-
1
-
-
70449713952
-
The NIH Human Microbiome Project
-
NIH HMP Working Group, Peterson J, Garges S, et al. The NIH Human Microbiome Project. Genome Res 2009;19:2317-23
-
(2009)
Genome Res
, vol.19
, pp. 2317-2323
-
-
Peterson, J.1
Garges, S.2
-
2
-
-
84977622019
-
Diet-microbiota interactions as moderators of human metabolism
-
Sonnenburg JL, Bäckhed F. Diet-microbiota interactions as moderators of human metabolism. Nature 2016;535:56-64
-
(2016)
Nature
, vol.535
, pp. 56-64
-
-
Sonnenburg, J.L.1
Bäckhed, F.2
-
3
-
-
84959338100
-
The role of the gut microbiome in the pathogenesis and treatment of obesity
-
Okeke F, Roland BC, Mullin GE. The role of the gut microbiome in the pathogenesis and treatment of obesity. Glob Adv Health Med 2014;3:44-57
-
(2014)
Glob Adv Health Med
, vol.3
, pp. 44-57
-
-
Okeke, F.1
Roland, B.C.2
Mullin, G.E.3
-
4
-
-
84963930821
-
Impact of the gut microbiota on inflammation, obesity, and metabolic disease
-
Boulangé CL, Neves AL, Chilloux J, et al. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med 2016;8:42
-
(2016)
Genome Med
, vol.8
, pp. 42
-
-
Boulangé, C.L.1
Neves, A.L.2
Chilloux, J.3
-
5
-
-
84991056627
-
Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome
-
Ussar S, Fujisaka S, Kahn CR. Interactions between host genetics and gut microbiome in diabetes and metabolic syndrome. Mol Metab 2016;5:795-803
-
(2016)
Mol Metab
, vol.5
, pp. 795-803
-
-
Ussar, S.1
Fujisaka, S.2
Kahn, C.R.3
-
6
-
-
84988372530
-
The gut microbiota and metabolic disease: current understanding and future perspectives
-
Arora T, Bäckhed F. The gut microbiota and metabolic disease: current understanding and future perspectives. J Intern Med 2016;280:339-49
-
(2016)
J Intern Med
, vol.280
, pp. 339-349
-
-
Arora, T.1
Bäckhed, F.2
-
9
-
-
84907557973
-
The microbial basis of inflammatory bowel diseases
-
Dalal SR, Chang EB. The microbial basis of inflammatory bowel diseases. J Clin Invest 2014;124:4190-6
-
(2014)
J Clin Invest
, vol.124
, pp. 4190-4196
-
-
Dalal, S.R.1
Chang, E.B.2
-
11
-
-
84992055659
-
Environmental control of autoimmune inflammation in the central nervous system
-
Rothhammer V, Quintana FJ. Environmental control of autoimmune inflammation in the central nervous system. Curr Opin Immunol 2016;43:46-53
-
(2016)
Curr Opin Immunol
, vol.43
, pp. 46-53
-
-
Rothhammer, V.1
Quintana, F.J.2
-
12
-
-
84981250455
-
The human microbiome in rheumatic autoimmune diseases: A comprehensive review
-
Coit P, Sawalha AH. The human microbiome in rheumatic autoimmune diseases: A comprehensive review. Clin Immunol 2016;170:70-9
-
(2016)
Clin Immunol
, vol.170
, pp. 70-79
-
-
Coit, P.1
Sawalha, A.H.2
-
13
-
-
84970003842
-
Polymicrobial-Host Interactions during Infection
-
Tay WH, Chong KK, Kline KA. Polymicrobial-Host Interactions during Infection. J Mol Biol 2016;428:3355-71
-
(2016)
J Mol Biol
, vol.428
, pp. 3355-3371
-
-
Tay, W.H.1
Chong, K.K.2
Kline, K.A.3
-
14
-
-
84963865443
-
Host-microbiome interactions in acute and chronic respiratory infections
-
Taylor SL, Wesselingh S, Rogers GB. Host-microbiome interactions in acute and chronic respiratory infections. Cell Microbiol 2016;18:652-62
-
(2016)
Cell Microbiol
, vol.18
, pp. 652-662
-
-
Taylor, S.L.1
Wesselingh, S.2
Rogers, G.B.3
-
15
-
-
84934968810
-
Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract
-
Shankar J, Solis NV, Mounaud S, et al. Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract. Sci Rep 2015;5:8131
-
(2015)
Sci Rep
, vol.5
, pp. 8131
-
-
Shankar, J.1
Solis, N.V.2
Mounaud, S.3
-
16
-
-
84962069627
-
An Omics Perspective on Candida Infections: Toward Next-Generation Diagnosis and Therapy
-
Smeekens SP, van de Veerdonk FL, Netea MG. An Omics Perspective on Candida Infections: Toward Next-Generation Diagnosis and Therapy. Front Microbiol 2016;7:154
-
(2016)
Front Microbiol
, vol.7
, pp. 154
-
-
Smeekens, S.P.1
van de Veerdonk, F.L.2
Netea, M.G.3
-
17
-
-
84978427487
-
Gram-Positive Uropathogens, Polymicrobial Urinary Tract Infection, and the Emerging Microbiota of the Urinary Tract
-
Kline KA, Lewis AL. Gram-Positive Uropathogens, Polymicrobial Urinary Tract Infection, and the Emerging Microbiota of the Urinary Tract. Microbiol Spectr 2016;4(2)
-
(2016)
Microbiol Spectr
, vol.4
, Issue.2
-
-
Kline, K.A.1
Lewis, A.L.2
-
18
-
-
84994126390
-
Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease
-
Cribbs SK, Beck JM. Microbiome in the pathogenesis of cystic fibrosis and lung transplant-related disease. Transl Res 2017;179:84-96
-
(2017)
Transl Res
, vol.179
, pp. 84-96
-
-
Cribbs, S.K.1
Beck, J.M.2
-
19
-
-
84963815353
-
Microbiome alterations in HIV infection a review
-
Williams B, Landay A, Presti RM. Microbiome alterations in HIV infection a review. Cell Microbiol 2016;18:645-51
-
(2016)
Cell Microbiol
, vol.18
, pp. 645-651
-
-
Williams, B.1
Landay, A.2
Presti, R.M.3
-
20
-
-
85018493034
-
Microbiome-driven carcinogenesis in colorectal cancer: models and mechanisms
-
Wang X, Yang Y, Huycke MM. Microbiome-driven carcinogenesis in colorectal cancer: models and mechanisms. Free Radic Biol Med 2017;105:3-15
-
(2017)
Free Radic Biol Med
, vol.105
, pp. 3-15
-
-
Wang, X.1
Yang, Y.2
Huycke, M.M.3
-
21
-
-
84956777636
-
Epidemiologic studies of the human microbiome and cancer
-
Vogtmann E, Goedert JJ. Epidemiologic studies of the human microbiome and cancer. Br J Cancer 2016;114:237-42
-
(2016)
Br J Cancer
, vol.114
, pp. 237-242
-
-
Vogtmann, E.1
Goedert, J.J.2
-
22
-
-
84963603074
-
Microbiome mediation of infections in the cancer setting
-
Taur Y, Pamer EG. Microbiome mediation of infections in the cancer setting. Genome Med 2016;8:40
-
(2016)
Genome Med
, vol.8
, pp. 40
-
-
Taur, Y.1
Pamer, E.G.2
-
23
-
-
84978861797
-
Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients
-
Shankar J, Nguyen MH, Crespo MM, et al. Looking Beyond Respiratory Cultures: Microbiome-Cytokine Signatures of Bacterial Pneumonia and Tracheobronchitis in Lung Transplant Recipients. Am J Transplant 2016;16:1766-78
-
(2016)
Am J Transplant
, vol.16
, pp. 1766-1778
-
-
Shankar, J.1
Nguyen, M.H.2
Crespo, M.M.3
-
24
-
-
85021792558
-
The Microbiome and Allogeneic Stem Cell Transplantation
-
Sporrer D, Gessner A, Hehlgans T, et al. The Microbiome and Allogeneic Stem Cell Transplantation. Curr Stem Cell Rep 2015;1:53-9
-
(2015)
Curr Stem Cell Rep
, vol.1
, pp. 53-59
-
-
Sporrer, D.1
Gessner, A.2
Hehlgans, T.3
-
25
-
-
84963613854
-
The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation
-
Langdon A, Crook N, Dantas G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med 2016;8:39
-
(2016)
Genome Med
