tutorial.bib

# This is the bibliography file for your tutorial.
#
# To add bibliography (bibtex) entries here, follow these steps:
#  1) Find the DOI for the article you want to cite
#  2) Go to https://doi2bib.org and fill in the DOI
#  3) Copy the resulting bibtex entry into this file
#
# To cite the example below, in your tutorial.md file
# use {% cite Batut2018 %}
#
# If you want to cite an online resourse (website etc)
# you can use the 'online' format (see below)
#
# You can remove the examples below

@misc{cdifficile,
  author = {{Helmholtz Centre for Infection Research}},
  title = {Clostridioides difficile},
  howpublished = {Helmholtz Centre for Infection Research},
  url = {https://www.helmholtz-hzi.de/wissen/wissensportal/clostridioides-difficile/},
  note = {Accessed: 3 April 2026}
}

@article{zanellaterrier2014recurrent,
  author = {Zanella Terrier, Marie Céline and Simonet, Martine Louis and Bichard, Philippe and Frossard, Jean Louis},
  title = {Recurrent Clostridium difficile infections: The importance of the intestinal microbiota},
  journal = {World Journal of Gastroenterology},
  year = {2014},
  volume = {20},
  number = {23},
  pages = {7416--7423},
  doi = {10.3748/wjg.v20.i23.7416}
}

@article{smillie2018strainfinder,
  author = {Smillie, Christopher S. and Sauk, Jenny and Gevers, Dirk and Friedman, Jonathan and Sung, Jonathan and Youngster, Ilan and Hohmann, Elizabeth L. and Staley, Christopher and Khoruts, Alexander and Sadowsky, Michael J. and Allegretti, Jessica R. and Smith, Mark B. and Xavier, Ramnik J. and Alm, Eric J.},
  title = {Strain tracking reveals the determinants of bacterial engraftment in the human gut following fecal microbiota transplantation},
  journal = {Cell Host \& Microbe},
  year = {2018},
  volume = {23},
  number = {2},
  pages = {229--240.e5},
  doi = {10.1016/j.chom.2018.01.003}
}

@article{samestr_podlesny,
  author = {Podlesny, Daniel and Arze, Cesar and Dörner, Elisabeth and Verma, Sandeep and Dutta, Sudhir and Walter, Jens and Fricke, W. Florian},
  title = {Metagenomic strain detection with SameStr: Identification of a persisting core gut microbiota transferable by fecal transplantation},
  journal = {Microbiome},
  year = {2022},
  volume = {10},
  number = {1},
  pages = {53},
  doi = {10.1186/s40168-022-01251-w}
}

@misc{kneaddata_website,
  author       = {{The Huttenhower Lab}},
  title        = {KneadData},
  year         = {n.d.},
  howpublished = {Harvard T.H. Chan School of Public Health},
  url          = {https://huttenhower.sph.harvard.edu/kneaddata},
  note         = {Accessed: 27 April 2026}
}
@article{blanco-miguez2023metaphlan4,
  author = {Blanco-Míguez, A. and Beghini, F. and Cumbo, F. and McIver, L. J. and Thompson, K. N. and Zolfo, M. and Manghi, P. and Dubois, L. and Huang, K. D. and Thomas, A. M. and Nickols, W. A. and Piccinno, G. and Piperni, E. and Punčochář, M. and Valles-Colomer, M. and Tett, A. and Giordano, F. and Davies, R. and Wolf, J. and Berry, S. E. and Spector, T. D. and Franzosa, E. A. and Pasolli, E. and Asnicar, F. and Huttenhower, C. and Segata, N.},
  title = {Extending and improving metagenomic taxonomic profiling with uncharacterized species using {MetaPhlAn} 4},
  journal = {Nature Biotechnology},
  year = {2023},
  volume = {41},
  number = {11},
  pages = {1633-1644},
  doi = {10.1038/s41587-023-01688-w}
}