Publications

  • C. Duitama Gonzalez, R. Vicedomini, T. Lemane, N. Rascovan, H. Richard, R. Chikhi, decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods, Microbiome (2023) doi: 10.1186/s40168-023-01670-3

  • C. Duitama Gonzalez, S. Rangavittal, R. Vicedomini, R. Chikhi, H. Richard, aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets, Iscience (2023). doi: 10.1016/j.isci.2023.108057

  • F. Meyer et al., Critical Assessment of Metagenome Interpretation: the second round of challenges, Nature Methods (2022). doi: 10.1038/s41592-022-01431-4

  • R. Vicedomini*, J.-P. Bouly*, E. Laine, A. Falciatore & A. Carbone, Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families, Molecular Biology and Evolution (2022). doi: 10.1093/molbev/msac070

  • R. Vicedomini, C. Quince, A. E. Darling & R. Chikhi, Strainberry: automated strain separation in low-complexity metagenomes using long reads, Nature Communications (2021). doi: 10.1038/s41467-021-24515-9

  • D. Danko et al., A global metagenomic map of urban microbiomes and antimicrobial resistance, Cell (2021). doi: 10.1016/j.cell.2021.05.002

  • R. Vicedomini, C. Blachon, F. Oteri & A. Carbone, MyCLADE: a multi-source domain annotation server for sequence functional exploration, Nucleic Acids Research, Web Server Issue (2021). doi: 10.1093/nar/gkab395

  • L. David, R. Vicedomini, H. Richard & A. Carbone, Targeted domain assembly for fast functional profiling of metagenomic datasets with S3A, Bioinformatics (2020). doi: 10.1093/bioinformatics/btaa272

  • A. Ugarte*, R. Vicedomini*, J. S. Bernardes & A. Carbone, A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling, Microbiome (2018). doi: 10.1186/s40168-018-0532-2

  • R. Vicedomini, F. Vezzi, S. Scalabrin, L. Arvestad & A. Policriti, Hierarchical assembly of pools, Bioinformatics and Biomedical Engineering, Lecture Notes in Computer Science, Springer International Publishing (2015). doi: 10.1007/978-3-319-16480-9_21

  • K. R. Bradnam et al., Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience (2013). doi: 10.1186/2047-217X-2-10

  • B. Nystedt, N. R. Street et al., The Norway spruce genome sequence and conifer genome evolution, Nature (2013). doi: 10.1038/nature12211

  • R. Vicedomini, F. Vezzi, S. Scalabrin, L. Arvestad & A. Policriti, GAM-NGS: genomic assemblies merger for next generation sequencing BMC Bioinformatics (2013). doi: 10.1186/1471-2105-14-S7-S6

Pre-prints

  • R. Vicedomini*, L. Polit*, S. Condemi, L. Longo & A. Carbone, Dietary adaptation in Neandertal, Denisovan and Sapiens revealed by gene copy number variation bioRxiv (2021). doi: 10.1101/2021.10.30.466563

PhD Thesis

  • Vicedomini R., Alignment and reconciliation strategies for large-scale de novo assembly, Doctoral Thesis, Università degli Studi di Udine (2016). [pdf]