, vol.8
, pp. 39
-
-
Langdon, A.1
Crook, N.2
Dantas, G.3
-
26
-
-
84951293450
-
Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance
-
Johanesen PA, Mackin KE, Hutton ML, et al. Disruption of the Gut Microbiome: Clostridium difficile Infection and the Threat of Antibiotic Resistance. Genes 2015;6:1347-60
-
(2015)
Genes
, vol.6
, pp. 1347-1360
-
-
Johanesen, P.A.1
Mackin, K.E.2
Hutton, M.L.3
-
27
-
-
84896092821
-
The Treatment-Naive Microbiome in New-Onset Crohn's Disease
-
Gevers D, Kugathasan S, Denson LA, et al. The Treatment-Naive Microbiome in New-Onset Crohn's Disease. Cell Host Microbe 2014;15:382-92
-
(2014)
Cell Host Microbe
, vol.15
, pp. 382-392
-
-
Gevers, D.1
Kugathasan, S.2
Denson, L.A.3
-
28
-
-
84962190540
-
Microbiome-based companion diagnostics: no longer science fiction?
-
Raes J. Microbiome-based companion diagnostics: no longer science fiction? Gut 2016;65:896-7
-
(2016)
Gut
, vol.65
, pp. 896-897
-
-
Raes, J.1
-
29
-
-
84978134353
-
Microbiome-wide association studies link dynamic microbial consortia to disease
-
Gilbert JA, Quinn RA, Debelius J, et al. Microbiome-wide association studies link dynamic microbial consortia to disease. Nature 2016;535:94-103
-
(2016)
Nature
, vol.535
, pp. 94-103
-
-
Gilbert, J.A.1
Quinn, R.A.2
Debelius, J.3
-
30
-
-
84979498467
-
Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease
-
Shaw KA, Bertha M, Hofmekler T, et al. Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease. Genome Med 2016;8:75
-
(2016)
Genome Med
, vol.8
, pp. 75
-
-
Shaw, K.A.1
Bertha, M.2
Hofmekler, T.3
-
31
-
-
84957565267
-
Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis
-
Bizzarro S, Laine ML, Buijs MJ, et al. Microbial profiles at baseline and not the use of antibiotics determine the clinical outcome of the treatment of chronic periodontitis. Sci Rep 2016;6:20205
-
(2016)
Sci Rep
, vol.6
, pp. 20205
-
-
Bizzarro, S.1
Laine, M.L.2
Buijs, M.J.3
-
32
-
-
84960359982
-
Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections
-
Gallo RL, Hultsch T, Farnaes L. Recognizing that the microbiome is part of the human immune system will advance treatment of both cancer and infections. J Am Acad Dermatol 2016;74:772-4
-
(2016)
J Am Acad Dermatol
, vol.74
, pp. 772-774
-
-
Gallo, R.L.1
Hultsch, T.2
Farnaes, L.3
-
33
-
-
84977507546
-
Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions
-
Zhang LS, Davies SS. Microbial metabolism of dietary components to bioactive metabolites: opportunities for new therapeutic interventions. Genome Med 2016;8:46
-
(2016)
Genome Med
, vol.8
, pp. 46
-
-
Zhang, L.S.1
Davies, S.S.2
-
34
-
-
85010200534
-
Intestinal microbial communities associated with acute enteric infections and disease recovery
-
Singh P, Teal TK, Marsh TL, et al. Intestinal microbial communities associated with acute enteric infections and disease recovery. Microbiome 2015;3:45
-
(2015)
Microbiome
, vol.3
, pp. 45
-
-
Singh, P.1
Teal, T.K.2
Marsh, T.L.3
-
35
-
-
84989352643
-
The Impact of the Gut Microbiota on Drug Metabolism and Clinical Outcome
-
Enright EF, Gahan CG, Joyce SA, et al. The Impact of the Gut Microbiota on Drug Metabolism and Clinical Outcome. Yale J Biol Med 2016;89:375-82
-
(2016)
Yale J Biol Med
, vol.89
, pp. 375-382
-
-
Enright, E.F.1
Gahan, C.G.2
Joyce, S.A.3
-
36
-
-
