Publications

Journals

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

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

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

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

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

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

  • 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. HIV-1-mediated insertional activation of STAT5B and BACH2 trigger viral reservoir in T regulatory cells. Nature Communications, Vol. 8:498 (2017). (Link)

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

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

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

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

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

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

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

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

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


Conferences

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

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

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

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

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

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

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

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

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


Editorials

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

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


Abstracts

  • Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Ivan Merelli. A Logistic Model Tree Based Approach For eQTL Data Prediction Integration. In Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB): 13th International Meeting, Stirling, UK, Sept 1-3, (2016).

  • Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Fabrizio Benedicenti, Erika Tenderini, Alessandra Biffi, Eugenio Montini. New Graph-Based Algorithm for Comprehensive Identification and Tracking Retroviral Integration Sites. In: 19th Annual Meeting of the American-Society-of-Gene-and-Cell-Therapy (ASGCT), Washington, DC, May 2016. MOLECULAR THERAPY Vol 24:S214-S215. (Link)

  • Stefano Beretta, Yuri Pirola, Valeria Ranzani, Grazisa Rossetti, Raoul Bonnal, Raffaella Rizzi, Gianluca Della Vedova, Massimiliano Pagani, Paola Bonizzoni. A tool for the comparison of transcript differential expression analysis pipelines. In: 13th annual meeting of the Bioinformatics Italian Society (BITS), Univ. of Salerno, Italy, June 2016. PeerJ Preprints 4 (July 2016), e2212v1. (Link)

  • Andrea Calabria, Giulio Spinozzi, Stefano Brasca, Stefano Beretta, Ivan Merelli, Fabrizio Benedicenti, Erika Tenderini, Luciano Milanesi, Eugenio Montini. A New Bioinformatics Pipeline for Retroviral Integration Site Analysis in Hematopoietic Stem Cell Gene Therapy Applications. In: 12th annual meeting of the Bioinformatics Italian Society (BITS), Milan, Italy. 2015.

  • Yuri Pirola, Raffaella Rizzi, Stefano Beretta, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni. PIntronNext: a fast method for detecting the gene structure due to alternative splicing via ESTs, mRNAs, and RNA-Seq data. EURASNET Symposium on Regulation of Gene Expression through RNA Splicing, Trieste, Italy, March 24-27, 2012.

  • Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, and Gianluca Della Vedova. Identification of Alternative Splicing variants from RNA-seq Data. In: Next Generation Sequencing Workshop. Oct. 2011.

  • Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, and Gianluca Della Vedova. Alternative Splicing from RNA-seq Data without the Genome. In: ISMB/ECCB - 8th Special Interest Group meeting on Alternative Splicing (AS-SIG). July 2011.


Posters

  • Stefano Beretta, Valentina Giansanti, Carlo Maj, Mauro Castelli, Ivo Gonçalves, and Ivan Merelli. HappyMirna: a Library to Integrate miRNA-Target Predictions using Machine Learning Techniques. In: Intelligent Systems for Molecular Biology (ISBM), Chicago, USA, 2018.

  • Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, and Paola Bonizzoni. ASGAL: Aligning RNA-Seq Data to a Splicing Graph to Detect Novel Alternative Splicing Events. In: Research in Computational Molecular Biology (RECOMB), Paris, France, 2018.

  • Stefano Beretta, Ivan Merelli, Alessandra Mezzelani, Maria Giulia Pini, Martina Landini, Nandia Galluccio, Maria Elisabetta Raggi, Anna Marabotti, Luciano Milanesi. An integrative approach to discover changes in the association of miRNA and target genes. In: 12th annual meeting of the Bioinformatics Italian Society (BITS), Milan, Italy, 2015.

  • Anna Paola Carrieri, Stefano Beretta, Gianluca Della Vedova, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi, Graziano Pesole, Paola Bonizzoni. An in-silico framework for comparing and validating transcripts predicted from single and paired-end reads. Next Generation Sequencing Workshop, Bari, Italy, Dec. 5-7, 2012.

  • Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi. Alternative Splicing from RNA-seq Data without the Genome. ISMB/ECCB - 8th Special Interest Group meeting on Alternative Splicing (AS-SIG), Vienna, Austria, July 15-16, (2011). (Poster)


Talks

  • Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi. Identification of Alternative Splicing variants from RNA-seq Data. Next Generation Sequencing Workshop, Bari, Italy, Oct. 12-14, (2011). (Presentation)

  • Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi. Alternative Splicing from RNA-seq Data without the Genome. ISMB/ECCB - 8th Special Interest Group meeting on Alternative Splicing (AS-SIG), Vienna, Austria, July 15-16, (2011). (Presentation)


PhD Thesis

  • Stefano Beretta. Algorithms for next generation sequencing data analysis. Univ. degli Studi di Milano-Bicocca, Milano, Italy, 2013. (Thesis)