RV
Riccardo Vicedomini
bioinformaticsMetagenomicsSoftwareMetagenomeComputational BiologyEvolution, MolecularHigh-Throughput Nucleotide SequencingSequence Analysis, DNAAlgorithmsB12-binding domain containing
On Valency
published · living versionsW_26xzgw86·v1 · currentpublished
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
with Keith R. Bradnam, Joseph N. Fass, Anton Alexandrov, Paul Baranay +86
1 version
Preprints & journals
18 papers in the corpus · 2013–2025MADRe: Strain-level metagenomic classification through assembly-driven database reduction.41871361 · Lipovac, Josipa, Šikić, Mile, Vicedomini, Riccardo et al.2026 · 2 citationsGigaScience. 2026;15
Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads.40478660 · Maurice, Nicolas, Lemaitre, Claire, Vicedomini, Riccardo et al.2025 · 4 citationsBioinformatics (Oxford, England). 2025;41(6)
Mapler: Assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads10.1101/2025.03.10.641994v1 · Maurice, N., Lemaitre, C., Vicedomini, R. et al.2025 · 0 citationsbioRxiv
MUSET: set of utilities for constructing abundance unitig matrices from sequencing data.39898792 · Vicedomini, Riccardo, Andreace, Francesco, Dufresne, Yoann et al.2025 · 4 citationsBioinformatics (Oxford, England). 2025;41(3)
Analysis of metagenomic data.40688383 · Liu, Shaopeng, Rodriguez, Judith S, Munteanu, Viorel et al.2025 · 89 citationsNature reviews. Methods primers. 2025;5
aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.37876815 · Duitama González, Camila, Rangavittal, Samarth, Vicedomini, Riccardo et al.2024 · 7 citationsiScience. 2023;26(11):108057
decOM: Similarity-based microbial source tracking of ancient oral samples using k-mer-based methods10.1101/2023.01.26.525439v1 · Duitama Gonzalez, C., Vicedomini, R., Lemane, T. et al.2023 · 15 citationsbioRxiv
Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families.35353898 · Vicedomini, R, Bouly, J P, Laine, E et al.2022 · 18 citationsMolecular biology and evolution. 2022;39(4)
Critical Assessment of Metagenome Interpretation: the second round of challenges.35396482 · Meyer, Fernando, Fritz, Adrian, Deng, Zhi-Luo et al.2022 · 384 citationsNature methods. 2022;19(4):429-440
Genetic dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation10.1101/2021.10.30.466563v2 · Vicedomini, R., Righetti, N., Polit, L. et al.2021 · 5 citationsbioRxiv
Strainberry: automated strain separation in low-complexity metagenomes using long reads.34301928 · Vicedomini, Riccardo, Quince, Christopher, Darling, Aaron E et al.2021 · 61 citationsNature communications. 2021;12(1):4485
MyCLADE: a multi-source domain annotation server for sequence functional exploration.34023906 · Vicedomini, Riccardo, Blachon, Clémence, Oteri, Francesco et al.2021 · 10 citationsNucleic acids research. 2021;49(W1):W452-W458
Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A.32330240 · David, Laurent, Vicedomini, Riccardo, Richard, Hugues et al.2020 · 4 citationsBioinformatics (Oxford, England). 2020;36(13):3975-3981
Multiple probabilistic models extract features from protein sequence data and resolve functional diversity of very different protein families10.1101/717249v2 · Vicedomini, R., Bouly, J.-P., Laine, E. et al.2019 · 1 citationbioRxiv
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling.30153857 · Ugarte, Ari, Vicedomini, Riccardo, Bernardes, Juliana et al.2019 · 49 citationsMicrobiome. 2018;6(1):149
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.23870653 · Bradnam, Keith R, Fass, Joseph N, Alexandrov, Anton et al.2014 · 671 citationsGigaScience. 2013;2(1):10
The Norway spruce genome sequence and conifer genome evolution.23698360 · Nystedt, Björn, Street, Nathaniel R, Wetterbom, Anna et al.2013 · 1,467 citationsNature. 2013;497(7451):579-84
GAM-NGS: genomic assemblies merger for next generation sequencing.23815503 · Vicedomini, Riccardo, Vezzi, Francesco, Scalabrin, Simone et al.2013 · 98 citationsBMC bioinformatics. 2013;14 Suppl 7:S6
Career total: 54 works. 18 are in this corpus.
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