84938244327
-
Human microbiota. Small molecules from the human microbiota
-
Donia MS, Fischbach MA. Human microbiota. Small molecules from the human microbiota. Science 2015;349:1254766
-
(2015)
Science
, vol.349
-
-
Donia, M.S.1
Fischbach, M.A.2
-
38
-
-
84989338122
-
The Hoops, Hopes, and Hypes of Human Microbiome Research
-
Bik EM. The Hoops, Hopes, and Hypes of Human Microbiome Research. Yale J Biol Med 2016;89:363-73
-
(2016)
Yale J Biol Med
, vol.89
, pp. 363-373
-
-
Bik, E.M.1
-
39
-
-
84969981398
-
The importance of the microbiome in epidemiologic research
-
Hanson BM, Weinstock GM. The importance of the microbiome in epidemiologic research. Ann Epidemiol 2016;26:301-5
-
(2016)
Ann Epidemiol
, vol.26
, pp. 301-305
-
-
Hanson, B.M.1
Weinstock, G.M.2
-
40
-
-
84970021127
-
Intricacies of assessing the human microbiome in epidemiologic studies
-
Robinson CK, Brotman RM, Ravel J. Intricacies of assessing the human microbiome in epidemiologic studies. Ann Epidemiol 2016;26:311-21
-
(2016)
Ann Epidemiol
, vol.26
, pp. 311-321
-
-
Robinson, C.K.1
Brotman, R.M.2
Ravel, J.3
-
41
-
-
84991233196
-
Integrity of the Human Faecal Microbiota following Long-Term Sample Storage
-
Kia E, Wagner Mackenzie B, Middleton D, et al. Integrity of the Human Faecal Microbiota following Long-Term Sample Storage. PLoS One 2016;11:e0163666
-
(2016)
PLoS One
, vol.11
-
-
Kia, E.1
Wagner Mackenzie, B.2
Middleton, D.3
-
42
-
-
84982224114
-
Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies
-
Song SJ, Amir A, Metcalf JL, et al. Preservation Methods Differ in Fecal Microbiome Stability, Affecting Suitability for Field Studies. mSystems 2016;1(3). pii: e00021-16
-
(2016)
mSystems
, vol.1
, Issue.3
-
-
Song, S.J.1
Amir, A.2
Metcalf, J.L.3
-
43
-
-
84995784036
-
Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room?
-
Shaw AG, Sim K, Powell E, et al. Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? Microbiome 2016;4:40
-
(2016)
Microbiome
, vol.4
, pp. 40
-
-
Shaw, A.G.1
Sim, K.2
Powell, E.3
-
44
-
-
84996671022
-
Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine
-
Hsieh YH, Peterson CM, Raggio A, et al. Impact of Different Fecal Processing Methods on Assessments of Bacterial Diversity in the Human Intestine. Front Microbiol 2016;7:1643
-
(2016)
Front Microbiol
, vol.7
, pp. 1643
-
-
Hsieh, Y.H.1
Peterson, C.M.2
Raggio, A.3
-
45
-
-
84959450570
-
Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
-
Clooney AG, Fouhy F, Sleator RD, et al. Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis. PLoS One 2016;11:e0148028
-
(2016)
PLoS One
, vol.11
-
-
Clooney, A.G.1
Fouhy, F.2
Sleator, R.D.3
-
46
-
-
84976478934
-
Privacy-preserving microbiome analysis using secure computation
-
Wagner J, Paulson JN, Wang X, et al. Privacy-preserving microbiome analysis using secure computation. Bioinformatics 2016;32:1873-9
-
(2016)
Bioinformatics
, vol.32
, pp. 1873-1879
-
-
Wagner, J.1
Paulson, J.N.2
Wang, X.3
-
47
-
-
84962799376
-
The real cost of sequencing: scaling computation to keep pace with data generation
-
Muir P, Li S, Lou S, et al. The real cost of sequencing: scaling computation to keep pace with data generation. Genome Biol 2016;17:53
-
(2016)
Genome Biol
, vol.17
, pp. 53
-
-
Muir, P.1
Li, S.2
Lou, S.3
-
48
-
-
84955094814
-
