Publications

Journals

  • BAR-Seq clonal tracking of gene-edited cells.
    Samuele Ferrari, Stefano Beretta, Aurelien Jacob, Davide Cittaro, Luisa Albano, Ivan Merelli, Luigi Naldini, Pietro Genovese. Nature Protocols, In Press, (2021). (Link)

  • Premature senescence and increased oxidative stress in the thymus of Down Syndrome patients.
    Genni E Marcovecchio, Francesca Ferrua, Elena Fontana, Stefano Beretta, Marco Genua, Ileana Bortolomai, Anastasia Conti, Davide Montin, Maria Teresa Cascarano, Sonia Bergante, Veronica Doria, Alessandro Giamberti, Donato Amodio, Caterina Cancrini, Adriano Carotti, Raffaella Di Micco, Ivan Merelli, Marita Bosticardo, Anna Villa. Frontiers in Immunology, Vol. 12:1830, (2021). (Link)

  • Modeling, optimization, and comparable efficacy of T cell and hematopoietic stem cell gene editing for treating hyper‐IgM syndrome.
    Valentina Vavassori, Elisabetta Mercuri, Genni E Marcovecchio, Maria C Castiello, Giulia Schiroli, Luisa Albano, Carrie Margulies, Frank Buquicchio, Elena Fontana, Stefano Beretta, Ivan Merelli, Andrea Cappelleri, Paola MV Rancoita, Vassilios Lougaris, Alessandro Plebani, Maria Kanariou, Arjan Lankester, Francesca Ferrua, Eugenio Scanziani, Cecilia Cotta‐Ramusino, Anna Villa, Luigi Naldini, Pietro Genovese. EMBO Molecular Medicine, Vol. 13:e13545, (2021). (Link)

  • Hematopoietic stem cell function in β-thalassemia is impaired and is rescued by targeting the bone marrow niche.
    Annamaria Aprile, Alessandro Gulino, Mariangela Storto, Isabella Villa, Stefano Beretta, Ivan Merelli, Alessandro Rubinacci, Maurilio Ponzoni, Sarah Marktel, Claudio Tripodo, Maria Rosa Lidonnici, Giuliana Ferrari. Blood, Vol. 136(5):610–622, (2020). (Link)

  • Efficient gene editing of human long-term hematopoietic stem cells validated by clonal tracking.
    Samuele Ferrari, Aurelien Jacob, Stefano Beretta, Giulia Unali, Luisa Albano, Valentina Vavassori, Davide Cittaro, Dejan Lazarevic, Chiara Brombin, Federica Cugnata, Anna Kajaste-Rudnitski, Ivan Merelli, Pietro Genovese, Luigi Naldini. Nature Biotechnology, Vol. 38(11):1298-1308, (2020). (Link)

  • Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era.
    Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni. Quantitative Biology, Vol. 7:278–292, (2019). (Link)

  • γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites.
    Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini. Bioinformatics, Vol. 36(5):1622-1624, (2019). (Link)

  • Precise gene editing preserves hematopoietic stem cell function following transient p53-mediated DNA damage response.
    Giulia Schiroli, Anastasia Conti, Samuele Ferrari, Lucrezia della Volpe, Aurelien Jacob, Luisa Albano, Stefano Beretta, Andrea Calabria, Valentina Vavassori, Patrizia Gasparini, Eralda Salataj, Delphine Ndiaye-Lobry, Chiara Brombin, Julie Chaumeil, Eugenio Montini, Ivan Merelli, Pietro Genovese, Luigi Naldini, Raffaella Di Micco. Cell Stem Cell, Vol. 24(4):551-565, (2019). (Link)

  • ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
    Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, and Paola Bonizzoni BMC Bioinformatics, Vol. 19(1):444, (2018). (Link)

  • HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.
    Stefano Beretta, Murray D. Patterson, Simone Zaccaria, Gianluca Della Vedova, and Paola Bonizzoni. BMC Bioinformatics, Vol. 19(1):252, (2018). (Link)

