Stefano Beretta

Senior Bioinformatician
TIGET — San Raffaele, Milan

Publications

  • Iron overload damages mitochondria and induces metabolic rewiring of hematopoietic stem cells towards glycolysis.
    Silvia Sighinolfi, Laura Cassina, Maria Rosa Lidonnici, Stefano Beretta, Davide Stefanoni, Mariangela Storto, Christina Mayerhofer, Trine A. Kristiansen, David T. Scadden, Ivan Merelli, Alessandra Boletta, Annamaria Aprile, Giuliana Ferrari. Blood, (2026). (Link)

  • Development and characterization of a model of mucopolysaccharidosis type IVA for evaluating therapies targeting bone disease.
    Margherita Berti, Selene Ceriotti, Ludovica Santi, Gaia Alberti, Stefano Beretta, et al. Disease Models & Mechanisms, Vol. 19(2):dmm052540, (2026).

  • TIGIT disruption rescues the antitumor activity of low avidity TCR-engineered T cells by increasing TCR signal strength.
    Martina Spiga, Alessia Potenza, Zulma Magnani, Stefano Beretta, Barbara Camisa, et al. Nature Communications, (2026).

  • Molecular and phenotypic blueprint of human hematopoiesis links proliferation stress to stem cell aging.
    Emanuele Lettera, Luca Basso-Ricci, Edoardo Carsana, Kety Giannetti, Teresa Tavella, Luca Seffin, Giacomo Farina, Nicolò Gualandi, Pamela Quaranta, Elena Lo Furno, Guido Pacini, Lucrezia della Volpe, Stefano Beretta, Anastasia Conti, et al. Journal of Experimental Medicine, Vol. 223(2):e20251805, (2025). (Link)

  • A cross-talk established by tumor-targeted cytokines rescues CAR T cell activity and engages host T cells against glioblastoma in mice.
    Federico Rossari, Giorgia Alvisi, Melania Cusimano, Stefano Beretta, Filippo Birocchi, et al. Science Translational Medicine, Vol. 17(805):eado9511, (2025).

  • Senescence and inflammation are unintended adverse consequences of CRISPR-Cas9/AAV6-mediated gene editing in hematopoietic stem cells.
    Anastasia Conti, Kety Giannetti, Federico Midena, Stefano Beretta, Nicolò Gualandi, et al. Cell Reports Medicine, Vol. 6(6), (2025).

  • Spatiotemporal liver dynamics shape hepatocellular heterogeneity and impact in vivo gene engineering.
    Michela Milani, Francesco Starinieri, Stefano Beretta, Marco Monti, Cesare Canepari, et al. Journal of Hepatology, (2025).

  • Tweaking lentiviral vector design balances efficacy and safety in liver-directed gene therapy for familial hypercholesterolemia.
    Cesare Canepari, Michela Milani, Sara Degl’Innocenti, Marco Monti, Monica Volpin, Stefano Beretta, et al. Molecular Therapy, (2025).

  • Reprogramming liver metastasis-associated macrophages toward an anti-tumoral phenotype through enforced miR-342 expression.
    Chiara Bresesti, Eleonora Carito, Marco Notaro, Giovanna Giacca, Sara Breggion, Thomas Kerzel, Carl Mirko Mercado, Stefano Beretta, Marco Monti, Ivan Merelli, et al. Cell Reports, Vol. 44(5), (2025).

  • In vivo armed macrophages curb liver metastasis through tumor-reactive T-cell rejuvenation.
    Marco Notaro, Maristella Borghetti, Chiara Bresesti, Giovanna Giacca, Thomas Kerzel, Carl Mirko Mercado, Stefano Beretta, Marco Monti, Ivan Merelli, et al. Nature Communications, Vol. 16(1):3471, (2025).

