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references.bibtex
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references.bibtex
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title="{The human gut microbiome as a screening tool for colorectal cancer}",
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journal={Cancer Prevention Research},
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pages={1112--1121},
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publisher={AACR}
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@article{siegel2014colorectal,
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journal={CA: a cancer journal for clinicians},
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title="{Vital signs: colorectal cancer screening test use--United States, 2012.}",
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year={2013}
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@article{hsia2000importance,
title="{The importance of health insurance as a determinant of cancer screening: evidence from the Women's Health Initiative}",
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publisher={Elsevier}
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number={5},
pages={508--516},
year={2010},
publisher={Elsevier}
}
@article{zackularMbio,
title="{The gut microbiome modulates colon tumorigenesis}",
author={Zackular, Joseph P and Baxter, Nielson T and Iverson, Kathryn D and Sadler, William D and Petrosino, Joseph F and Chen, Grace Y and Schloss, Patrick D},
journal={MBio},
volume={4},
number={6},
pages={e00692--13},
year={2013},
publisher={Am Soc Microbiol}
}
@article{kostic2012genomic,
title="{Genomic analysis identifies association of Fusobacterium with colorectal carcinoma}",
author={Kostic, Aleksandar D and Gevers, Dirk and Pedamallu, Chandra Sekhar and Michaud, Monia and Duke, Fujiko and Earl, Ashlee M and Ojesina, Akinyemi I and Jung, Joonil and Bass, Adam J and Tabernero, Josep and others},
journal={Genome research},
volume={22},
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pages={292--298},
year={2012},
publisher={Cold Spring Harbor Lab}
}
@article{kostic2013fusobacterium,
title="{Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment}",
author={Kostic, Aleksandar D and Chun, Eunyoung and Robertson, Lauren and Glickman, Jonathan N and Gallini, Carey Ann and Michaud, Monia and Clancy, Thomas E and Chung, Daniel C and Lochhead, Paul and Hold, Georgina L and others},
journal={Cell host \& microbe},
volume={14},
number={2},
pages={207--215},
year={2013},
publisher={Elsevier}
}
@article{wu2009human,
title="{A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses}",
author={Wu, Shaoguang and Rhee, Ki-Jong and Albesiano, Emilia and Rabizadeh, Shervin and Wu, Xinqun and Yen, Hung-Rong and Huso, David L and Brancati, Frederick L and Wick, Elizabeth and McAllister, Florencia and others},
journal={Nature medicine},
volume={15},
number={9},
pages={1016--1022},
year={2009},
publisher={Nature Publishing Group}
}
@article{arthur2012intestinal,
title="{Intestinal inflammation targets cancer-inducing activity of the microbiota}",
author={Arthur, Janelle C and Perez-Chanona, Ernesto and M{\"u}hlbauer, Marcus and Tomkovich, Sarah and Uronis, Joshua M and Fan, Ting-Jia and Campbell, Barry J and Abujamel, Turki and Dogan, Belgin and Rogers, Arlin B and others},
journal={science},
volume={338},
number={6103},
pages={120--123},
year={2012},
publisher={American Association for the Advancement of Science}
}
@article{wang2012structural,
title="{Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers}",
author={Wang, Tingting and Cai, Guoxiang and Qiu, Yunping and Fei, Na and Zhang, Menghui and Pang, Xiaoyan and Jia, Wei and Cai, Sanjun and Zhao, Liping},
journal={The ISME journal},
volume={6},
number={2},
pages={320--329},
year={2012},
publisher={Nature Publishing Group}
}
@article{chen2013decreased,
title="{Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma}",
author={Chen, Hui-Min and Yu, Ya-Nan and Wang, Ji-Lin and Lin, Yan-Wei and Kong, Xuan and Yang, Chang-Qing and Yang, Li and Liu, Zhan-Ju and Yuan, Yao-Zong and Liu, Fei and others},
journal={The American journal of clinical nutrition},
volume={97},
number={5},
pages={1044--1052},
year={2013},
publisher={Am Soc Nutrition}
}
@article{chen2012human,
title="{Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer}",
author={Chen, Weiguang and Liu, Fanlong and Ling, Zongxin and Tong, Xiaojuan and Xiang, Charlie},
journal={PloS one},
volume={7},
number={6},
pages={e39743},
year={2012}
}
@article{shen2010molecular,
title="{Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas}",
