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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. Among authors: rizzi r. 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.
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: rizzi r. BMC Bioinformatics. 2018 Nov 20;19(1):444. doi: 10.1186/s12859-018-2436-3. BMC Bioinformatics. 2018. PMID: 30458725 Free PMC article.
Transcriptome assembly and alternative splicing analysis.
Bonizzoni P, Della Vedova G, Pesole G, Picardi E, Pirola Y, Rizzi R. Bonizzoni P, et al. Among authors: rizzi r. Methods Mol Biol. 2015;1269:173-88. doi: 10.1007/978-1-4939-2291-8_11. Methods Mol Biol. 2015. PMID: 25577379
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text.
Pirola Y, Rizzi R, Picardi E, Pesole G, Della Vedova G, Bonizzoni P. Pirola Y, et al. Among authors: rizzi r. BMC Bioinformatics. 2012 Apr 12;13 Suppl 5(Suppl 5):S2. doi: 10.1186/1471-2105-13-S5-S2. BMC Bioinformatics. 2012. PMID: 22537006 Free PMC article.
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing.
Martelli PL, D'Antonio M, Bonizzoni P, Castrignanò T, D'Erchia AM, D'Onorio De Meo P, Fariselli P, Finelli M, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Rizzi R, Rossi I, Valletti A, Zauli A, Zambelli F, Casadio R, Pesole G. Martelli PL, et al. Among authors: rizzi r. Nucleic Acids Res. 2011 Jan;39(Database issue):D80-5. doi: 10.1093/nar/gkq1073. Epub 2010 Nov 4. Nucleic Acids Res. 2011. PMID: 21051348 Free PMC article.
Computational methods for alternative splicing prediction.
Bonizzoni P, Rizzi R, Pesole G. Bonizzoni P, et al. Among authors: rizzi r. Brief Funct Genomic Proteomic. 2006 Mar;5(1):46-51. doi: 10.1093/bfgp/ell011. Epub 2006 Feb 20. Brief Funct Genomic Proteomic. 2006. PMID: 16769678 Review.
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences.
Bonizzoni P, Rizzi R, Pesole G. Bonizzoni P, et al. Among authors: rizzi r. BMC Bioinformatics. 2005 Oct 5;6:244. doi: 10.1186/1471-2105-6-244. BMC Bioinformatics. 2005. PMID: 16207377 Free PMC article.
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.
Castrignanò T, Rizzi R, Talamo IG, De Meo PD, Anselmo A, Bonizzoni P, Pesole G. Castrignanò T, et al. Among authors: rizzi r. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W440-3. doi: 10.1093/nar/gkl324. Nucleic Acids Res. 2006. PMID: 16845044 Free PMC article.
Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array.
Bonizzoni P, Della Vedova G, Pirola Y, Previtali M, Rizzi R. Bonizzoni P, et al. Among authors: rizzi r. J Comput Biol. 2019 Sep;26(9):948-961. doi: 10.1089/cmb.2018.0230. Epub 2019 May 29. J Comput Biol. 2019. PMID: 31140836
FSG: Fast String Graph Construction for De Novo Assembly.
Bonizzoni P, Vedova GD, Pirola Y, Previtali M, Rizzi R. Bonizzoni P, et al. Among authors: rizzi r. J Comput Biol. 2017 Oct;24(10):953-968. doi: 10.1089/cmb.2017.0089. Epub 2017 Jul 17. J Comput Biol. 2017. PMID: 28715269
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