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Maxime Borry
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Reconstruction of ancient microbial genomes from the human gut
MC Wibowo, Z Yang, M Borry, A Hübner, KD Huang, BT Tierney, ...
Nature 594 (7862), 234-239, 2021
1742021
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager
JAF Yates, TC Lamnidis, M Borry, AA Valtueña, Z Fagernäs, S Clayton, ...
PeerJ 9, e10947, 2021
64*2021
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content
M Borry, B Cordova, A Perri, M Wibowo, TP Honap, J Ko, J Yu, K Britton, ...
PeerJ 8, e9001, 2020
412020
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir
JA Fellows Yates, A Andrades Valtueña, ÅJ Vågene, B Cribdon, ...
Scientific Data 8 (1), 31, 2021
292021
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly
M Borry, A Hübner, AB Rohrlach, C Warinner
PeerJ 9, e11845, 2021
242021
Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic
M Klapper, A Hübner, A Ibrahim, I Wasmuth, M Borry, VG Haensch, ...
Science 380 (6645), 619-624, 2023
142023
CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content. PeerJ 8: e9001
M Borry, B Cordova, A Perri, M Wibowo, TP Honap, J Ko, J Yu, K Britton, ...
82020
Sourcepredict: Prediction of metagenomic sample sources using dimension reduction followed by machine learning classification
M Borry
Journal of Open Source Software 4, 1540, 2019
82019
Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Sci Data 8: 31
JA Fellows Yates, A Andrades Valtueña, ÅJ Vågene, B Cribdon, ...
62021
PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly. PeerJ 9: e11845
M Borry, A Hübner, AB Rohrlach, C Warinner
62021
sam2lca: Lowest Common Ancestor for SAM/BAM/CRAM alignment files
M Borry, A Hübner, C Warinner
Journal of Open Source Software 7 (74), 4360, 2022
22022
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
M Borry, A Forsythe, A Andrades Valtueña, A Hübner, A Ibrahim, ...
F1000Research 12, 926, 2023
12023
TAXPASTA: TAXonomic Profile Aggregation and STAndardisation
ME Beber, M Borry, S Stamouli, JAF Yates
Journal of Open Source Software 8 (87), 5627, 2023
12023
nf-core/taxprofiler: highly parallelised and flexible pipeline for metagenomic taxonomic classification and profiling
S Stamouli, ME Beber, T Normark, TA Christensen, L Andersson-Li, ...
bioRxiv, 2023.10. 20.563221, 2023
12023
Expanding the ancient DNA bioinformatics toolbox, and its applications to archeological microbiomes
M Borry
2023
Foldit, un jeu pour faire de la recherche
F BERNARDON, M BORRY, M POTHIER
La Recherche (Imprimé), 68-71, 2012
2012
Facilitating accessible, rapid, and appropriate processing o f ancient metagenomic data with AMDirT [version 1; peer
M Borry, A Forsythe, AA Valtueña, A Hübner, A Ibrahim, A Quagliariello, ...
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Articles 1–17