Abstracts & Posters

Abstracts

Assessing Stealth and Sensed Base Editing in Human Hematopoietic Stem/Progenitor Cells.
M. Fiumara, S. Ferrari, A. Omer, S. Beretta, L. Albano, I. Merelli, L. Naldini. In Blood, Vol 138 (Supplement_1), p. 3976, November 2021. (Link)
Therapy-Induced Senescence As an Anti-Cancer and Immune-Stimulatory Strategy.
D. Gilioli, S. Fusco, K. Giannetti, V. Gambacorta, T. Tavella, C. Liberatore, S. Beretta, M. Schönlein, I. Merelli, F. Ciceri, L. Vago, C. A Schmitt, R. Di Micco. In Blood, Vol 138 (Supplement_1), p. 4419, November 2021. (Link)
Triggering P53 Activation and Trapping of Transcriptionally Active Recombinant AAV Sequences Are Inadvertent Consequences of HSC Genome Editing.
S. Ferrari, A. Jacob, M. Laugel, V. Blouin, S. Beretta, V. Vavassori, L. Albano, I. Merelli, E. Ayuso, O. Adjali, M. Penaud-Budloo, P. Genovese, L. Naldini. In MOLECULAR THERAPY, Vol. 29, no. 4, pp. 95-96, 2021.
Inducible Tumor-Targeted Interferon-alpha Gene Therapy Inhibits Glioblastoma Multiforme in Mouse Model without Adverse Systemic Effects.
F. Birocchi, M. Cusimano, F. Rossari, S. Beretta, A. Ranghetti, M. Genua, R. Ostuni, S. Colombo, I. Merelli, P. Rancoita, B. Costa, A. Peter, N. Coltella, L. Naldini. In MOLECULAR THERAPY, Vol. 29, no. 4, pp. 57-58, 2021.
Dissecting the Transcriptional and Epigenetic Landscape of hiPSC-Derived Neural Stem and Progenitor Cells: Implications for Cell Therapy Approaches.
V. Meneghini, M. Luciani, C. Garsia, L. Petiti, I. Cifola, S. Beretta, I. Merelli, C. Peano, A. Miccio, A. Gritti. In MOLECULAR THERAPY, Vol. 29, no. 4, pp. 70, 2021.
Gene-Based Immune Reprogramming Overcomes the Immunosuppressive Microenvironment of Liver Metastases and Enables Protective T Cell Responses.
T. Kerzel, F. Pedica, S. Beretta, E. Scarmadella, T. Canu, R. Norata, L. Sergi Sergi, M. Genua, R. Ostuni, A. Kajaste-Rudnitski, A. Esposito, M. Oshima, F. Sanvito, M.L. Squadrito, L. Naldini. In MOLECULAR THERAPY, Vol. 29, no. 4, pp. 57, 2021.
Clonal Tracking Uncovers Barriers and Validates New Strategies to Enhance Gene Editing in Human Hematopoietic Stem Cells.
A. Jacob, S. Ferrari, S. Beretta, G. Unali, L. Albano, V. Vavassori, D. Cittaro, D. Lazarevic, C. Brombin, F. Cugnata, A. Kajaste-Rudnitski, I. Merelli, P. Genovese, L. Naldini. In MOLECULAR THERAPY, Vol. 28, no. 4, pp. 4-5, 2020.
BAR-seq: a Novel Barcode Strategy to Track Clones in Human Edited Hematopoietic Stem Cells.
S. Ferrari, A. Jacob, S. Beretta, D. Cittaro, L. Albano, G. Unali, V. Vavassori, D. Lazarevic, C. Brombin, F. Cugnata, A. Kajaste-Rudnitski, I. Merelli, P. Genovese, L. Naldini. In: Research in Computational Molecular Biology (RECOMB), Italy, 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.
V. Gambacorta, D. Gnani, L. Zito, S. Beretta, L. Zanotti, O. Giacomo, D. Cittaro, I. Merelli, F. Ciceri, R. Di Micco, L. Vago. In Blood, Vol 134 (Supplement_1), p. 514, November 2019. (Link)
Longitudinal Tracking of Acute Myeloid Leukemia Stem Cells in Xenografts and Patients By microRNA Reporters and Single Cell RNA Sequencing.
M. Naldini, G. Casirati, M. Barcella, S. Beretta, I. Merelli, C. Caserta, G. Desantis, F. Pavesi, F. Ciceri, B. Gentner. In Blood, Vol 134 (Supplement_1), p. 916, November 2019. (Link)
Cell cycle “push-up” to boost targeted genome editing in hematopoietic stem cells.
A. Jacob, S. Ferrari, L. Albano, M. Fiumara, V. Vavassori, D. Cittaro, S. Beretta, D. Lazarevic, I. Merelli, L. Naldini, P. Genovese. In HUMAN GENE THERAPY, Vol. 30, no. 11, pp. A183-A183, 2019.
Impact of DNA damage response activation in haematopoietic stem and progenitor cells upon gene-targeting.
A. Conti, L. Della Volpe, G. Schiroli, S. Beretta, I. Merelli, P. Genovese, L. Naldini, R. Di Micco. In HUMAN GENE THERAPY, Vol. 29, no. 12, pp. A57-A57, 2018.
Single cell transcriptomic analysis of gene edited HSPC uncovers molecular targets to improve long-term cell repopulation ability.
G. Schiroli, S. Ferrari, A. Jacob, A. Conti, L. Albano, S. Beretta, I. Merelli, R. Di Micco, L. Naldini, P. Genovese. In HUMAN GENE THERAPY, Vol. 29, no. 12, pp. A104-A104, 2018.
A Logistic Model Tree Based Approach For eQTL Data Prediction Integration.
S. Beretta, M. Castelli, I. Gonçalves, I. Kel, I. Merelli. In Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB): 13th International Meeting, Stirling, UK, Sept 1-3, (2016).
New Graph-Based Algorithm for Comprehensive Identification and Tracking Retroviral Integration Sites.
A. Calabria, S. Beretta, I. Merelli, G. Spinozzi, S. Brasca, F. Benedicenti, E. Tenderini, A. Biffi, E. Montini. 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)
A tool for the comparison of transcript differential expression analysis pipelines.
S. Beretta, Y. Pirola, V. Ranzani, G. Rossetti, R. Bonnal, R. Rizzi, G. Della Vedova, M. Pagani, P. Bonizzoni. In: 13th annual meeting of the Bioinformatics Italian Society (BITS), Univ. of Salerno, Italy, June 2016. PeerJ Preprints 4 (July 2016), e2212v1. (Link)
A New Bioinformatics Pipeline for Retroviral Integration Site Analysis in Hematopoietic Stem Cell Gene Therapy Applications.
A. Calabria, G. Spinozzi, S. Brasca, S. Beretta, I. Merelli, F. Benedicenti, E. Tenderini, L. Milanesi, E. Montini. In: 12th annual meeting of the Bioinformatics Italian Society (BITS), Milan, Italy. 2015.
PIntronNext: a fast method for detecting the gene structure due to alternative splicing via ESTs, mRNAs, and RNA-Seq data.
Y. Pirola, R. Rizzi, S. Beretta, E. Picardi, G. Pesole, G. Della Vedova, P. Bonizzoni. EURASNET Symposium on Regulation of Gene Expression through RNA Splicing, Trieste, Italy, March 24-27, 2012.
Identification of Alternative Splicing variants from RNA-seq Data.
S. Beretta, P. Bonizzoni, R. Rizzi, G. Della Vedova. In: Next Generation Sequencing Workshop. Oct. 2011.
Alternative Splicing from RNA-seq Data without the Genome.
S. Beretta, P. Bonizzoni, R. Rizzi, G. Della Vedova. In: ISMB/ECCB - 8th Special Interest Group meeting on Alternative Splicing (AS-SIG). July 2011.

