@Manual{SE,
  title = {SummarizedExperiment: SummarizedExperiment container},
  author = {Martin Morgan and Valerie Obenchain and Jim Hester and Hervé Pagès},
  year = {2021},
  note = {R package version 1.23.3},
  url = {https://bioconductor.org/packages/SummarizedExperiment},
}

@Article{treeio,
  title = {treeio: an R package for phylogenetic tree input and output with richly annotated and associated data.},
  author = {Li-Gen Wang and Tommy Tsan-Yuk Lam and Shuangbin Xu and Zehan Dai and Lang Zhou and Tingze Feng and Pingfan Guo and Casey W. Dunn and Bradley R. Jones and Tyler Bradley and Huachen Zhu and Yi Guan and Yong Jiang and Guangchuang Yu},
  year = {2020},
  journal = {Molecular Biology and Evolution},
  volume = {37},
  issue = {2},
  pages = {599-603},
  doi = {10.1093/molbev/msz240},
}

@Manual{tidytree,
  title = {tidytree: A Tidy Tool for Phylogenetic Tree Data Manipulation},
  author = {Guangchuang Yu},
  year = {2021},
  note = {R package version 0.3.4.992},
  url = {https://yulab-smu.top/treedata-book/},
}

@Manual{Biostrings,
  title = {Biostrings: Efficient manipulation of biological strings},
  author = {H. Pagès and P. Aboyoun and R. Gentleman and S. DebRoy},
  year = {2021},
  note = {R package version 2.61.2},
  url = {https://bioconductor.org/packages/Biostrings},
}

@Article{ggtreeExtra,
  title = {ggtreeExtra: Compact visualization of richly annotated phylogenetic data},
  author = {Shuangbin Xu and Zehan Dai and Pingfan Guo and Xiaocong Fu and Shanshan Liu and Lang Zhou and Wenli Tang and Tingze Feng and Meijun Chen and Li Zhan and Tianzi Wu and Erqiang Hu and Yong Jiang and Xiaochen Bo and Guangchuang Yu},
  journal = {Molecular Biology and Evolution},
  volume = {38},
  issue = {9},
  pages = {4039-4042},
  year = {2021},
  month = {06},
  issn = {0737-4038},
  doi = {10.1093/molbev/msab166},
  pmid = {34097064},
  url = {https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msab166/6294410},
}

@article{qiime2,
  title={Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2},
  author={Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian C and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and others},
  journal={Nature biotechnology},
  volume={37},
  number={8},
  pages={852--857},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{dada2,
  title={DADA2: high-resolution sample inference from Illumina amplicon data},
  author={Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
  journal={Nature methods},
  volume={13},
  number={7},
  pages={581--583},
  year={2016},
  publisher={Nature Publishing Group}
}

@article{metaphlan,
  title={Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3},
  author={Beghini, Francesco and McIver, Lauren J and Blanco-M{\'\i}guez, Aitor and Dubois, Leonard and Asnicar, Francesco and Maharjan, Sagun and Mailyan, Ana and Manghi, Paolo and Scholz, Matthias and Thomas, Andrew Maltez and others},
  journal={Elife},
  volume={10},
  pages={e65088},
  year={2021},
  publisher={eLife Sciences Publications Limited}
}

@article{ps,
         author = {Paul J. McMurdie and Susan Holmes},
         journal = {PLoS ONE},
         pages = {e61217},
         title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
         volume = {8},
         number = {4},
         year = {2013},
         doi={10.1371/journal.pone.0061217},
         url = {http://dx.plos.org/10.1371/journal.pone.0061217},
}

@Article{TSE,
  title = {TreeSummarizedExperiment: a S4 class for data with hierarchical structure},
  author = {Ruizhu Huang and Charlotte Soneson and Felix G.M. Ernst and Kevin C. Rue-Albrecht and Guangchuang Yu and Stephanie C. Hicks and Mark D. Robinson},
  journal = {F1000Research},
  year = {2021},
  volume = {9},
  pages = {1246},
  url = {https://f1000research.com/articles/9-1246},
}

