Publications

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.