Posters

HappyMirna: a Library to Integrate miRNA-Target Predictions using Machine Learning Techniques.
S. Beretta, V. Giansanti, C. Maj, M. Castelli, I. Gonçalves, I. Merelli. In: Intelligent Systems for Molecular Biology (ISBM), Chicago, USA, 2018.
ASGAL: Aligning RNA-Seq Data to a Splicing Graph to Detect Novel Alternative Splicing Events.
L. Denti, R. Rizzi, S. Beretta, G. Della Vedova, M. Previtali, P. Bonizzoni. In: Research in Computational Molecular Biology (RECOMB), Paris, France, 2018.
An integrative approach to discover changes in the association of miRNA and target genes.
S. Beretta, I. Merelli, A. Mezzelani, M. Giulia Pini, M. Landini, N. Galluccio, M. Elisabetta Raggi, A. Marabotti, L. Milanesi. In: 12th annual meeting of the Bioinformatics Italian Society (BITS), Milan, Italy, 2015.
An in-silico framework for comparing and validating transcripts predicted from single and paired-end reads.
A. Paola Carrieri, S. Beretta, G. Della Vedova, E. Picardi, Y. Pirola, R. Rizzi, G. Pesole, P. Bonizzoni. Next Generation Sequencing Workshop, Bari, Italy, Dec. 5-7, 2012.
Alternative Splicing from RNA-seq Data without the Genome.
S. Beretta, P. Bonizzoni, G. Della Vedova, R. Rizzi. ISMB/ECCB - 8th Special Interest Group meeting on Alternative Splicing (AS-SIG), Vienna, Austria, July 15-16, (2011). (Poster)

Talks

Identification of Alternative Splicing variants from RNA-seq Data.
S. Beretta, P. Bonizzoni, G. Della Vedova, R. Rizzi. Next Generation Sequencing Workshop, Bari, Italy, Oct. 12-14, (2011). (Presentation)
Alternative Splicing from RNA-seq Data without the Genome.
S. Beretta, P. Bonizzoni, G. Della Vedova, R. Rizzi. ISMB/ECCB - 8th Special Interest Group meeting on Alternative Splicing (AS-SIG), Vienna, Austria, July 15-16, (2011). (Presentation)