, 2009, Quantifying environmental adaptation of metabolic pathways in metagenomics., Proc Natl Acad Sci U S A, 106, 1374, 10.1073/pnas.0808022106
I Sharon, 2009, A Statistical Framework for the Functional Analysis of Metagenomes., 496
K Kurokawa, 2007, Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes., DNA Res, 14, 169, 10.1093/dnares/dsm018
JR White, 2009, Statistical methods for detecting differentially abundant features in clinical metagenomic samples., PLoS Comput Biol, 5, e1000352, 10.1371/journal.pcbi.1000352
BL Cantarel, 2012, Complex Carbohydrate Utilization by the Healthy Human Microbiome. PLoS One.
Y Ye, 2009, A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes., PLoS Comput Biol, 5, e1000465, 10.1371/journal.pcbi.1000465
N Segata, 2011, Metagenomic biomarker discovery and explanation., Genome Biol, 12, R60, 10.1186/gb-2011-12-6-r60
J Martin, 2012, Optimizing Read Mapping to Reference Genomes to determine composition and species prevalence in microbial communities. PLoS One.
H Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform., Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324
M Kanehisa, 2010, KEGG for representation and analysis of molecular networks involving diseases and drugs., Nucleic Acids Res, 38, D355, 10.1093/nar/gkp896
RC Edgar, 2010, Search and clustering orders of magnitude faster than BLAST., Bioinformatics, 26, 2460, 10.1093/bioinformatics/btq461
R Caspi, 2010, The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases., Nucleic Acids Res, 38, D473, 10.1093/nar/gkp875
IH Witten, 1991, The zero-frequency problem: Estimating the probabilities of novel events in adaptive text compression., IEEE Trans Inf Theory, 37, 1085, 10.1109/18.87000
C Hastings, 1947, Low moments for small samples: a comparative study of order statistics., Ann Math Stat, 18, 413, 10.1214/aoms/1177730388
K Mavromatis, 2007, Use of simulated data sets to evaluate the fidelity of metagenomic processing methods., Nat Methods, 4, 495, 10.1038/nmeth1043
Y Huang, 2003, Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli., Science, 301, 616, 10.1126/science.1087619
D Ware, 2005, Utilization of putrescine by Streptococcus pneumoniae during growth in choline-limited medium., J Microbiol, 43, 398
AE Magurran, 2004, Measuring Biological Diversity. Wiley-Blackwell.
S Lavorel, 2008, Assessing functional diversity in the field–methodology matters! Funct Ecol, 22, 134
S Villeger, 2008, New multidimensional functional diversity indices for a multifaceted framework in functional ecology., Ecology, 89, 2290, 10.1890/07-1206.1
PD Schloss, 2008, A statistical toolbox for metagenomics: assessing functional diversity in microbial communities., BMC Bioinformatics, 9, 34, 10.1186/1471-2105-9-34
J Raes, 2011, Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data., Mol Syst Biol, 7, 473, 10.1038/msb.2011.6
EC Pielou, 1975, Indices of diversity and evenness.