author={Shen, Xiang Jun and Rawls, John F and Randall, Thomas A and Burcall, Lauren and Mpande, Caroline and Jenkins, Natascha and Jovov, Biljana and Abdo, Zaid and Sandler, Robert S and Keku, Temitope O},
journal={Gut microbes},
volume={1},
number={3},
pages={138--147},
year={2010},
publisher={Taylor \& Francis}
}
@article{miseq,
title="{Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform}",
author={Kozich, James J and Westcott, Sarah L and Baxter, Nielson T and Highlander, Sarah K and Schloss, Patrick D},
journal={Applied and environmental microbiology},
volume={79},
number={17},
pages={5112--5120},
year={2013},
publisher={Am Soc Microbiol}
}
@article{mothur,
title="{Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities}",
author={Schloss, Patrick D and Westcott, Sarah L and Ryabin, Thomas and Hall, Justine R and Hartmann, Martin and Hollister, Emily B and Lesniewski, Ryan A and Oakley, Brian B and Parks, Donovan H and Robinson, Courtney J and others},
journal={Applied and environmental microbiology},
volume={75},
number={23},
pages={7537--7541},
year={2009},
publisher={Am Soc Microbiol}
}
@article{heitman2009prevalence,
title="{Prevalence of adenomas and colorectal cancer in average risk individuals: a systematic review and meta-analysis}",
author={Heitman, Steven J and Ronksley, Paul E and Hilsden, Robert J and Manns, Braden J and Rostom, Alaa and Hemmelgarn, Brenda R},
journal={Clinical Gastroenterology and Hepatology},
volume={7},
number={12},
pages={1272--1278},
year={2009},
publisher={Elsevier}
}
@article{hundt2009comparative,
title="{Comparative evaluation of immunochemical fecal occult blood tests for colorectal adenoma detection}",
author={Hundt, Sabrina and Haug, Ulrike and Brenner, Hermann},
journal={Annals of Internal Medicine},
volume={150},
number={3},
pages={162--169},
year={2009},
publisher={Am Coll Physicians}
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@article{calle2011auc,
title="{AUC-RF: A new strategy for genomic profiling with random forest}",
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number={2},
pages={121--132},
year={2011},
publisher={Karger Publishers}
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title="{Classification and regression by randomForest}",
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year={2002}
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@article{delong1988comparing,
title="{Comparing the areas under two or more correlated receiver operating characteristic curves: a nonparametric approach}",
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publisher={JSTOR}
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@article{robin2011proc,
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author={Robin, Xavier and Turck, Natacha and Hainard, Alexandre and Tiberti, Natalia and Lisacek, Fr{\'e}d{\'e}rique and Sanchez, Jean-Charles and M{\"u}ller, Markus},
journal={BMC bioinformatics},
volume={12},
number={1},
pages={1},
year={2011},
publisher={BioMed Central}
}
@article{pepe2009estimation,
title="{Estimation and comparison of receiver operating characteristic curves}",
author={Pepe, Margaret and Longton, Gary and Janes, Holly},
journal={The Stata Journal},
volume={9},
number={1},
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year={2009},
publisher={NIH Public Access}
}
@article{youden1950index,
title="{Index for rating diagnostic tests}",
author={Youden, William J},
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publisher={Wiley Online Library}
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@article{mira2014microbial,
title="{Microbial mucosal colonic shifts associated with the development of colorectal cancer reveal the presence of different bacterial and archaeal biomarkers}",
author={Mira-Pascual, L and Cabrera-Rubio, R and Ocon, S and Costales, P and Parra, A and Suarez, A and Moris, F and Rodrigo, L and Mira, A and Collado, MC},
journal={Journal of gastroenterology},
volume={50},
number={2},
pages={167--179},
year={2014},
publisher={Springer}
}
@article{imperiale2014multitarget,
title="{Multitarget stool DNA testing for colorectal-cancer screening}",
author={Imperiale, Thomas F and Ransohoff, David F and Itzkowitz, Steven H and Levin, Theodore R and Lavin, Philip and Lidgard, Graham P and Ahlquist, David A and Berger, Barry M},
journal={New England Journal of Medicine},
volume={370},
number={14},
pages={1287--1297},
year={2014},
publisher={Mass Medical Soc}
}
@article{levi2009sensitivity,
title="{Sensitivity, but not specificity, of a quantitative immunochemical fecal occult blood test for neoplasia is slightly increased by the use of low-dose aspirin, NSAIDs, and anticoagulants}",
author={Levi, Zohar and Rozen, Paul and Hazazi, Rachel and Vilkin, Alex and Waked, Amal and Maoz, Eran and Birkenfeld, Shlomo and Lieberman, Nicky and Klang, Shmuel and Niv, Yaron},