Perils and potentials of self-selected entry to epidemiological studies and surveys
-
Keiding N, Louis TA. Perils and potentials of self-selected entry to epidemiological studies and surveys. J R Stat Soc Ser A Stat Soc 2016;179:319-76
-
(2016)
J R Stat Soc Ser A Stat Soc
, vol.179
, pp. 319-376
-
-
Keiding, N.1
Louis, T.A.2
-
49
-
-
77955554377
-
Experience with multiple control groups in a large population-based case-control study on genetic and environmental risk factors
-
Pomp ER, Van Stralen KJ, Le Cessie S, et al. Experience with multiple control groups in a large population-based case-control study on genetic and environmental risk factors. Eur J Epidemiol 2010;25:459-66
-
(2010)
Eur J Epidemiol
, vol.25
, pp. 459-466
-
-
Pomp, E.R.1
Van Stralen, K.J.2
Le Cessie, S.3
-
50
-
-
85100906014
-
-
Waltham, MA: UpToDate; 2016. Cited 2016 Nov 6
-
Han MK, Dransfield MT, Martinez F. Chronic obstructive pulmonary disease: Definition, clinical manifestations, diagnosis, and staging UpToDate. Waltham, MA: UpToDate; 2016. Cited 2016 Nov 6. Available online: http://www.uptodate.com/contents/chronic-obstructive-pulmonary-disease-definition-clinical-manifestations-diagnosis-and-staging
-
Chronic obstructive pulmonary disease: Definition, clinical manifestations, diagnosis, and staging UpToDate
-
-
Han, M.K.1
Dransfield, M.T.2
Martinez, F.3
-
51
-
-
84918522966
-
Commercial Smartphone-Based Devices and Smart Applications for Personalized Healthcare Monitoring and Management
-
Vashist SK, Schneider EM, Luong JH. Commercial Smartphone-Based Devices and Smart Applications for Personalized Healthcare Monitoring and Management. Diagnostics (Basel) 2014;4:104-28
-
(2014)
Diagnostics (Basel)
, vol.4
, pp. 104-128
-
-
Vashist, S.K.1
Schneider, E.M.2
Luong, J.H.3
-
52
-
-
84996542226
-
Research on the human virome: where are we and what is next
-
Zou S, Caler L, Colombini-Hatch S, et al. Research on the human virome: where are we and what is next. Microbiome 2016;4:32
-
(2016)
Microbiome
, vol.4
, pp. 32
-
-
Zou, S.1
Caler, L.2
Colombini-Hatch, S.3
-
53
-
-
52449129099
-
Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories
-
Woo PC, Lau SK, Teng JL, et al. Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 2008;14:908-34
-
(2008)
Clin Microbiol Infect
, vol.14
, pp. 908-934
-
-
Woo, P.C.1
Lau, S.K.2
Teng, J.L.3
-
54
-
-
84859972408
-
Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
-
Schoch CL, Seifert KA, Huhndorf S, et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proc Natl Acad Sci U S A 2012;109:6241-6
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 6241-6246
-
-
Schoch, C.L.1
Seifert, K.A.2
Huhndorf, S.3
-
55
-
-
84962666391
-
Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome
-
Willis AL, Calton JB, Carr TF, et al. Dead or alive: Deoxyribonuclease I sensitive bacteria and implications for the sinus microbiome. Am J Rhinol Allergy 2016;30:94-8
-
(2016)
Am J Rhinol Allergy
, vol.30
, pp. 94-98
-
-
Willis, A.L.1
Calton, J.B.2
Carr, T.F.3
-
56
-
-
84957431829
-
Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
-
Ranjan R, Rani A, Metwally A, et al. Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing. Biochem Biophys Res Commun 2016;469:967-77
-
(2016)
Biochem Biophys Res Commun
, vol.469
, pp. 967-977
-
-
Ranjan, R.1
Rani, A.2
Metwally, A.3