@Article{tidyverse,
  title = {Welcome to the {tidyverse}},
  author = {Hadley Wickham and Mara Averick and Jennifer Bryan and Winston Chang and Lucy D'Agostino McGowan and Romain François and Garrett Grolemund and Alex Hayes and Lionel Henry and Jim Hester and Max Kuhn and Thomas Lin Pedersen and Evan Miller and Stephan Milton Bache and Kirill Müller and Jeroen Ooms and David Robinson and Dana Paige Seidel and Vitalie Spinu and Kohske Takahashi and Davis Vaughan and Claus Wilke and Kara Woo and Hiroaki Yutani},
  year = {2019},
  journal = {Journal of Open Source Software},
  volume = {4},
  number = {43},
  pages = {1686},
  doi = {10.21105/joss.01686},
}

@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},
         number={2},
         pages={292--298},
         year={2012},
         publisher={Cold Spring Harbor Lab},
         doi={10.1101/gr.126573.111},
         url={https://genome.cshlp.org/content/22/2/292.long}
}

@article{yu2017ggtree,
         title={ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data},
         author={Guangchuang Yu and David Smith and Huachen Zhu and Yi Guan and Tommy Tsan-Yuk Lam},
         journal={Methods in Ecology and Evolution},
         volume={8},
         issue={1},
         pages={28--36},
         year={2017},
         doi={10.1111/2041-210X.12628},
         url={http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract},
         publisher={Wiley Online Library}
}

@article{yu2018two,
         title={Two methods for mapping and visualizing associated data on phylogeny using ggtree},
         author={Guangchuang Yu and Tommy Tsan-Yuk Lam and Huachen Zhu and Yi Guan},
         journal={Molecular Biology and Evolution},
         volume={35},
         issue = {2},
         pages={3041--3043},
         year={2018},
         doi = {10.1093/molbev/msy194}, 
         url = {https://doi.org/10.1093/molbev/msy194},
         publisher={Oxford University Press}
}

@article{Nicola2011LEfSe,
         title={Metagenomic biomarker discovery and explanation},
         author={Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett and Curtis Huttenhower},
         journal={Genome Biology},
         year={2011},
         volume={12},
         issue = {6},
         pages={R60},
         doi = {10.1186/gb-2011-12-6-r60},
         url = {https://doi.org/10.1186/gb-2011-12-6-r60}
}

@article{Jari2019vegan,
         title = {vegan: Community Ecology Package},
         author = {Jari Oksanen and F. Guillaume Blanchet and Michael Friendly and Roeland Kindt and Pierre Legendre and Dan McGlinn and Peter R. Minchin and R. B. O'Hara and Gavin L. Simpson and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner},
         year = {2019},
         note = {R package version 2.5-5},
         url = {https://CRAN.R-project.org/package=vegan},
}

@article{siegel2004rarefaction,
         title={Rarefaction curves},
         author={Siegel, Andrew F},
         journal={Encyclopedia of statistical sciences},
         volume={10},
         year={2004},
         publisher={Wiley Online Library},
         doi={10.1002/0471667196.ess2195.pub2},
         url={https://onlinelibrary.wiley.com/doi/abs/10.1002/0471667196.ess2195.pub2}
}

@article{tothill2008novel,
         title={Novel molecular subtypes of serous and endometrioid ovarian cancer linked to clinical outcome},
         author={Tothill, Richard W and Tinker, Anna V and George, Joshy and Brown, Robert and Fox, Stephen B and Lade, Stephen and Johnson, Daryl S and Trivett, Melanie K and Etemadmoghadam, Dariush and Locandro, Bianca and others},
         journal={Clinical cancer research},
         volume={14},
         number={16},
         pages={5198--5208},
         year={2008},
         doi={10.1158/1078-0432.CCR-08-0196},
         url={https://clincancerres.aacrjournals.org/content/14/16/5198},
         publisher={AACR}
}

