Luca DENTI

"I know that I know nothing" (Socrates)

Publications

  1. S. Ciccolella, L. Denti, J. Avila Cartes, G. Della Vedova, Y. Pirola, R. Rizzi, P. Bonizzoni
    Differential Analysis of Alternative Splicing Events in gene regions using Residual Neural Networks
    bioRxiv (2024)

  2. J. Avila Cartes, P. Bonizzoni, S. Ciccolella, G. Della Vedova, L. Denti, X. Didelot, D.C. Monti, Y. Pirola
    RecGraph: adding recombinations to sequence-to-graph alignment
    Bioinformatics (2024)

  3. J. Avila Cartes, P. Bonizzoni, S. Ciccolella, G. Della Vedova, L. Denti
    PangeBlocks: customized construction of pangenome graphs via maximal blocks
    BMC Bioinformatics (2024)

  4. S. Mahadevaraju, S. Pal, P. Bhaskar, B.D. McDonald, L. Benner, L. Denti, D. Cozzi, P. Bonizzoni, T.M. Przytycka, B. Oliver
    Diverse somatic Transformer and sex chromosome karyotype pathways regulate gene expression in Drosophila gonad development
    eLife (2024)

  5. L. Denti*, P. Khorsand*, P. Bonizzoni, F. Hormozdiari, R. Chikhi
    SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads
    Nature Methods (2023)

  6. D. Cozzi, P. Bonizzoni, L. Denti
    ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs
    ITAT Proceedings (2023)

  7. S. Ciccolella, D. Cozzi, G. Della Vedova, S. Kuria, P. Bonizzoni, L. Denti
    Differential quantification of alternative splicing events on spliced pangenome graphs
    bioRxiv (2023)

  8. S. Ciccolella*, L. Denti*, P. Bonizzoni, G. Della Vedova, Y. Pirola*, and M. Previtali*
    MALVIRUS: an integrated web application for viral variant calling
    BMC Bioinformatics (2022)

  9. G. Bernardini*, L. Denti, M. Previtali
    Alignment-Free Genotyping of Known Variations with MALVA
    Methods in Molecular Biology (2022)

  10. P. Khorsand*, L. Denti*, Human Genome Structural Variant Consortium, P. Bonizzoni, R. Chikhi, F. Hormozdiari
    Comparative genome analysis using sample-specific string detection in accurate long reads
    Bioinformatics Advances (2021)

  11. L. Denti*, Y. Pirola*, M. Previtali*, T. Ceccato, G. Della Vedova, R. Rizzi, P. Bonizzoni
    Shark: fishing relevant reads in an RNA-Seq sample
    Bioinformatics (2020)

  12. S. Ciccolella, G. Bernardini, P. Bonizzoni, M. Previtali, G. Della Vedova
    Triplet-based similarity score for fully multi-labeled trees with poly-occurring labels
    Bioinformatics (2020)

  13. L. Denti*, M. Previtali*, G. Bernardini, A. Schönhuth, P. Bonizzoni
    MALVA: genotyping by Mapping-free ALlele detection of known VAriants
    Iscience (2019)

  14. S. Beretta, L. Denti, M. Previtali
    Graph Theory and Definitions
    Encyclopedia of Bioinformatics and Computational Biology (2019)

  15. S. Beretta, L. Denti, M. Previtali
    Network Properties
    Encyclopedia of Bioinformatics and Computational Biology (2019)

  16. L. Denti, R. Rizzi, S. Beretta, G. Della Vedova, M. Previtali, P. Bonizzoni
    ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
    BMC Bioinformatics (2018)

  17. S. Beretta, P. Bonizzoni, L. Denti, M. Previtali, R. Rizzi
    Mapping RNA-seq data to a transcript graph via approximate pattern matching to a hypertext
    AlCoB (2017)


Talks

  1. ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs
    ITAT23. Tatranské Matliare, Slovakia

  2. SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads
    RECOMB2023 - Instanbul, Turkey

  3. Structural Variations Discovery from Specific Strings
    Nov. 9, 2022. Comenius University (invited by Tomas Vinar)

  4. Comparative genome analysis using sample-specific string detection in accurate long reads
    HiTSeq2021 - Lyon, France (virtual)

  5. Comparative genome analysis using sample-specific string detection in accurate long reads
    DSB2021 - Milano, Italy (virtual)

  6. Dynamic quasi-minimal perfect hash function for k-mers (work-in-progress talk)
    DSB2020 - Rennes, France

  7. MALVA: genotyping by Mapping-free ALlele detection of known VAriants
    BITS2019 - Palermo, Italy

  8. MALVA: genotyping by Mapping-free ALlele detection of known VAriants
    RECOMBSEQ2019 - Washington DC, USA

  9. Mapping RNA-seq data to a transcript graph via approximate pattern matching to a hypertext
    AlCoB2017 - Aveiro, Portugal


Posters

  1. MALVA: genotyping by Mapping-free ALlele detection of known VAriants
    RECOMB2019

  2. ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
    RECOMB2018 Best Poster Award