J Xu, 2007, Evolution of symbiotic bacteria in the distal human intestine., PLoS Biol, 5, e156, 10.1371/journal.pbio.0050156
MY Ahn, 1998, Characterization of a Bacteroides species from human intestine that degrades glycosaminoglycans., Can J Microbiol, 44, 423, 10.1139/cjm-44-5-423
EC Martens, 2009, Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm., J Biol Chem, 284, 24673, 10.1074/jbc.R109.022848
K Gloux, 2010, Microbes and Health Sackler Colloquium: A metagenomic {beta}-glucuronidase uncovers a core adaptive function of the human intestinal microbiome., Proc Natl Acad Sci U S A, 108, 4539, 10.1073/pnas.1000066107
C Humblot, 2007, Beta-glucuronidase in human intestinal microbiota is necessary for the colonic genotoxicity of the food-borne carcinogen 2-amino-3-methylimidazo[4,5-f]quinoline in rats., Carcinogenesis, 28, 2419, 10.1093/carcin/bgm170
K Takasuna, 1996, Involvement of beta-glucuronidase in intestinal microflora in the intestinal toxicity of the antitumor camptothecin derivative irinotecan hydrochloride (CPT-11) in rats., Cancer Res, 56, 3752
I Vlodavsky, 1999, Mammalian heparanase: gene cloning, expression and function in tumor progression and metastasis., Nat Med, 5, 793, 10.1038/10518
M Waterman, 2007, Heparanase upregulation by colonic epithelium in inflammatory bowel disease., Mod Pathol, 20, 8, 10.1038/modpathol.3800710
GW Yip, 2006, Therapeutic value of glycosaminoglycans in cancer., Mol Cancer Ther, 5, 2139, 10.1158/1535-7163.MCT-06-0082
A Schmidtchen, 2001, Dermatan sulphate is released by proteinases of common pathogenic bacteria and inactivates antibacterial alpha-defensin., Mol Microbiol, 39, 708, 10.1046/j.1365-2958.2001.02251.x
JM Laparra, 2010, Interactions of gut microbiota with functional food components and nutraceuticals., Pharmacol Res, 61, 219, 10.1016/j.phrs.2009.11.001
ZQ Wang, 2007, Bacterial flavodoxins support nitric oxide production by Bacillus subtilis nitric-oxide synthase., J Biol Chem, 282, 2196, 10.1074/jbc.M608206200
J Vermeiren, 2009, Nitric oxide production by the human intestinal microbiota by dissimilatory nitrate reduction to ammonium., J Biomed Biotechnol, 2009, 284718, 10.1155/2009/284718
MD Mailman, 2007, The NCBI dbGaP database of genotypes and phenotypes., Nat Genet, 39, 1181, 10.1038/ng1007-1181
TR Klaenhammer, 2005, Genomic features of lactic acid bacteria effecting bioprocessing and health., FEMS Microbiol Rev, 29, 393, 10.1016/j.fmrre.2005.04.007
AL Francl, 2010, The PTS transporters of Lactobacillus gasseri ATCC 33323., BMC Microbiol, 10, 77, 10.1186/1471-2180-10-77
O Koren, 2011, Human oral, gut, and plaque microbiota in patients with atherosclerosis., Proc Natl Acad Sci U S A, 108, 4592, 10.1073/pnas.1011383107
DB Goldstein, 2009, Common genetic variation and human traits., N Engl J Med, 360, 1696, 10.1056/NEJMp0806284
A Dupuy, 2007, Critical review of published microarray studies for cancer outcome and guidelines on statistical analysis and reporting., J Natl Cancer Inst, 99, 147, 10.1093/jnci/djk018
R Clarke, 2008, The properties of high-dimensional data spaces: implications for exploring gene and protein expression data., Nat Rev Cancer, 8, 37, 10.1038/nrc2294
CT Walsh, 2010, Natural products version 2.0: connecting genes to molecules., J Am Chem Soc, 132, 2469, 10.1021/ja909118a
DG Burrin, 2009, Metabolic fate and function of dietary glutamate in the gut., Am J Clin Nutr, 90, 850S, 10.3945/ajcn.2009.27462Y
D Dalevi, 2008, Annotation of metagenome short reads using proxygenes., Bioinformatics, 24, i7, 10.1093/bioinformatics/btn276
PJ Turnbaugh, 2008, An invitation to the marriage of metagenomics and metabolomics., Cell, 134, 708, 10.1016/j.cell.2008.08.025
S Freilich, 2009, Metabolic-network-driven analysis of bacterial ecological strategies., Genome Biol, 10, R61, 10.1186/gb-2009-10-6-r61
N Klitgord, 2011, Ecosystems biology of microbial metabolism., Curr Opin Biotechnol, 22, 541, 10.1016/j.copbio.2011.04.018
C Manichanh, 2006, Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach., Gut, 55, 205, 10.1136/gut.2005.073817
OL Petchey, 2006, Functional diversity: back to basics and looking forward., Ecol Lett, 9, 741, 10.1111/j.1461-0248.2006.00924.x
J Yang, 2008, VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics., Nucleic Acids Res, 36, D539, 10.1093/nar/gkm951
B Liu, 2009, ARDB–Antibiotic Resistance Genes Database., Nucleic Ccids Res, 37, D443, 10.1093/nar/gkn656
J Goll, 2012, A case study for large-scale human microbiome analysis using JCVI's Metagenomics Reports (METAREP). PLoS One.