A Bayesian framework for identifying consistent patterns of microbial abundance between body sites
Tóm tắt
Từ khóa
Tài liệu tham khảo
Callahan, B. J., P. J. McMurdie and S. P. Holmes (2017): “Exact sequence variants should replace operational taxonomic units in marker-gene data analysis,” ISME J., 11, 2639–2643.10.1038/ismej.2017.11928731476
Chai, H., H. Jiang, L. Lin and L. Liu (2018): “A marginalized two-part beta regression model for microbiome compositional data,” PLoS Comput. Biol., 14, e1006329.30036363
Chen, E. Z. and H. Li (2016): “A two-part mixed-effects model for analyzing longitudinal microbiome compositional data,” Bioinformatics, 32, 2611–2617.2718720010.1093/bioinformatics/btw308
Chen, C., C. Hemme, J. Beleno, Z. J. Shi, D. Ning, Y. Qin, Q. Tu, M. Jorgensen, Z. He, L. Wu and J. Zhou (2018): “Oral microbiota of periodontal health and disease and their changes after nonsurgical periodontal therapy,” ISME J., 12, 1210–1224.10.1038/s41396-017-0037-129339824
Chiranjeevi, T., O. H. Prasad, U. Prasad, A. K. Kumar, V. Chakravarthi, P. B. Rao, P. Sarma, N. Reddy and M. Bhaskar (2014): “Identification of microbial pathogens in periodontal disease and diabetic patients of south indian population,” Bioinformation, 10, 241–244.2496652810.6026/97320630010241
Chung, M., N. Zhao, R. Meier, D. C. Koestler, G. Wu, E. D. Castillo, B. J. Paster, K. T. Kelsey and D. S. Michaud (2019): “Oral, gut, and pancreatic microbiome are correlated and exhibit consist co-abundance in patients with pancreatic diseases and cancer,” [Manuscript in Progress].
Cohen, J. (1960): “A coefficient of agreement for nominal scales,” Educ. Psychol. Meas., 20, 37–46.10.1177/001316446002000104
del Castillo, E., R. Meier, M. Chung, D. C. Koestler, T. Chen, B. J. Paster, K. P. Charpentier, K. T. Kelsey, J. Izard and D. S. Michaud (2019): “The microbiomes of pancreatic and duodenum tissue overlap and are highly subject specific but differ between pancreatic cancer and noncancer subjects,” Cancer Epidemiol. Biomark. Prev., 28, 370–383.10.1158/1055-9965.EPI-18-0542
Faith, J. J., J. L. Guruge, M. Charbonneau, S. Subramanian, H. Seedorf, A. L. Goodman, J. C. Clemente, R. Knight, A. C. Heath, R. L. Leibel, M. Rosenbaum and J. I. Gordon (2013): “The long-term stability of the human gut microbiota,” Science, 341, 1237439.2382894110.1126/science.1237439
Fan, X., A. V. Alekseyenko, J. Wu, B. A. Peters, E. J. Jacobs, S. M. Gapstur, M. P. Purdue, C. C. Abnet, R. Stolzenberg-Solomon, G. Miller, J. Ravel, R. B. Hayes and J. Ahn (2016): “Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study,” Gut, 67, 120–127.27742762
Fardini, Y., X. Wang, S. Témoin, S. Nithianantham, D. Lee, M. Shoham and Y. W. Han (2011): “Fusobacterium nucleatum adhesin FadA binds vascular endothelial cadherin and alters endothelial integrity,” Mol. Microbiol., 82, 1468–1480.10.1111/j.1365-2958.2011.07905.x22040113
Fleiss, J. L. (1971): “Measuring nominal scale agreement among many raters,” Psychol. Bull., 76, 378–382.10.1037/h0031619
Gloor, G. B., J. M. Macklaim, V. Pawlowsky-Glahn and J. J. Egozcue (2017): “Microbiome datasets are compositional: and this is not optional,” Front. Microbiol., 8, 2224.10.3389/fmicb.2017.0222429187837
Goodman, B. and H. Gardner (2018): “The microbiome and cancer,” J. Pathol., 244, 667–676.2937713010.1002/path.5047
Lu, H., Z. Ren, A. Li, J. Li, S. Xu, H. Zhang, J. Jiang, J. Yang, Q. Luo, K. Zhou, S. Zheng and L. Li (2019): “Tongue coating microbiome data distinguish patients with pancreatic head cancer from healthy controls,” J. Oral Microbiol., 11, 1563409.3072891510.1080/20002297.2018.1563409
Meier, R. (2019): “R scripts for simulation studies, analyses and examples related to pasta,” https://github.com/richard-meier/PASTA_scripts. [Online; accessed 08-April-2019].
Michaud, D. S., J. Izard, C. S. Wilhelm-Benartzi, D.-H. You, V. A. Grote, A. Tjønneland, C. C. Dahm, K. Overvad, M. Jenab, V. Fedirko, M. C. Boutron-Ruault, F. Clavel-Chapelon, A. Racine, R. Kaaks, H. Boeing, J. Foerster, A. Trichopoulou, P. Lagiou, D. Trichopoulos, C. Sacerdote, S. Sieri, D. Palli, R. Tumino, S. Panico, P. D. Siersema, P. H. Peeters, E. Lund, A. Barricarte, J.-M. Huerta, E. Molina-Montes, M. Dorronsoro, J. R. Quirós, E. J. Duell, W. Ye, M. Sund, B. Lindkvist, D. Johansen, K.-T. Khaw, N. Wareham, R. C. Travis, P. Vineis, H. B. B. de Mesquita and E. Riboli (2012): “Plasma antibodies to oral bacteria and risk of pancreatic cancer in a large european prospective cohort study,” Gut, 62, 1764–1770.
Peng, X., G. Li and Z. Liu (2016): “Zero-inflated beta regression for differential abundance analysis with metagenomics data,” J. Comput. Biol., 23, 102–110.10.1089/cmb.2015.015726675626
Pushalkar, S., M. Hundeyin, D. Daley, C. P. Zambirinis, E. Kurz, A. Mishra, N. Mohan, B. Aykut, M. Usyk, L. E. Torres, G. Werba, K. Zhang, Y. Guo, Q. Li, N. Akkad, S. Lall, B. Wadowski, J. Gutierrez, J. A. K. Rossi, J. W. Herzog, B. Diskin, A. Torres-Hernandez, J. Leinwand, W. Wang, P. S. Taunk, S. Savadkar, M. Janal, A. Saxena, X. Li, D. Cohen, R. B. Sartor, D. Saxena and G. Miller (2018): “The pancreatic cancer microbiome promotes oncogenesis by induction of innate and adaptive immune suppression,” Cancer Discov., 8, 403–416.10.1158/2159-8290.CD-17-113429567829
Schober, P., C. Boer and L. A. Schwarte (2018): “Correlation coefficients,” Anesth. Analg., 126, 1763–1768.10.1213/ANE.000000000000286429481436
Shi, P., A. Zhang and H. Li (2016): “Regression analysis for microbiome compositional data,” Ann. Appl. Stat., 10, 1019–1040.10.1214/16-AOAS928
Tsilimigras, M. C. and A. A. Fodor (2016): “Compositional data analysis of the microbiome: fundamentals, tools, and challenges,” Ann. Epidemiol., 26, 330–335.2725573810.1016/j.annepidem.2016.03.002
Xia, Y., J. Sun and D.-G. Chen (2018): “Modeling zero-inflated microbiome data.” In: Jiahuan Chen, (ed.), Statistical Analysis of Microbiome Data with R. Springer, Singapore. pp. 453–496.