TY - JOUR AU - Parsonnet, J. AU - Friedman, G. D. AU - Vandersteen, D. P. AU - Chang, Y. AU - Vogelman, J. H. AU - Orentreich, N. PY - 1991 DA - 1991// TI - Helicobacter pylori infection and the risk of gastric carcinoma JO - N Engl J Med VL - 325 UR - https://doi.org/10.1056/NEJM199110173251603 DO - 10.1056/NEJM199110173251603 ID - Parsonnet1991 ER - TY - JOUR AU - Castellarin, M. AU - Warren, R. L. AU - Freeman, J. D. AU - Dreolini, L. AU - Krzywinski, M. AU - Strauss, J. PY - 2012 DA - 2012// TI - Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.126516.111 DO - 10.1101/gr.126516.111 ID - Castellarin2012 ER - TY - JOUR AU - Kostic, A. D. AU - Gevers, D. AU - Pedamallu, C. S. AU - Michaud, M. AU - Duke, F. AU - Earl, A. M. PY - 2012 DA - 2012// TI - Genomic analysis identifies association of Fusobacterium with colorectal carcinoma JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.126573.111 DO - 10.1101/gr.126573.111 ID - Kostic2012 ER - TY - JOUR AU - Rubinstein, M. R. AU - Wang, X. AU - Liu, W. AU - Hao, Y. AU - Cai, G. AU - Han, Y. W. PY - 2013 DA - 2013// TI - Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-Cadherin/??-Catenin signaling via its FadA adhesin JO - Cell Host Microbe VL - 14 UR - https://doi.org/10.1016/j.chom.2013.07.012 DO - 10.1016/j.chom.2013.07.012 ID - Rubinstein2013 ER - TY - JOUR AU - Kostic, A. D. AU - Chun, E. AU - Robertson, L. AU - Glickman, J. N. AU - Gallini, C. A. AU - Michaud, M. PY - 2013 DA - 2013// TI - Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment JO - Cell Host Microbe VL - 14 UR - https://doi.org/10.1016/j.chom.2013.07.007 DO - 10.1016/j.chom.2013.07.007 ID - Kostic2013 ER - TY - JOUR AU - Consortium, T. H. M. P. PY - 2013 DA - 2013// TI - Structure, function and diversity of the healthy human microbiome JO - Nature VL - 486 ID - Consortium2013 ER - TY - JOUR AU - Fujimura, K. E. AU - Slusher, N. A. AU - Cabana, M. D. AU - Lynch, S. V. PY - 2010 DA - 2010// TI - Role of the gut microbiota in defining human health JO - Expert Rev Anti Infect Ther VL - 8 UR - https://doi.org/10.1586/eri.10.14 DO - 10.1586/eri.10.14 ID - Fujimura2010 ER - TY - JOUR AU - Ma, B. AU - Forney, L. J. AU - Ravel, J. PY - 2012 DA - 2012// TI - Vaginal microbiome: rethinking health and disease JO - Annu Rev Microbiol VL - 66 UR - https://doi.org/10.1146/annurev-micro-092611-150157 DO - 10.1146/annurev-micro-092611-150157 ID - Ma2012 ER - TY - JOUR AU - Peterson, S. N. AU - Snesrud, E. AU - Liu, J. AU - Ong, A. C. AU - Kilian, M. AU - Schork, N. J. AU - Bretz, W. PY - 2013 DA - 2013// TI - The dental plaque microbiome in health and disease JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0058487 DO - 10.1371/journal.pone.0058487 ID - Peterson2013 ER - TY - JOUR AU - Struzycka, I. PY - 2014 DA - 2014// TI - The oral microbiome in dental caries JO - Pol J Microbiol VL - 63 ID - Struzycka2014 ER - TY - JOUR AU - Chaturvedi, A. K. AU - Anderson, W. F. AU - Lortet-Tieulent, J. AU - Paula Curado, M. AU - Ferlay, J. AU - Franceschi, S. PY - 2013 DA - 2013// TI - Worldwide trends in incidence rates for oral cavity and oropharyngeal cancers JO - J Clin Oncol VL - 31 UR - https://doi.org/10.1200/JCO.2013.50.3870 DO - 10.1200/JCO.2013.50.3870 ID - Chaturvedi2013 ER - TY - JOUR AU - Jemal, A. AU - Bray, F. AU - Center, M. M. AU - Ferlay, J. AU - Ward, E. AU - Forman, D. PY - 2011 DA - 2011// TI - Global cancer statistics JO - CA Cancer J Clin VL - 61 UR - https://doi.org/10.3322/caac.20107 DO - 10.3322/caac.20107 ID - Jemal2011 ER - TY - JOUR AU - Sturgis, E. M. AU - Wei, Q. AU - Spitz, M. R. PY - 2004 DA - 2004// TI - Descriptive epidemiology and risk factors for head and neck cancer JO - Semin Oncol VL - 31 UR - https://doi.org/10.1053/j.seminoncol.2004.09.013 DO - 10.1053/j.seminoncol.2004.09.013 ID - Sturgis2004 ER - TY - JOUR AU - Sturgis, E. M. AU - Ang, K. K. PY - 2011 DA - 2011// TI - The epidemic of HPV-associated oropharyngeal cancer is here: is it time to change our treatment paradigms? JO - J Natl Compr Canc Netw VL - 9 ID - Sturgis2011 ER - TY - JOUR AU - Wu, J. AU - Peters, B. A. AU - Dominianni, C. AU - Zhang, Y. AU - Pei, Z. AU - Yang, L. PY - 2016 DA - 2016// TI - Cigarette smoking and the oral microbiome in a large study of American adults JO - ISME J VL - 10 UR - https://doi.org/10.1038/ismej.2016.37 DO - 10.1038/ismej.2016.37 ID - Wu2016 ER - TY - JOUR AU - Leclercq, S. AU - Matamoros, S. AU - Cani, P. D. AU - Neyrinck, A. M. AU - Jamar, F. AU - Stärkel, P. PY - 2014 DA - 2014// TI - Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1415174111 DO - 10.1073/pnas.1415174111 ID - Leclercq2014 ER - TY - JOUR AU - Bebek, G. AU - Bennett, K. L. AU - Funchain, P. AU - Campbell, R. AU - Seth, R. AU - Scharpf, J. PY - 2012 DA - 2012// TI - Microbiomic subprofiles and MDR1 promoter methylation in head and neck squamous cell carcinoma JO - Hum Mol Genet VL - 21 UR - https://doi.org/10.1093/hmg/ddr593 DO - 10.1093/hmg/ddr593 ID - Bebek2012 ER - TY - JOUR AU - Schmidt, B. L. AU - Kuczynski, J. AU - Bhattacharya, A. AU - Huey, B. AU - Corby, P. M. AU - Queiroz, E. L. S. PY - 2014 DA - 2014// TI - Changes in abundance of oral microbiota associated with oral cancer JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0098741 DO - 10.1371/journal.pone.0098741 ID - Schmidt2014 ER - TY - JOUR AU - Gong, H. AU - Shi, Y. AU - Zhou, X. AU - Wu, C. AU - Cao, P. AU - Xu, C. PY - 2014 DA - 2014// TI - Microbiota in the throat and risk factors for laryngeal carcinoma JO - Appl Environ Microbiol VL - 80 UR - https://doi.org/10.1128/AEM.02329-14 DO - 10.1128/AEM.02329-14 ID - Gong2014 ER - TY - JOUR AU - Hooper, S. J. AU - Crean, S. J. AU - Fardy, M. J. AU - Lewis, M. A. AU - Spratt, D. A. AU - Wade, W. G. PY - 2007 DA - 2007// TI - A molecular analysis of the bacteria present within oral squamous cell carcinoma JO - J Med Microbiol VL - 56 UR - https://doi.org/10.1099/jmm.0.46918-0 DO - 10.1099/jmm.0.46918-0 ID - Hooper2007 ER - TY - JOUR AU - Hooper, S. J. AU - Crean, S. J. AU - Lewis, M. A. O. AU - Spratt, D. A. AU - Wade, W. G. AU - Wilson, M. J. PY - 2006 DA - 2006// TI - Viable bacteria present within oral squamous cell carcinoma tissue JO - J Clin Microbiol VL - 44 UR - https://doi.org/10.1128/JCM.44.5.1719-1725.2006 DO - 10.1128/JCM.44.5.1719-1725.2006 ID - Hooper2006 ER - TY - JOUR AU - Gong, H. -. L. AU - Shi, Y. AU - Zhou, L. AU - Wu, C. -. P. AU - Cao, P. -. Y. AU - Tao, L. PY - 2013 DA - 2013// TI - The composition of microbiome in larynx and the throat biodiversity between laryngeal squamous cell carcinoma patients and control population JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0066476 DO - 10.1371/journal.pone.0066476 ID - Gong2013 ER - TY - JOUR AU - Edge, S. B. AU - Compton, C. C. PY - 2010 DA - 2010// TI - The American Joint Committee on Cancer: the 7th edition of the AJCC cancer staging manual and the future of TNM JO - Ann Surg Oncol VL - 17 UR - https://doi.org/10.1245/s10434-010-0985-4 DO - 10.1245/s10434-010-0985-4 ID - Edge2010 ER - TY - JOUR AU - Dauphin, L. A. AU - Stephens, K. W. AU - Eufinger, S. C. AU - Bowen, M. D. PY - 2010 DA - 2010// TI - Comparison of five commercial DNA extraction kits for the recovery of Yersinia pestis DNA from bacterial suspensions and spiked environmental samples JO - J Appl Microbiol VL - 108 UR - https://doi.org/10.1111/j.1365-2672.2009.04404.x DO - 10.1111/j.1365-2672.2009.04404.x ID - Dauphin2010 ER - TY - JOUR AU - Tamariz, J. AU - Voynarovska, K. AU - Prinz, M. AU - Caragine, T. PY - 2006 DA - 2006// TI - The application of ultraviolet irradiation to exogenous sources of DNA in plasticware and water for the amplification of low copy number DNA JO - J Forensic Sci VL - 51 UR - https://doi.org/10.1111/j.1556-4029.2006.00172.x DO - 10.1111/j.1556-4029.2006.00172.x ID - Tamariz2006 ER - TY - JOUR AU - Rideout, J. R. AU - He, Y. AU - Navas-Molina, J. A. AU - Walters, W. A. AU - Ursell, L. K. AU - Gibbons, S. M. PY - 2014 DA - 2014// TI - Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences JO - PeerJ VL - 2 UR - https://doi.org/10.7717/peerj.545 DO - 10.7717/peerj.545 ID - Rideout2014 ER - TY - JOUR AU - DeSantis, T. Z. AU - Hugenholtz, P. AU - Larsen, N. AU - Rojas, M. AU - Brodie, E. L. AU - Keller, K. PY - 2006 DA - 2006// TI - Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB JO - Appl Environ Microbiol VL - 72 UR - https://doi.org/10.1128/AEM.03006-05 DO - 10.1128/AEM.03006-05 ID - DeSantis2006 ER - TY - JOUR AU - McDonald, D. AU - Price, M. N. AU - Goodrich, J. AU - Nawrocki, E. P. AU - DeSantis, T. Z. AU - Probst, A. PY - 2012 DA - 2012// TI - An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2011.139 DO - 10.1038/ismej.2011.139 ID - McDonald2012 ER - TY - JOUR AU - Edgar, R. C. PY - 2010 DA - 2010// TI - Search and clustering orders of magnitude faster than BLAST JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq461 DO - 10.1093/bioinformatics/btq461 ID - Edgar2010 ER - TY - JOUR AU - Caporaso, J. G. AU - Bittinger, K. AU - Bushman, F. D. AU - DeSantis, T. Z. AU - Andersen, G. L. AU - Knight, R. PY - 2010 DA - 2010// TI - PyNAST: a flexible tool for aligning sequences to a template alignment JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp636 DO - 10.1093/bioinformatics/btp636 ID - Caporaso2010 ER - TY - JOUR AU - Price, M. N. AU - Dehal, P. S. AU - Arkin, A. P. PY - 2010 DA - 2010// TI - FastTree 2--approximately maximum-likelihood trees for large alignments JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0009490 DO - 10.1371/journal.pone.0009490 ID - Price2010 ER - TY - JOUR AU - Hill, T. C. J. AU - Walsh, K. A. AU - Harris, J. A. AU - Moffett, B. F. PY - 2003 DA - 2003// TI - Using ecological diversity measures with bacterial communities JO - FEMS Microbiol Ecol VL - 43 UR - https://doi.org/10.1111/j.1574-6941.2003.tb01040.x DO - 10.1111/j.1574-6941.2003.tb01040.x