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Modeling alternative splicing variants from RNA-Seq data with isoform graphs.
Beretta S, Bonizzoni P, Vedova GD, Pirola Y, Rizzi R. Beretta S, et al. J Comput Biol. 2014 Jan;21(1):16-40. doi: 10.1089/cmb.2013.0112. Epub 2013 Nov 7. J Comput Biol. 2014. PMID: 24200390 Free PMC article.
Further steps in TANGO: improved taxonomic assignment in metagenomics.
Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G. Alonso-Alemany D, et al. Among authors: beretta s. Bioinformatics. 2014 Jan 1;30(1):17-23. doi: 10.1093/bioinformatics/btt256. Epub 2013 May 3. Bioinformatics. 2014. PMID: 23645816
SPIRE, a modular pipeline for eQTL analysis of RNA-Seq data, reveals a regulatory hotspot controlling miRNA expression in C. elegans.
Kel I, Chang Z, Galluccio N, Romeo M, Beretta S, Diomede L, Mezzelani A, Milanesi L, Dieterich C, Merelli I. Kel I, et al. Among authors: beretta s. Mol Biosyst. 2016 Oct 18;12(11):3447-3458. doi: 10.1039/c6mb00453a. Mol Biosyst. 2016. PMID: 27722582
VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.
Spinozzi G, Calabria A, Brasca S, Beretta S, Merelli I, Milanesi L, Montini E. Spinozzi G, et al. Among authors: beretta s. BMC Bioinformatics. 2017 Nov 25;18(1):520. doi: 10.1186/s12859-017-1937-9. BMC Bioinformatics. 2017. PMID: 29178837 Free PMC article.
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads.
Beretta S, Patterson MD, Zaccaria S, Della Vedova G, Bonizzoni P. Beretta S, et al. BMC Bioinformatics. 2018 Jul 3;19(1):252. doi: 10.1186/s12859-018-2253-8. BMC Bioinformatics. 2018. PMID: 29970002 Free PMC article.
Improving eQTL Analysis Using a Machine Learning Approach for Data Integration: A Logistic Model Tree Solution.
Beretta S, Castelli M, Gonçalves I, Kel I, Giansanti V, Merelli I. Beretta S, et al. J Comput Biol. 2018 Oct;25(10):1091-1105. doi: 10.1089/cmb.2017.0167. Epub 2018 Jul 27. J Comput Biol. 2018. PMID: 30052049
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events.
Denti L, Rizzi R, Beretta S, Vedova GD, Previtali M, Bonizzoni P. Denti L, et al. Among authors: beretta s. BMC Bioinformatics. 2018 Nov 20;19(1):444. doi: 10.1186/s12859-018-2436-3. BMC Bioinformatics. 2018. PMID: 30458725 Free PMC article.
HIV-1-mediated insertional activation of STAT5B and BACH2 trigger viral reservoir in T regulatory cells.
Cesana D, Santoni de Sio FR, Rudilosso L, Gallina P, Calabria A, Beretta S, Merelli I, Bruzzesi E, Passerini L, Nozza S, Vicenzi E, Poli G, Gregori S, Tambussi G, Montini E. Cesana D, et al. Among authors: beretta s. Nat Commun. 2017 Sep 8;8(1):498. doi: 10.1038/s41467-017-00609-1. Nat Commun. 2017. PMID: 28887441 Free PMC article.
Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response.
Schiroli G, Conti A, Ferrari S, Della Volpe L, Jacob A, Albano L, Beretta S, Calabria A, Vavassori V, Gasparini P, Salataj E, Ndiaye-Lobry D, Brombin C, Chaumeil J, Montini E, Merelli I, Genovese P, Naldini L, Di Micco R. Schiroli G, et al. Among authors: beretta s. Cell Stem Cell. 2019 Apr 4;24(4):551-565.e8. doi: 10.1016/j.stem.2019.02.019. Epub 2019 Mar 21. Cell Stem Cell. 2019. PMID: 30905619 Free PMC article.
DSM-5 Alternative Model of Personality Disorder Dysfunctional Personality Traits as Predictors of Self-Reported Aggression in an Italian Sample of Consecutively Admitted, Personality-Disordered Psychotherapy Patients.
Somma A, Krueger RF, Markon KE, Alajmo VBM, Arlotta E, Beretta S, Boni F, Busso SL, Manini R, Nazzaro G, Maffei C, Fossati A. Somma A, et al. Among authors: beretta s. J Pers Disord. 2019 Jun 17:1-20. doi: 10.1521/pedi_2019_33_430. Online ahead of print. J Pers Disord. 2019. PMID: 31206343
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