@article{banerjee2015computed,
         title={A computed tomography radiogenomic biomarker predicts microvascular invasion and clinical outcomes in hepatocellular carcinoma},
         author={Banerjee, Sudeep and Wang, David S and Kim, Hyun J and Sirlin, Claude B and Chan, Michael G and Korn, Ronald L and Rutman, Aaron M and Siripongsakun, Surachate and Lu, David and Imanbayev, Galym and others},
         journal={Hepatology},
         volume={62},
         number={3},
         pages={792--800},
         year={2015},
         doi={10.1002/hep.27877},
         url={https://aasldpubs.onlinelibrary.wiley.com/doi/full/10.1002/hep.27877},
         publisher={Wiley Online Library}
}

@article{zhang2019leveraging,
         title={Leveraging fecal bacterial survey data to predict colorectal tumors},
         author={Zhang, Bangzhou and Xu, Shuangbin and Xu, Wei and Chen, Qiongyun and Chen, Zhangran and Fan, Yanyun and Zhang, Huangkai and Liu, Qi and Yang, Jie and Yang, JInfeng and others},
         journal={Frontiers in genetics},
         volume={10},
         pages={447},
         year={2019},
         doi={10.3389/fgene.2019.00447},
         url={https://www.frontiersin.org/articles/10.3389/fgene.2019.00447/full},
         publisher={Frontiers}

}

@article{yu2017metagenomic,
         title={Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer},
         author={Yu, Jun and Feng, Qiang and Wong, Sunny Hei and Zhang, Dongya and yi Liang, Qiao and Qin, Youwen and Tang, Longqing and Zhao, Hui and Stenvang, Jan and Li, Yanli and others},
         journal={Gut},
         volume={66},
         number={1},
         pages={70--78},
         year={2017},
         doi={10.1136/gutjnl-2015-309800},
         url={https://gut.bmj.com/content/66/1/70.full},
         publisher={BMJ Publishing Group}
}

@article{ren2019gut,
         title={Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma},
         author={Ren, Zhigang and Li, Ang and Jiang, Jianwen and Zhou, Lin and Yu, Zujiang and Lu, Haifeng and Xie, Haiyang and Chen, Xiaolong and Shao, Li and Zhang, Ruiqing and others},
         journal={Gut},
         volume={68},
         number={6},
         pages={1014--1023},
         year={2019},
         doi={10.1136/gutjnl-2017-315084},
         url={https://gut.bmj.com/content/68/6/1014.full},
         publisher={BMJ Publishing Group}
}

@article{wirbel2019meta,
         title={Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer},
         author={Wirbel, Jakob and Pyl, Paul Theodor and Kartal, Ece and Zych, Konrad and Kashani, Alireza and Milanese, Alessio and Fleck, Jonas S and Voigt, Anita Y and Palleja, Albert and Ponnudurai, Ruby and others},
         journal={Nature medicine},
         volume={25},
         number={4},
         pages={679},
         year={2019},
         doi={10.1038/s41591-019-0406-6},
         url={https://www.nature.com/articles/s41591-019-0406-6},
         publisher={Nature Publishing Group}
}