ID - Hill2003 ER - TY - JOUR AU - Barker, G. M. PY - 2008 DA - 2008// TI - Phylogenetic diversity: a quantitative framework for measurement of priority and achievement in biodiversity conservation JO - Biol J Linn Soc VL - 76 UR - https://doi.org/10.1111/j.1095-8312.2002.tb02081.x DO - 10.1111/j.1095-8312.2002.tb02081.x ID - Barker2008 ER - TY - JOUR AU - Lozupone, C. AU - Knight, R. PY - 2005 DA - 2005// TI - UniFrac: a new phylogenetic method for comparing microbial communities JO - Appl Environ Microbiol VL - 71 UR - https://doi.org/10.1128/AEM.71.12.8228-8235.2005 DO - 10.1128/AEM.71.12.8228-8235.2005 ID - Lozupone2005 ER - TY - JOUR AU - Lozupone, C. A. AU - Hamady, M. AU - Kelley, S. T. AU - Knight, R. PY - 2007 DA - 2007// TI - Quantitative and qualitative beta diversity measures lead to different insights into factors that structure microbial communities JO - Appl Environ Microbiol VL - 73 UR - https://doi.org/10.1128/AEM.01996-06 DO - 10.1128/AEM.01996-06 ID - Lozupone2007 ER - TY - JOUR AU - Caporaso, J. G. AU - Kuczynski, J. AU - Stombaugh, J. AU - Bittinger, K. AU - Bushman, F. D. AU - Costello, E. K. PY - 2010 DA - 2010// TI - QIIME allows analysis of high-throughput community sequencing data JO - Nat Methods VL - 7 UR - https://doi.org/10.1038/nmeth.f.303 DO - 10.1038/nmeth.f.303 ID - Caporaso2010 ER - TY - JOUR AU - Anderson, M. J. PY - 2001 DA - 2001// TI - A new method for non-parametric multivariate analysis of variance JO - Austral Ecol VL - 26 ID - Anderson2001 ER - TY - STD TI - Sarkar D. SpringerLink (Online service). Lattice multivariate data visualization with R. Use R! J Stat Software. 2008;25(ii):1-265. http://dsarkar.fhcrc.org/lattice/. UR - http://dsarkar.fhcrc.org/lattice/ ID - ref38 ER - TY - JOUR AU - Asnicar, F. AU - Weingart, G. AU - Tickle, T. L. AU - Huttenhower, C. AU - Segata, N. PY - 2015 DA - 2015// TI - Compact graphical representation of phylogenetic data and metadata with GraPhlAn JO - PeerJ VL - 3 UR - https://doi.org/10.7717/peerj.1029 DO - 10.7717/peerj.1029 ID - Asnicar2015 ER - TY - STD TI - Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M, et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol. 2010;Chapter 19:Unit 19.10.1–21 ID - ref40 ER - TY - JOUR AU - Dewhirst, F. E. AU - Chen, T. AU - Izard, J. AU - Paster, B. J. AU - Tanner, A. C. R. AU - Yu, W. H. PY - 2010 DA - 2010// TI - The human oral microbiome JO - J Bacteriol VL - 192 UR - https://doi.org/10.1128/JB.00542-10 DO - 10.1128/JB.00542-10 ID - Dewhirst2010 ER - TY - JOUR AU - Ahn, J. AU - Yang, L. AU - Paster, B. J. AU - Ganly, I. AU - Morris, L. AU - Pei, Z. PY - 2011 DA - 2011// TI - Oral microbiome profiles: 16 s rRNA pyrosequencing and microarray assay comparison JO - PLoS One VL - 6 UR - https://doi.org/10.1371/journal.pone.0022788 DO - 10.1371/journal.pone.0022788 ID - Ahn2011 ER - TY - JOUR AU - Segata, N. AU - Haake, S. K. AU - Mannon, P. AU - Lemon, K. P. AU - Waldron, L. AU - Gevers, D. PY - 2012 DA - 2012// TI - Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-6-r42 DO - 10.1186/gb-2012-13-6-r42 ID - Segata2012 ER - TY - JOUR AU - Bik, E. M. AU - Long, C. D. AU - Armitage, G. C. AU - Loomer, P. AU - Emerson, J. AU - Mongodin, E. F. PY - 2010 DA - 2010// TI - Bacterial diversity in the oral cavity of 10 