-
57
-
-
84963799511
-
Strain-level dissection of the contribution of the gut microbiome to human metabolic disease
-
Zhang C, Zhao L. Strain-level dissection of the contribution of the gut microbiome to human metabolic disease. Genome Med 2016;8:41
-
(2016)
Genome Med
, vol.8
, pp. 41
-
-
Zhang, C.1
Zhao, L.2
-
58
-
-
84892728434
-
Sequencing depth and coverage: key considerations in genomic analyses
-
Sims D, Sudbery I, Ilott NE, et al. Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet 2014;15:121-32
-
(2014)
Nat Rev Genet
, vol.15
, pp. 121-132
-
-
Sims, D.1
Sudbery, I.2
Ilott, N.E.3
-
59
-
-
84978127724
-
Metagenome-wide association studies: fine-mining the microbiome
-
Wang J, Jia H. Metagenome-wide association studies: fine-mining the microbiome. Nat Rev Microbiol 2016;14:508-22
-
(2016)
Nat Rev Microbiol
, vol.14
, pp. 508-522
-
-
Wang, J.1
Jia, H.2
-
60
-
-
84946919159
-
Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis
-
Conceição-Neto N, Zeller M, Lefrère H, et al. Modular approach to customise sample preparation procedures for viral metagenomics: a reproducible protocol for virome analysis. Sci Rep 2015;5:16532
-
(2015)
Sci Rep
, vol.5
, pp. 16532
-
-
Conceição-Neto, N.1
Zeller, M.2
Lefrère, H.3
-
61
-
-
84986559375
-
Metagenomics and the Human Virome in Asymptomatic Individuals
-
Rascovan N, Duraisamy R, Desnues C. Metagenomics and the Human Virome in Asymptomatic Individuals. Annu Rev Microbiol 2016;70:125-41
-
(2016)
Annu Rev Microbiol
, vol.70
, pp. 125-141
-
-
Rascovan, N.1
Duraisamy, R.2
Desnues, C.3
-
62
-
-
84920644670
-
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
-
Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014;12:87
-
(2014)
BMC Biol
, vol.12
, pp. 87
-
-
Salter, S.J.1
Cox, M.J.2
Turek, E.M.3
-
63
-
-
84884251320
-
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform
-
Kozich JJ, Westcott SL, Baxter NT, et al. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013;79:5112-20
-
(2013)
Appl Environ Microbiol
, vol.79
, pp. 5112-5120
-
-
Kozich, J.J.1
Westcott, S.L.2
Baxter, N.T.3
-
64
-
-
79960852002
-
Addressing challenges in the production and analysis of illumina sequencing data
-
Kircher M, Heyn P, Kelso J. Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 2011;12:382
-
(2011)
BMC Genomics
, vol.12
, pp. 382
-
-
Kircher, M.1
Heyn, P.2
Kelso, J.3
-
65
-
-
84897111313
-
Prevention, diagnosis and treatment of high-throughput sequencing data pathologies
-
Zhou X, Rokas A. Prevention, diagnosis and treatment of high-throughput sequencing data pathologies. Mol Ecol 2014;23:1679-700
-
(2014)
Mol Ecol
, vol.23
, pp. 1679-1700
-
-
Zhou, X.1
Rokas, A.2
-
66
-
-
72949107142
-
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
-
Schloss PD, Westcott SL, Ryabin T, et al. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 2009;75:7537-41
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 7537-7541
-
-
Schloss, P.D.1
Westcott, S.L.2
Ryabin, T.3
-
67
-
-
84857596874
-
Using QIIME to analyze 16S rRNA gene sequences from microbial communities
-
Chapter 10, Unit 10.7
-
Kuczynski J, Stombaugh J, Walters WA, et al. Using QIIME to analyze 16S rRNA gene sequences from microbial communities. Curr Protoc Bioinformatics 2011;Chapter 10:Unit 10.7
-
(2011)
Curr Protoc Bioinformatics
-
-
Kuczynski, J.1
