Publications

James A. Fellows Yates, Christina Warinner, Aida Andrades Valtueña, Maxime Borry, Meriam Guellil, Alexander Herbig, Alina Hiß, Alexander Hübner, Arthur Kocher, Thiseas C. Lamnidis, Megan E. Michel, Kevin Nota, Nikolay Oskolkov, Aleksandra Laura Pach, Vilma Pérez, Clemens Schmid, Irina M. Velsko, Robin Warner, Giulia Zampirolo, Teresa Zeibig. Introduction to Ancient Metagenomics Textbook. Zenodo, 2024.

Maxime Borry et al. Facilitating Accessible, Rapid, and Appropriate Processing of Ancient Metagenomic Data with AMDirT. F1000Research, 2024.

Moritz E. Beber, Maxime Borry, Sofia Stamouli, James A. Fellows Yates. TAXPASTA: TAXonomic Profile Aggregation and STAndardisation. Journal of Open Source Software, 2023.

Martin Klapper, Alexander Hübner, Anan Ibrahim, Ina Wasmuth, Maxime Borry, Veit G. Haensch, Shuaibing Zhang, Walid K. Al-Jammal, Harikumar Suma, James A. Fellows Yates, Jasmin Frangenberg, Irina M. Velsko, Somak Chowdhury, Rosa Herbst, Evgeni V. Bratovanov, Hans-Martin Dahse, Therese Horch, Christian Hertweck, Manuel Ramon González Morales, Lawrence Guy Straus, Ivan Vilotijevic, Christina Warinner, Pierre Stallforth. Natural Products from Reconstructed Bacterial Genomes of the Middle and Upper Paleolithic. Science, 2023.

Sofia Stamouli, Moritz E. Beber, Tanja Normark, Thomas A. Christensen, Lili Andersson-Li, Maxime Borry, Mahwash Jamy, nf-core community, James A. Fellows Yates. nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling. bioRxiv, 2023.

Maxime Borry, Alexander Hübner, Christina Warinner. sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files. Journal of Open Source Software, 2022.

Maxime Borry, Alexander Hübner, Adam B. Rohrlach, Christina Warinner. PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ, 2021.

Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Hübner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto García-Ortiz, Angélica Martínez-Hernández, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Sünje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc, Aleksandar D. Kostic. Reconstruction of ancient microbial genomes from the human gut. Nature, 2021.

James A. Fellows Yates, Thiseas C. Lamnidis, Maxime Borry, Aida Andrades Valtueña, Zandra Fagernäs, Stephen Clayton, Maxime U. Garcia, Judith Neukamm, Alexander Peltzer. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ, 2021.

James A. Fellows Yates, Aida Andrades Valtueña, Åshild J. Vågene, Becky Cribdon, Irina M. Velsko, Maxime Borry, Miriam J. Bravo-Lopez, Antonio Fernandez-Guerra, Eleanor J. Green, Shreya L. Ramachandran, Peter D. Heintzman, Maria A. Spyrou, Alexander Hübner, Abigail S. Gancz, Jessica Hider, Aurora F. Allshouse, Valentina Zaro, Christina Warinner. Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 2021.

Maxime Borry et al. CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ, 2020.

Maxime Borry. Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification. Journal of Open Source Software, 2019.