  • Identification of hepatocyte-primed cholangiocytes in the homeostatic liver by in vivo lentiviral gene transfer to mice and non-human primates.
    Michela Milani, Francesco Starinieri, Anna Fabiano, Stefano Beretta, Tiziana Plati, Cesare Canepari, et al. Cell Reports, Vol. 44(3), (2025).

  • Human iPSC-derived neural stem cells displaying radial glia signature exhibit long-term safety in mice.
    Marco Luciani, Chiara Garsia, Stefano Beretta, Ingrid Cifola, Clelia Peano, Ivan Merelli, Luca Petiti, Annarita Miccio, Vasco Meneghini, Angela Gritti. Nature Communications, Vol. 15(1):9433, (2024). (Link)

  • A p38 MAPK-ROS axis fuels proliferation stress and DNA damage during CRISPR-Cas9 gene editing in hematopoietic stem and progenitor cells.
    Lucrezia Della Volpe, Federico Midena, Roberta Vacca, Teresa Tavella, Laura Alessandrini, Giacomo Farina, Chiara Brandas, Elena Lo Furno, Kety Giannetti, Edoardo Carsana, Stefano Beretta, et al. Cell Reports Medicine, Vol. 5(11), (2024).

  • Transcriptomic analysis of BM-MSCs identified EGR1 as a transcription factor to fully exploit their therapeutic potential.
    Ludovica Santi, Stefano Beretta, Margherita Berti, Evelyn Oliva Savoia, Laura Passerini, Marilena Mancino, Giada De Ponti, Gaia Alberti, Pamela Quaranta, Luca Basso-Ricci, et al. Biochimica et Biophysica Acta (BBA) – Molecular Cell Research, Vol. 1871(8):119818, (2024).

  • VisualZoneR: A computational protocol to identify compartmental zones from single-cell spatial transcriptomics using R.
    Thomas Kerzel, Stefano Beretta, Luigi Naldini, Mario Leonardo Squadrito. STAR Protocols, Vol. 5:103196, (2024). (Link)

  • Genotoxic effects of base and prime editing in human hematopoietic stem cells.
    Martina Fiumara, Samuele Ferrari, Attya Omer-Javed, Stefano Beretta, Luisa Albano, Daniele Canarutto, Angelica Varesi, Chiara Gaddoni, Chiara Brombin, Federica Cugnata, Erika Zonari, Matteo Maria Naldini, Matteo Barcella, Bernhard Gentner, Ivan Merelli, Luigi Naldini. Nature Biotechnology, Vol. 42:877–891, (2024). (Link)

  • In vivo macrophage engineering reshapes the tumor microenvironment leading to eradication of liver metastases.
    Thomas Kerzel, Giovanna Giacca, Stefano Beretta, Chiara Bresesti, Marco Notaro, Giulia Maria Scotti, Chiara Balestrieri, Tamara Canu, Miriam Redegalli, Federica Pedica, Marco Genua, Renato Ostuni, Anna Kajaste-Rudnitski, Masanobu Oshima, Giovanni Tonon, Ivan Merelli, Luca Aldrighetti, Paolo Dellabona, Nadia Coltella, Claudio Doglioni, Paola M.V. Rancoita, Francesca Sanvito, Luigi Naldini, Mario Leonardo Squadrito. Cancer Cell, Vol. 41:1892–1910.e10, (2023). (Link)

  • InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration.
    Ivan Merelli, Stefano Beretta, Daniela Cesana, Alessandro Gennari, Fabrizio Benedicenti, Giulio Spinozzi, Daniele Cesini, Eugenio Montini, Daniele D’Agostino, Andrea Calabria. Database, Vol. 2023, (2023). (Link)

  • The transcription factor HIF2α partakes in the differentiation block of acute myeloid leukemia.
    Daniela Magliulo, Matilde Simoni, Carolina Caserta, Cristina Fracassi, Serena Belluschi, Kety Giannetti, Raffaella Pini, Ettore Zapparoli, Stefano Beretta, Martina Uggè, et al. EMBO Molecular Medicine, Vol. 15, (2023). (Link)