healthy individuals JO - ISME J VL - 4 UR - https://doi.org/10.1038/ismej.2010.30 DO - 10.1038/ismej.2010.30 ID - Bik2010 ER - TY - JOUR AU - Pushalkar, S. AU - Ji, X. AU - Li, Y. AU - Estilo, C. AU - Yegnanarayana, R. AU - Singh, B. PY - 2012 DA - 2012// TI - Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma JO - BMC Microbiol VL - 12 UR - https://doi.org/10.1186/1471-2180-12-144 DO - 10.1186/1471-2180-12-144 ID - Pushalkar2012 ER - TY - JOUR AU - Takeshita, T. AU - Kageyama, S. AU - Furuta, M. AU - Tsuboi, H. AU - Takeuchi, K. AU - Shibata, Y. PY - 2016 DA - 2016// TI - Bacterial diversity in saliva and oral health-related conditions: the Hisayama Study JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep22164 DO - 10.1038/srep22164 ID - Takeshita2016 ER - TY - JOUR AU - Slaughter, D. P. AU - Southwick, H. W. AU - Smejkal, W. PY - 1953 DA - 1953// TI - Field cancerization in oral stratified squamous epithelium; clinical implications of multicentric origin JO - Cancer VL - 6 UR - https://doi.org/3.0.CO;2-Q DO - 3.0.CO;2-Q ID - Slaughter1953 ER - TY - JOUR AU - Wong, V. K. AU - Turmezei, T. D. PY - 2011 DA - 2011// TI - Actinomycosis JO - Britiish Med J VL - 343 ID - Wong2011 ER - TY - JOUR AU - Hozumi, M. AU - Ogawa, M. AU - Sugimura, T. AU - Takeuchi, T. AU - Umezawa, H. PY - 1972 DA - 1972// TI - Inhibition of tumorigenesis in mouse skin by leupeptin, a protease inhibitor from actinomycetes JO - Cancer Res VL - 32 ID - Hozumi1972 ER - TY - JOUR AU - Schulze, A. AU - Harris, A. L. PY - 2012 DA - 2012// TI - How cancer metabolism is tuned for proliferation and vulnerable to disruption JO - Nature VL - 491 UR - https://doi.org/10.1038/nature11706 DO - 10.1038/nature11706 ID - Schulze2012 ER - TY - JOUR AU - Hamady, M. AU - Knight, R. PY - 2009 DA - 2009// TI - Microbial community profiling for human microbiome projects: Tools, techniques, and challenges JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.085464.108 DO - 10.1101/gr.085464.108 ID - Hamady2009 ER - TY - JOUR AU - Ley, R. E. AU - Lozupone, C. A. AU - Hamady, M. AU - Knight, R. AU - Gordon, J. I. PY - 2008 DA - 2008// TI - Worlds within worlds: evolution of the vertebrate gut microbiota JO - Nat Rev Microbiol VL - 6 UR - https://doi.org/10.1038/nrmicro1978 DO - 10.1038/nrmicro1978 ID - Ley2008 ER - TY - JOUR AU - Ley, R. E. AU - Hamady, M. AU - Lozupone, C. AU - Turnbaugh, P. J. AU - Ramey, R. R. AU - Bircher, J. S. PY - 2008 DA - 2008// TI - Evolution of mammals and their gut microbes JO - Science VL - 320 UR - https://doi.org/10.1126/science.1155725 DO - 10.1126/science.1155725 ID - Ley2008 ER - TY - JOUR AU - McKenna, P. AU - Hoffmann, C. AU - Minkah, N. AU - Aye, P. P. AU - Lackner, A. AU - Liu, Z. PY - 2008 DA - 2008// TI - The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis JO - PLoS Pathog VL - 4 UR - https://doi.org/10.1371/journal.ppat.0040020 DO - 10.1371/journal.ppat.0040020 ID - McKenna2008 ER - TY - JOUR AU - Smith, B. C. AU - McAndrew, T. AU - Chen, Z. AU - Harari, A. AU - Barris, D. M. AU - Viswanathan, S. PY - 2012 DA - 2012// TI - The cervical microbiome over 7 years and a comparison of methodologies for its characterization JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0040425 DO - 10.1371/journal.pone.0040425 ID - Smith2012 ER -