journal={The American journal of gastroenterology},
volume={104},
number={4},
pages={933--938},
year={2009},
publisher={Nature Publishing Group}
}
@article{kapidzic2015gender,
title="{Gender differences in fecal immunochemical test performance for early detection of colorectal neoplasia}",
author={Kapidzic, Atija and van der Meulen, Miriam P and Hol, Lieke and van Roon, Aafke HC and Looman, Caspar WN and Lansdorp-Vogelaar, Iris and van Ballegooijen, Marjolein and van Vuuren, Anneke J and Reijerink, Jacqueline CIY and van Leerdam, Monique E and others},
journal={Clinical Gastroenterology and Hepatology},
volume={13},
number={8},
pages={1464--1471},
year={2015},
publisher={Elsevier}
}
@article{symonds2015factors,
title="{Factors affecting faecal immunochemical test positive rates: demographic, pathological, behavioural and environmental variables}",
author={Symonds, Erin L and Osborne, Joanne M and Cole, Stephen R and Bampton, Peter A and Fraser, Robert JL and Young, Graeme P},
journal={Journal of medical screening},
volume={22},
number={4},
pages={187--193},
year={2015},
publisher={SAGE Publications}
}
@article{ding2014dynamics,
title="{Dynamics and associations of microbial community types across the human body}",
author={Ding, Tao and Schloss, Patrick D},
journal={Nature},
volume={509},
number={7500},
pages={357--360},
year={2014},
publisher={Nature Publishing Group}
}
@article{pryde2002microbiology,
title="{The microbiology of butyrate formation in the human colon}",
author={Pryde, Susan E and Duncan, Sylvia H and Hold, Georgina L and Stewart, Colin S and Flint, Harry J},
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number={2},
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year={2002},
publisher={The Oxford University Press}
}
@article{zeller2014potential,
title="{Potential of fecal microbiota for early-stage detection of colorectal cancer}",
author={Zeller, Georg and Tap, Julien and Voigt, Anita Y and Sunagawa, Shinichi and Kultima, Jens Roat and Costea, Paul I and Amiot, Aur{\'e}lien and B{\"o}hm, J{\"u}rgen and Brunetti, Francesco and Habermann, Nina and others},
journal={Molecular systems biology},
volume={10},
number={11},
pages={766},
year={2014},
publisher={EMBO Press}
}
@article{warren2013co,
title="{Co-occurrence of anaerobic bacteria in colorectal carcinomas}",
author={Warren, Ren{\'e} L and Freeman, Douglas J and Pleasance, Stephen and Watson, Peter and Moore, Richard A and Cochrane, Kyla and Allen-Vercoe, Emma and Holt, Robert A},
journal={Microbiome},
volume={1},
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pages={16},
year={2013},
publisher={BioMed Central Ltd}
}
@article{schubert2015antibiotic,
title="{Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile}",
author={Schubert, Alyxandria M and Sinani, Hamide and Schloss, Patrick D},
journal={MBio},
volume={6},
number={4},
pages={e00974--15},
year={2015},
publisher={Am Soc Microbiol}
}
@article{rex2009american,
title="{American College of Gastroenterology guidelines for colorectal cancer screening 2008}",
author={Rex, Douglas K and Johnson, David A and Anderson, Joseph C and Schoenfeld, Phillip S and Burke, Carol A and Inadomi, John M},
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year={2009},
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doi={10.1371/journal.pone.0062815},
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publisher={Public Library of Science ({PLoS})},
volume={8},
number={5},
pages={e62815},
title="{Impact of Colonoscopy Bowel Preparation on Intestinal Microbiota}",
author={Claire L. O'Brien and Gwen E. Allison and Florian Grimpen and Paul Pavli},
journal={{PLoS} {ONE}}
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title={Periodontal pathogens Porphyromonas gingivalis and Fusobacterium nucleatum promote tumor progression in an oral-specific chemical carcinogenesis model.},
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publisher={BMJ Publishing Group Ltd and British Society of Gastroenterology}
}
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@article{ding2014dynamics,
title={Dynamics and associations of microbial community types across the human body},
author={Ding, Tao and Schloss, Patrick D},
journal={Nature},
volume={509},
number={7500},
pages={357--360},
year={2014},
publisher={Nature Publishing Group}
}
@article{feng2015gut,
title={Gut microbiome development along the colorectal adenoma--carcinoma sequence},
author={Feng, Qiang and Liang, Suisha and Jia, Huijue and Stadlmayr, Andreas and Tang, Longqing and Lan, Zhou and Zhang, Dongya and Xia, Huihua and Xu, Xiaoying and Jie, Zhuye and others},
journal={Nature communications},
volume={6},
year={2015},
publisher={Nature Publishing Group}
}