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aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets

 Camila Duitama González , Samarth Rangavittal , Riccardo Vicedomini , Rayan Chikhi , Hugues Richard
iScience, 2023, 26 (11), pp.108057. ⟨10.1016/j.isci.2023.108057⟩
Article dans une revue hal-04303607v1
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MyCLADE: a multi-source domain annotation server for sequence functional exploration

 Riccardo Vicedomini , Clémence Blachon , Francesco Oteri , Alessandra Carbone
Nucleic Acids Research, 2021, 49 (W1), pp.W452 - W458. ⟨10.1093/nar/gkab395⟩
Article dans une revue hal-03294232v1
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Metagenomic assembly of complex ecosystems with highly accurate long-reads

 Nicolas Maurice , Claire Lemaitre , Clémence Frioux , Riccardo Vicedomini
Journées 2024 du PEPR Agroécologie et Numérique, Jan 2024, Rennes, France. pp.1-1, 2024
Poster de conférence hal-04425626v1
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decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods

 Camila Duitama González , Riccardo Vicedomini , Téo Lemane , Nicolas Rascovan , Hugues Richard , et al.
Microbiome, 2023, 11 (1), pp.1-12. ⟨10.1186/s40168-023-01670-3⟩
Article dans une revue hal-04303600v1
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Unlocking the Soil Microbiome: Unraveling Soil Microbial Complexity Using Long-Read Metagenomics

 Carole Belliardo , Nicolas Maurice , Clémence Frioux , Claire Lemaitre , Riccardo Vicedomini , et al.
EAGS 2024 - The International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. , pp.1-1, 2024
Poster de conférence hal-04509213v1
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Strainberry: automated strain separation in low-complexity metagenomes using long reads

 Riccardo Vicedomini , Christopher Quince , Aaron Darling , Rayan Chikhi
Nature Communications, 2021, 12 (1), pp.4485. ⟨10.1038/s41467-021-24515-9⟩
Article dans une revue hal-03412884v1
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A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

 Ari Ugarte , Riccardo Vicedomini , Juliana Bernardes , Alessandra Carbone
Microbiome, 2018, 6, pp.149. ⟨10.1186/s40168-018-0532-2⟩
Article dans une revue hal-01875977v1
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Exploring and quantifying the soil genetic diversity captured by long and short-read shotgun metagenomic sequencing

 Carole Belliardo , Samuel Mondy , Arthur Pere , Claire Lemaitre , Riccardo Vicedomini , et al.
Journées 2024 du programme Agroécologie et Numérique, Jan 2024, Rennes, France. , pp.1-1, 2024
Poster de conférence hal-04423917v1
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A global metagenomic map of urban microbiomes and antimicrobial resistance

 David Danko , Daniela Bezdan , Evan Afshin , Sofia Ahsanuddin , Chandrima Bhattacharya , et al.
Cell, 2021, 184 (13), pp.3376-3393.e17. ⟨10.1016/j.cell.2021.05.002⟩
Article dans une revue hal-03357730v1
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Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

 Keith Bradnam , Joseph Fass , Anton Alexandrov , Paul Baranay , Michael Bechner , et al.
GigaScience, 2013, 2 (1), pp.10. ⟨10.1186/2047-217X-2-10⟩
Article dans une revue hal-00868822v1
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Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A

 Laurent David , Riccardo Vicedomini , Hugues Richard , Alessandra Carbone
Bioinformatics, 2020, 36 (13), pp.3975-3981. ⟨10.1093/bioinformatics/btaa272⟩
Article dans une revue hal-02935519v1
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Critical Assessment of Metagenome Interpretation: the second round of challenges

 Fernando Meyer , Adrian Fritz , Zhi-Luo Deng , David Koslicki , Till Robin Lesker , et al.
Nature Methods, 2022, 19 (4), pp.429-440. ⟨10.1038/s41592-022-01431-4⟩
Article dans une revue hal-03832903v1
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