Publications
Papers
2026
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DIANA: Deep Learning Identification and Assessment of Ancient DNA — Duitama González, C., Lopopolo, M., Nishimura, L., Faure, R., & Duchene, S. — bioRxiv read here
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Streptococcus pyogenes emm1 and emm12 lineages in China — You, Y., Yu, D., […] Duitama González, C., […] & Yang, Y. — Nature Microbiology read here
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The phylodynamic threshold of measurably evolving populations — Weber, A., Kende, J., Duitama González, C., Översti, S., & Duchene, S. — Molecular Biology and Evolution 43(6) read here
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Benchmarking BEAGLE to find optimal parameters for BEAST X — Fosse, S., Duchene, S., & Duitama González, C. — bioRxiv read here
2025
- MUSET: Set of utilities for the construction of abundance unitig matrices from sequencing data — Vicedomini, R., Andreace, F., Dufresne, Y., Chikhi, R., & Duitama González, C. — Bioinformatics read here
2023
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aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets — González, C. D., Rangavittal, S., Vicedomini, R., Chikhi, R., & Richard, H. — iScience 26(11) read here
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decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods — Duitama González, C., Vicedomini, R., Lemane, T., Rascovan, N., Richard, H., & Chikhi, R. — Microbiome 11(1), 243 read here