  • Lipid Nanoparticles Allow Efficient and Harmless Ex Vivo Gene Editing of Human Hematopoietic Cells.
    Valentina Vavassori, Samuele Ferrari, Stefano Beretta, Claudia Asperti, Luisa Albano, Andrea Annoni, Chiara Gaddoni, Angelica Varesi, Monica Soldi, Alessandro Cuomo, et al. Blood, (2023). (Link)

  • Mesenchymal stromal cells improve the transplantation outcome of CRISPR-Cas9 gene-edited human HSPCs.
    Stefania Crippa, Anastasia Conti, Valentina Vavassori, Samuele Ferrari, Stefano Beretta, Silvia Rivis, Roberto Bosotti, Serena Scala, Stefania Pirroni, Raisa Jofra-Hernandez, et al. Molecular Therapy, Vol. 31(1):230–248, (2023). (Link)

  • Choice of template delivery mitigates the genotoxic risk and adverse impact of editing in human hematopoietic stem cells.
    Samuele Ferrari, Aurelien Jacob, Daniela Cesana, Marianne Laugel, Stefano Beretta, Angelica Varesi, Giulia Unali, Anastasia Conti, Daniele Canarutto, Luisa Albano, et al. Cell Stem Cell, Vol. 29(10):1428–1444, (2022). (Link)

  • Targeted inducible delivery of immunoactivating cytokines reprograms glioblastoma microenvironment and inhibits growth in mouse models.
    Filippo Birocchi, Melania Cusimano, Federico Rossari, Stefano Beretta, Paola MV Rancoita, Anna Ranghetti, Stefano Colombo, Barbara Costa, Peter Angel, Francesca Sanvito, et al. Science Translational Medicine, Vol. 14(653):eabl4106, (2022). (Link)

  • Integrated Multiomic Profiling Identifies the Epigenetic Regulator PRC2 as a Therapeutic Target to Counteract Leukemia Immune Escape and Relapse.
    Valentina Gambacorta, Stefano Beretta, Martina Ciccimarra, Laura Zito, Kety Giannetti, Angela Andrisani, Daniela Gnani, Lucia Zanotti, Giacomo Oliveira, Matteo Giovanni Carrabba, Davide Cittaro, Ivan Merelli, Fabio Ciceri, Raffaella di Micco, Luca Vago. Cancer Discovery, (2022). (Link)

  • Oncogene-induced senescence in hematopoietic progenitors features myeloid restricted hematopoiesis, chronic inflammation and histiocytosis.
    Riccardo Biavasco, Emanuele Lettera, Kety Giannetti, Diego Gilioli, Stefano Beretta, Anastasia Conti, Serena Scala, Daniela Cesana, Pierangela Gallina, Margherita Norelli, Luca Basso-Ricci, Attilio Bondanza, Giulio Cavalli, Maurilio Ponzoni, Lorenzo Dagna, Claudio Doglioni, Alessandro Aiuti, Ivan Merelli, Raffaella Di Micco, Eugenio Montini. Nature Communications, Vol. 12:4559, (2021). (Link)

  • 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, Vol. 16:2991–3025, (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, 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, 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, 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, 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, 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. 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, (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, (2013). (Link)

  • 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 Studies.
    Valentina Giansanti, Stefano Beretta, Daniele Cesini, Daniele D’Agostino, Ivan Merelli. In 27th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, pp. 329–333, (2019). (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, Ivan Merelli. In 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 — AlCoB 2017, LNCS, 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 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 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 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 Computability in Europe (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 Language and Automata Theory and Applications (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 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia PA, USA, (2012). (Link)

Abstracts

  • Assessing Stealth and Sensed Base Editing in Human Hematopoietic Stem/Progenitor Cells.
    Martina Fiumara, Samuele Ferrari, Attya Omer, Stefano Beretta, Luisa Albano, Ivan Merelli, Luigi Naldini. Blood, Vol. 138:3976, (2021). (Link)