Stombaugh, J.2
Walters, W.A.3
-
68
-
-
84897542122
-
CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota
-
White JR, Maddox C, White O, et al. CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota. Microbiome 2013;1:6
-
(2013)
Microbiome
, vol.1
, pp. 6
-
-
White, J.R.1
Maddox, C.2
White, O.3
-
69
-
-
84930000752
-
LotuS: an efficient and user-friendly OTU processing pipeline
-
Hildebrand F, Tadeo R, Voigt AY, et al. LotuS: an efficient and user-friendly OTU processing pipeline. Microbiome 2014;2:30
-
(2014)
Microbiome
, vol.2
, pp. 30
-
-
Hildebrand, F.1
Tadeo, R.2
Voigt, A.Y.3
-
70
-
-
84930225510
-
MICCA: a complete and accurate software for taxonomic profiling of metagenomic data
-
Albanese D, Fontana P, De Filippo C, et al. MICCA: a complete and accurate software for taxonomic profiling of metagenomic data. Sci Rep 2015;5:9743
-
(2015)
Sci Rep
, vol.5
, pp. 9743
-
-
Albanese, D.1
Fontana, P.2
De Filippo, C.3
-
71
-
-
84899090573
-
Kraken: ultrafast metagenomic sequence classification using exact alignments
-
Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014;15:R46
-
(2014)
Genome Biol
, vol.15
-
-
Wood, D.E.1
Salzberg, S.L.2
-
72
-
-
84964994621
-
MetaPhlAn2 for enhanced metagenomic taxonomic profiling
-
Truong DT, Franzosa EA, Tickle TL, et al. MetaPhlAn2 for enhanced metagenomic taxonomic profiling. Nat Methods 2015;12:902-3
-
(2015)
Nat Methods
, vol.12
, pp. 902-903
-
-
Truong, D.T.1
Franzosa, E.A.2
Tickle, T.L.3
-
73
-
-
84929174408
-
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
-
Ounit R, Wanamaker S, Close TJ, et al. CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers. BMC Genomics 2015;16:236
-
(2015)
BMC Genomics
, vol.16
, pp. 236
-
-
Ounit, R.1
Wanamaker, S.2
Close, T.J.3
-
74
-
-
84963963850
-
Fast and sensitive taxonomic classification for metagenomics with Kaiju
-
Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun 2016;7:11257
-
(2016)
Nat Commun
, vol.7
, pp. 11257
-
-
Menzel, P.1
Ng, K.L.2
Krogh, A.3
-
75
-
-
84962263095
-
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
-
Silva GG, Green KT, Dutilh BE, et al. SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. Bioinformatics 2016;32:354-61
-
(2016)
Bioinformatics
, vol.32
, pp. 354-361
-
-
Silva, G.G.1
Green, K.T.2
Dutilh, B.E.3
-
76
-
-
84992223578
-
MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data
-
Ulyantsev VI, Kazakov SV, Dubinkina VB, et al. MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. Bioinformatics 2016;32:2760-7
-
(2016)
Bioinformatics
, vol.32
, pp. 2760-2767
-
-
Ulyantsev, V.I.1
Kazakov, S.V.2
Dubinkina, V.B.3
-
77
-
-
84946412300
-
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
-
Peabody MA, Van Rossum T, Lo R, et al. Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities. BMC Bioinformatics 2015;16:363
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 363
-
-
Peabody, M.A.1
Van Rossum, T.2
Lo, R.3
-
78
-
-
84934989481
-
Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities
-
Majaneva M, Hyytiäinen K, Varvio SL, et al. Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities. PLoS One 2015;10:e0130035
-
(2015)
PLoS One
, vol.10
-
-
Majaneva, M.1
Hyytiäinen, K.2
Varvio, S.L.3
-
79
-
-
84954556725
-
An evaluation of the accuracy and speed of metagenome analysis tools
