메뉴 건너뛰기




Volumn 5, Issue 12, 2017, Pages

Insights into study design and statistical analyses in translational microbiome studies

Author keywords

Microbiome; Statistical analysis; Statistical models; Study design; Translational research

Indexed keywords

HIGH THROUGHPUT SEQUENCING; INFORMATION PROCESSING; MICROBIOME; NONHUMAN; PHENOTYPE; SIMULATION; STATISTICAL ANALYSIS; STUDY DESIGN; TRANSLATIONAL RESEARCH; WHOLE GENOME SEQUENCING;

EID: 85021833670     PISSN: 23055839     EISSN: 23055847     Source Type: Journal    
DOI: 10.21037/atm.2017.01.13     Document Type: Review
Times cited : (18)

References (95)
  • 1
    • 70449713952 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 8
    • 85027930713 scopus 로고    scopus 로고
    • The microbiome-systemic diseases connection
    • van der Meulen TA, Harmsen H, Bootsma H, et al. The microbiome-systemic diseases connection. Oral Dis 2016;22:719-34
    • (2016) Oral Dis , vol.22 , pp. 719-734
    • van der Meulen, T.A.1    Harmsen, H.2    Bootsma, H.3
  • 9
    • 84907557973 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 51
    • 84918522966 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • Measurement of Diversity
    • Simpson EH. Measurement of Diversity. Nature 1949;163:688
    • (1949) Nature , vol.163 , pp. 688
    • Simpson, E.H.1
  • 90
    • 0000245743 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.