  • Therapy-Induced Senescence As an Anti-Cancer and Immune-Stimulatory Strategy.
    Diego Gilioli, Simona Fusco, Kety Giannetti, Valentina Gambacorta, Teresa Tavella, Carmine Liberatore, Stefano Beretta, Martin Schonlein, Ivan Merelli, Fabio Ciceri, Luca Vago, Clemens A. Schmitt, Raffaella Di Micco. Blood, Vol. 138:4419, (2021). (Link)

  • Triggering P53 Activation and Trapping of Transcriptionally Active Recombinant AAV Sequences Are Inadvertent Consequences of HSC Genome Editing.
    Samuele Ferrari, Aurelien Jacob, Marianne Laugel, Veronique Blouin, Stefano Beretta, Valentina Vavassori, Luisa Albano, Ivan Merelli, et al. Molecular Therapy, Vol. 29(4):95–96, (2021).

  • Inducible Tumor-Targeted Interferon-alpha Gene Therapy Inhibits Glioblastoma Multiforme in Mouse Model without Adverse Systemic Effects.
    Filippo Birocchi, Melania Cusimano, Federico Rossari, Stefano Beretta, Anna Ranghetti, Marco Genua, Renato Ostuni, Stefano Colombo, Ivan Merelli, Paola Rancoita, et al. Molecular Therapy, Vol. 29(4):57–58, (2021).

  • Dissecting the Transcriptional and Epigenetic Landscape of hiPSC-Derived Neural Stem and Progenitor Cells: Implications for Cell Therapy Approaches.
    Vasco Meneghini, Marco Luciani, Chiara Garsia, Luca Petiti, Ingrid Cifola, Stefano Beretta, Ivan Merelli, Clelia Peano, Annarita Miccio, Angela Gritti. Molecular Therapy, Vol. 29(4):70, (2021).

  • Gene-Based Immune Reprogramming Overcomes the Immunosuppressive Microenvironment of Liver Metastases and Enables Protective T Cell Responses.
    Thomas Kerzel, Federica Pedica, Stefano Beretta, Eloise Scarmadella, Tamara Canu, Rossana Norata, Lucia Sergi Sergi, Marco Genua, Renato Ostuni, Anna Kajaste-Rudnitski, et al. Molecular Therapy, Vol. 29(4):57, (2021).

  • Clonal Tracking Uncovers Barriers and Validates New Strategies to Enhance Gene Editing in Human Hematopoietic Stem Cells.
    Aurelien Jacob, Samuele Ferrari, Stefano Beretta, Giulia Unali, Luisa Albano, Valentina Vavassori, Davide Cittaro, Dejan Lazarevic, Chiara Brombin, Federica Cugnata, et al. Molecular Therapy, Vol. 28(4):4–5, (2020).

  • BAR-seq: a Novel Barcode Strategy to Track Clones in Human Edited Hematopoietic Stem Cells.
    Samuele Ferrari, Aurelien Jacob, Stefano Beretta, Davide Cittaro, Luisa Albano, Giulia Unali, Valentina Vavassori, Dejan Lazarevic, Chiara Brombin, Federica Cugnata, Anna Kajaste-Rudnitski, Ivan Merelli, Pietro Genovese, Luigi Naldini. Research in Computational Molecular Biology (RECOMB), (2020).