  • Learning the Structure of Bayesian Networks: A Quantitative Assessment of the Effect of Different Algorithmic Schemes.
    Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Roberto Henriques, and Daniele Ramazzotti. Complexity, Vol. 2018, Article ID 1591878, (2018). (Link)

  • Improving eQTL Analysis using a Machine Learning Approach for Data Integration: a Logistic Model Tree Solution.
    Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Valentina Giansanti, and Ivan Merelli. Journal of Computational Biology, Vol.25(10):1091-1105, (2018). (Link)

  • A Scalable Genetic Programming Approach to Integrate miRNA-Target Predictions: Comparing Different Parallel Implementations of M3GP.
    Stefano Beretta, Mauro Castelli, Luis Muñoz, Leonardo Trujillo, Yuliana Martinez, Ales Popovic, Luciano Milanesi, and Ivan Merelli. Complexity, Vol. 2018, Article ID 4963139, (2018). (Link)

  • VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.
    Giulio Spinozzi, Andrea Calabria, Stefano Brasca, Stefano Beretta, Ivan Merelli, Luciano Milanesi, Eugenio Montini. BMC Bioinformatics, Vol. 18:520 (2017). (Link)

  • HIV-1-mediated insertional activation of STAT5B and BACH2 trigger viral reservoir in T regulatory cells.
    Daniela Cesana, Francesca R. Santoni de Sio, Laura Rudilosso, Pierangela Gallina, Andrea Calabria, Stefano Beretta, Ivan Merelli, Elena Bruzzesi, Laura Passerini, Silvia Nozza, Elisa Vicenzi, Guido Poli, Silvia Gregori, Giuseppe Tambussi, Eugenio Montini. Nature Communications, Vol. 8:498 (2017). (Link)

  • SPIRE: a modular pipeline for eQTL analysis of RNA-Seq data reveals a regulatory hotspot controlling miRNA expression.
    Ivan Kel, Zisong Chang, Nadia Galluccio, Margherita Romeo, Stefano Beretta, Luisa Diomede, Alessandra Mezzelani, Luciano Milanesi, Christoph Dieterich, Ivan Merelli. Molecular BioSystems, Vol. 12(11):3447-3458 (2016). (Link)

  • Corrigendum to “Parameterized tractability of the maximum-duo preservation string mapping problem”.
    Stefano Beretta, Mauro Castelli, Riccardo Dondi. Theoretical Computer Science, Vol. 653:108-110 (2016). (Link)

  • Parameterized tractability of the maximum-duo preservation string mapping problem.
    Stefano Beretta, Mauro Castelli, Riccardo Dondi. Theoretical Computer Science, Vol. 646:16-25 (2016). (Link)

  • Correcting Gene Trees by Leaf Insertions: Complexity and Approximation.
    Stefano Beretta, Riccardo Dondi. Proceedings of {ICTCS} 2015, the 16th Italian Conference on Theoretical Computer Science, Electronic Notes in Theoretical Computer Science, Vol. 322:35-50 (2016). (Link)

  • Correcting gene tree by removal and modification: Tractability and approximability.
    Stefano Beretta, Mauro Castelli, Riccardo Dondi. Journal of Discrete Algorithms, Vol. 33:115-129 (2015). (Link)

  • Covering Pairs in Directed Acyclic Graphs.
    Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola. The Computer Journal, Vol. 58(7):1673-1686 (2015). (Link)

  • Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs.
    Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi. Journal of Computational Biology, Vol. 21(1):16-40 (January 2014). (Link)

  • Further Steps in TANGO: Improved Taxonomic Assignment in Metagenomics.
    Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente. Bioinformatics, Vol. 30(1):17-23 (2014). (Link)

  • A hybrid genetic algorithm for the repetition free longest common subsequence problem.
    Mauro Castelli, Stefano Beretta, Leonardo Vanneschi. Operations Research Letters, Vol. 41(6):644–649 (November 2013). (Link)