@article{He289,
          author = {He, Zhen and Gharaibeh, Raad Z and Newsome, Rachel C and Pope, Jllian L and Dougherty, Michael W and Tomkovich, Sarah and Pons, Benoit and Mirey, Gladys and Vignard, Julien and Hendrixson, David R and Jobin, Christian},
          title = { Campylobacter jejuni promotes colorectal tumorigenesis through the action of cytolethal distending toxin},
          volume = {68},
          number = {2},
          pages = {289--300},
          year = {2019},
          doi = {10.1136/gutjnl-2018-317200},
          publisher = {BMJ Publishing Group},
          abstract = {Objective Campylobacter jejuni produces a genotoxin, cytolethal distending toxin (CDT), which has DNAse activity and causes DNA double-strand breaks. Although C. jejuni infection has been shown to promote intestinal inflammation, the impact of this bacterium on carcinogenesis has never been examined.Design Germ-free (GF) ApcMin/+ mice, fed with 1\% dextran sulfate sodium, were used to test tumorigenesis potential of CDT-producing C. jejuni. Cells and enteroids were exposed to bacterial lysates to determine DNA damage capacity via γH2AX immunofluorescence, comet assay and cell cycle assay. To examine the interplay of CDT-producing C. jejuni, gut microbiome and host in tumorigenesis, colonic RNA-sequencing and faecal 16S rDNA sequencing were performed. Rapamycin was administrated to investigate the prevention of CDT-producing C. jejuni-induced tumorigenesis.Results GF ApcMin/+ mice colonised with human clinical isolate C. jejuni81{\textendash}176 developed significantly more and larger tumours when compared with uninfected mice. C. jejuni with a mutated cdtB subunit, mutcdtB, attenuated C. jejuni-induced tumorigenesis in vivo and decreased DNA damage response in cells and enteroids. C. jejuni infection induced expression of hundreds of colonic genes, with 22 genes dependent on the presence of cdtB. The C. jejuni-infected group had a significantly different microbial gene expression profile compared with the mutcdtB group as shown by metatranscriptomic data, and different microbial communities as measured by 16S rDNA sequencing. Finally, rapamycin could diminish the tumorigenic capability of C. jejuni.Conclusion Human clinical isolate C. jejuni 81{\textendash}176 promotes colorectal cancer and induces changes in microbial composition and transcriptomic responses, a process dependent on CDT production.},
          issn = {0017-5749},
          URL = {https://gut.bmj.com/content/68/2/289},
          eprint = {https://gut.bmj.com/content/68/2/289.full.pdf},
          journal = {Gut}
}

@article{wu2013dysbiosis,
         title={Dysbiosis signature of fecal microbiota in colorectal cancer patients},
         author={Wu, Na and Yang, Xi and Zhang, Ruifen and Li, Jun and Xiao, Xue and Hu, Yongfei and Chen, Yanfei and Yang, Fengling and Lu, Na and Wang, Zhiyun and others},
         journal={Microbial ecology},
         volume={66},
         number={2},
         pages={462--470},
         year={2013},
         doi={10.1007/s00248-013-0245-9},
         url={https://link.springer.com/article/10.1007/s00248-013-0245-9},
         publisher={Springer}
}

@article{amer2017microbiome,
         title={The microbiome of potentially malignant oral leukoplakia exhibits enrichment for Fusobacterium, Leptotrichia, Campylobacter, and Rothia species},
         author={Amer, Abdrazak and Galvin, Sheila and Healy, Claire M and Moran, Gary P},
         journal={Frontiers in microbiology},
         volume={8},
         pages={2391},
         year={2017},
         doi={10.3389/fmicb.2017.02391},
         url={https://doi.org/10.3389/fmicb.2017.02391},
         publisher={Frontiers}
}

@article{callahan2016dada2,
         title={DADA2: high-resolution sample inference from Illumina amplicon data},
         author={Callahan, Benjamin J and McMurdie, Paul J and Rosen, Michael J and Han, Andrew W and Johnson, Amy Jo A and Holmes, Susan P},
         journal={Nature methods},
         volume={13},
         number={7},
         pages={581},
         year={2016},
         doi={10.1038/nmeth.3869},
         url={https://www.nature.com/articles/nmeth.3869},
         publisher={Nature Publishing Group}
}

@article{bolyen2019qiime2,
         title={Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2},
	 author={Bolyen, Evan and Rideout, Jai Ram and Dillon, Matthew R and Bokulich, Nicholas A and Abnet, Christian C and Al-Ghalith, Gabriel A and Alexander, Harriet and Alm, Eric J and Arumugam, Manimozhiyan and Asnicar, Francesco and others},
	 journal={Nature biotechnology},
	 volume={37},
	 number={8},
	 pages={852--857},
	 year={2019},
         doi={10.1038/s41587-019-0209-9},
         url={https://www.nature.com/articles/s41587-019-0209-9},
	 publisher={Nature Publishing Group}
}