-
Lindgreen S, Adair KL, Gardner PP. An evaluation of the accuracy and speed of metagenome analysis tools. Sci Rep 2016;6:19233
-
(2016)
Sci Rep
, vol.6
, pp. 19233
-
-
Lindgreen, S.1
Adair, K.L.2
Gardner, P.P.3
-
80
-
-
85005983418
-
Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data
-
Richardson RT, Bengtsson-Palme J, Johnson RM. Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data. Mol Ecol Resour 2017;17:760-9
-
(2017)
Mol Ecol Resour
, vol.17
, pp. 760-769
-
-
Richardson, R.T.1
Bengtsson-Palme, J.2
Johnson, R.M.3
-
81
-
-
84901363655
-
Waste not, want not: why rarefying microbiome data is inadmissible
-
McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol 2014;10:e1003531
-
(2014)
PLoS Comput Biol
, vol.10
-
-
McMurdie, P.J.1
Holmes, S.2
-
82
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. Differential expression analysis for sequence count data. Genome Biol 2010;11:R106
-
(2010)
Genome Biol
, vol.11
-
-
Anders, S.1
Huber, W.2
-
83
-
-
84923930979
-
A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses
-
Shankar J, Szpakowski S, Solis NV, et al. A systematic evaluation of high-dimensional, ensemble-based regression for exploring large model spaces in microbiome analyses. BMC Bioinformatics 2015;16:31
-
(2015)
BMC Bioinformatics
, vol.16
, pp. 31
-
-
Shankar, J.1
Szpakowski, S.2
Solis, N.V.3
-
84
-
-
84950998192
-
Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity
-
He Y, Caporaso JG, Jiang XT, et al. Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity. Microbiome 2015;3:20
-
(2015)
Microbiome
, vol.3
, pp. 20
-
-
He, Y.1
Caporaso, J.G.2
Jiang, X.T.3
-
87
-
-
0041813144
-
ColorBrewer.org: An Online Tool for Selecting Colour Schemes for Maps
-
Harrower M, Brewer CA. ColorBrewer.org: An Online Tool for Selecting Colour Schemes for Maps. Cartogr J 2003;40:27-37
-
(2003)
Cartogr J
, vol.40
, pp. 27-37
-
-
Harrower, M.1
Brewer, C.A.2
-
88
-
-
84940644968
-
A Mathematical Theory of Communication
-
Shannon CE. A Mathematical Theory of Communication. Bell System Technical Journal 1948;27:379-423
-
(1948)
Bell System Technical Journal
, vol.27
, pp. 379-423
-
-
Shannon, C.E.1
-
89
-
-
33344464667
-
Measurement of Diversity
-
Simpson EH. Measurement of Diversity. Nature 1949;163:688
-
(1949)
Nature
, vol.163
, pp. 688
-
-
Simpson, E.H.1
-
90
-
-
0000245743
-
Statistical Modeling: The Two Cultures (with comments and a rejoinder by the author)
-
Breiman L. Statistical Modeling: The Two Cultures (with comments and a rejoinder by the author). Stat Sci 2001;16:199-231
-
(2001)
Stat Sci
, vol.16
, pp. 199-231
-
-
Breiman, L.1
-
91
-
-
0031526204
-
Approaches for Bayesian variable selection
-
George EI, McCulloch RE. Approaches for Bayesian variable selection. Statistica Sinica 1997;7:339-73
-
(1997)
Statistica Sinica
, vol.7
, pp. 339-373
-
-
George, E.I.1
McCulloch, R.E.2
-
92
-
-
0035478854
-
Random Forests
-
Breiman L. Random Forests. Mach Learn 2001;45:5-32
-
(2001)
Mach Learn
, vol.45
, pp. 5-32
-
-
Breiman, L.1
-
93
-
-
16244401458
-
Regularization and variable selection via the elastic net
-
Zou H, Hastie T. Regularization and variable selection via the elastic net. J R Stat Soc Series B Stat Methodol 2005;67:301-20
-
(2005)
J R Stat Soc Series B Stat Methodol
, vol.67
, pp. 301-320
-
-
Zou, H.1
Hastie, T.2
|