Conferences

  • Comparing Deep and Machine Learning Approaches in Bioinformatics: A miRNA-Target Prediction Case Study.
    Valentina Giansanti, Mauro Castelli, Stefano Beretta, Ivan Merelli. In. International Conference on Computational Science (ICCS), LNCS, pp. 31-44, (2019). (Link)

  • Parallel Computing in Deep Learning: Bioinformatics Case Studiesa.
    Valentina Giansanti, Stefano Beretta, Daniele Cesini, Daniele D’Agostino, Ivan Merelli. In 2019 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE. pp. 329-333, (2018). (Link)

  • Computing Empirical P-Values for Estimating Gene-Gene Interactions in Genome-Wide Association Studies: A Parallel Computing Approach.
    Valentina Giansanti, Daniele D’Agostino, Carlo Maj, Stefano Beretta, and Ivan Merelli. In 2018 26th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, pp. 406–409, (2018). (Link)

  • Mapping RNA-seq Data to a Transcript Graph via Approximate Pattern Matching to a Hypertext.
    Stefano Beretta, Paola Bonizzoni, Luca Denti, Marco Previtali, Raffaella Rizzi. In Algorithms for Computational Biology - 4th International Conference, AlCoB 2017, Aveiro, Portugal, pp. 49-61, (2017). (Link)

  • Rank miRNA: a web tool for identifying polymorphisms altering miRNA target sites.
    Stefano Beretta, Carlo Maj, Ivan Merelli. In BBC2017 Workshop - International Conference on Computational Science (ICCS), Procedia Computer Science, Vol 108:1125-1134, (2017). (Link)

  • Low-Power Architectures for miRNA-Target Genome Wide Analysis.
    Stefano Beretta, Lucia Morganti, Elena Corni, Andrea Ferraro, Daniele Cesini, Daniele D’Agostino, Luciano Milanesi, Ivan Merelli. In 2017 25th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP), IEEE, pp. 309-312, (2017). (Link)

  • Combining Bayesian Approaches and Evolutionary Techniques for the Inference of Breast Cancer Networks.
    Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Merelli, Daniele Ramazzotti. In Proceedings of the 8th International Joint Conference on Computational Intelligence (IJCCI). pp. 217-224, (2016). (Link)

  • A Machine Learning Approach for the Integration of miRNA-target Predictions.
    Stefano Beretta, Mauro Castelli, Yuliana Martínez, Luis Muñoz, Sara Silva, Leonardo Trujillo, Luciano Milanesi, Ivan Merelli. In 2016 24th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing (PDP), IEEE, pp. 528-534, (2016). (Link)

  • Gene Tree Correction by Leaf Removal and Modification: Tractability and Approximability.
    Stefano Beretta, Riccardo Dondi. In A. Beckmann et al. (Eds.): CiE 2014, LNCS 8493, pp. 42-52, (2014). (Link)

  • Covering Pairs in Directed Acyclic Graphs.
    Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola. In A.-H. Dediu et al. (Eds.): LATA 2014, LNCS 8370, pp. 126-137, (2014). (Link)

  • Reconstructing isoform graphs from RNA-Seq data.
    Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi. In Bioinformatics and Biomedicine (BIBM), 2012 IEEE International Conference, Philadelphia PA, USA, Oct. 4-7, (2012). (Link) (Presentation)


Editorials

  • 9th Workshop on Biomedical and Bioinformatics Challenges for Computer Science - BBC2016.
    Stefano Beretta, Mario Cannataro, Mauro Castelli. International Conference On Computational Science (ICCS). Procedia Computer Science, Vol 80:962-964, (2016). (Link)

  • 8th Workshop on Biomedical and Bioinformatics Challenges for Computer Science - BBC2015.
    Stefano Beretta, Mario Cannataro, Riccardo Dondi. International Conference On Computational Science (ICCS). Procedia Computer Science, Vol 51:680-682, (2015). (Link)