  • Integrated Epigenetic Profiling Identifies EZH2 As a Therapeutic Target to Re-Establish Immune Recognition of Leukemia Relapses with Loss of HLA Class II Expression.
    Valentina Gambacorta, Daniela Gnani, Laura Zito, Stefano Beretta, Lucia Zanotti, Giacomo Oliveira, Davide Cittaro, Ivan Merelli, Fabio Ciceri, Raffaella Di Micco, Luca Vago. Blood, Vol. 134(Suppl. 1):514, (2019). (Link)

  • Longitudinal Tracking of Acute Myeloid Leukemia Stem Cells in Xenografts and Patients By microRNA Reporters and Single Cell RNA Sequencing.
    Matteo Maria Naldini, Gabriele Casirati, Matteo Barcella, Stefano Beretta, Ivan Merelli, Carolina Caserta, Giacomo Desantis, Francesca Pavesi, Fabio Ciceri, Bernhard Gentner. Blood, Vol. 134(Suppl. 1):916, (2019). (Link)

  • Cell cycle “push-up” to boost targeted genome editing in hematopoietic stem cells.
    Aurelien Jacob, Samuele Ferrari, Luisa Albano, Martina Fiumara, Valentina Vavassori, Davide Cittaro, Stefano Beretta, Dejan Lazarevic, Ivan Merelli, Luigi Naldini, et al. Human Gene Therapy, Vol. 30(11):A183, (2019).

  • Impact of DNA damage response activation in haematopoietic stem and progenitor cells upon gene-targeting.
    Anastasia Conti, Lucrezia della Volpe, Giulia Schiroli, Stefano Beretta, Ivan Merelli, Pietro Genovese, Luigi Naldini, Raffaella Di Micco. Human Gene Therapy, Vol. 29(12):A57, (2018).

  • Single cell transcriptomic analysis of gene edited HSPC uncovers molecular targets to improve long-term cell repopulation ability.
    Giulia Schiroli, Samuele Ferrari, Aurelien Jacob, Anastasia Conti, Luisa Albano, Stefano Beretta, Ivan Merelli, Raffaella Di Micco, Luigi Naldini, Pietro Genovese. Human Gene Therapy, Vol. 29(12):A104, (2018).

  • A Logistic Model Tree Based Approach For eQTL Data Prediction Integration.
    Stefano Beretta, Mauro Castelli, Ivo Gonçalves, Ivan Kel, Ivan Merelli. CIBB — 13th International Meeting, Stirling, UK, (2016).

  • A tool for the comparison of transcript differential expression analysis pipelines.
    Stefano Beretta, Yuri Pirola, Valeria Ranzani, Grazisa Rossetti, Raoul Bonnal, Raffaella Rizzi, Gianluca Della Vedova, Massimiliano Pagani, Paola Bonizzoni. BITS — 13th Annual Meeting, Salerno, Italy, (2016). (Link)

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

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

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

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

Posters

  • HaploVir: Inferring Viral Haplotypes from Deep Sequencing of a Mixture of Strains using a Path Decomposition Algorithm.
    Stefano Beretta, Paola Bonizzoni, Andrea Calabria, Daniela Cesana, Ivan Merelli. Intelligent Systems for Molecular Biology (ISMB), (2018).

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

  • 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, Paola Bonizzoni. Research in Computational Molecular Biology (RECOMB), (2018). (Link)

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

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

  • Graph Isomorphism.
    Riccardo Dondi, Stefano Beretta, et al. In Encyclopedia of Bioinformatics and Computational Biology, Vol. 2, pp. 509–517. Elsevier, (2025).

  • Graph Algorithms.
    Riccardo Dondi, Stefano Beretta, et al. In Encyclopedia of Bioinformatics and Computational Biology, Vol. 2, pp. 518–531. Elsevier, (2025).

  • Graph theory and definitions.
    Stefano Beretta, Luca Denti, Marco Previtali. In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Vol. 1, pp. 922–927. Elsevier, (2019). (Link)

  • Network properties.
    Stefano Beretta, Luca Denti, Marco Previtali. In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Vol. 1, pp. 928–932. Elsevier, (2019). (Link)

  • Algorithms for strings and sequences: Pairwise alignment.
    Stefano Beretta. In Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Vol. 1, pp. 22–29. Elsevier, (2019). (Link)

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

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