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2010 – today
- 2018
[j14]Luca Denti, Raffaella Rizzi, Stefano Beretta, Gianluca Della Vedova, Marco Previtali, Paola Bonizzoni:
ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events. BMC Bioinformatics 19(1): 444:1-444:21 (2018)- [c9]Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Divide and Conquer Computation of the Multi-string BWT and LCP Array. CiE 2018: 107-117 - 2017
- [j13]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
An External-Memory Algorithm for String Graph Construction. Algorithmica 78(2): 394-424 (2017) - [j12]Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco:
Species-Driven Persistent Phylogeny. Fundam. Inform. 154(1-4): 47-63 (2017) - [j11]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
FSG: Fast String Graph Construction for De Novo Assembly. Journal of Computational Biology 24(10): 953-968 (2017) - [j10]Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco:
A colored graph approach to perfect phylogeny with persistent characters. Theor. Comput. Sci. 658: 60-73 (2017) - [c8]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. AlCoB 2017: 49-61 - [c7]Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez:
Character-Based Phylogeny Construction and Its Application to Tumor Evolution. CiE 2017: 3-13 - [i5]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Computing the BWT and LCP array of a Set of Strings in External Memory. CoRR abs/1705.07756 (2017) - 2016
- [j9]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
LSG: An External-Memory Tool to Compute String Graphs for Next-Generation Sequencing Data Assembly. Journal of Computational Biology 23(3): 137-149 (2016) - [c6]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. ISBRA 2016: 27-39 - [i4]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data. CoRR abs/1604.03587 (2016) - [i3]Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia, Marco Previtali, Raffaella Rizzi:
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings. CoRR abs/1607.08342 (2016) - 2014
- [j8]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 21(1): 16-40 (2014) - [c5]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. WABI 2014: 311-325 - [i2]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. CoRR abs/1405.7520 (2014) - 2012
- [j7]Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni:
PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text. BMC Bioinformatics 13(S-5): S2 (2012) - [c4]Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova:
Reconstructing isoform graphs from RNA-Seq data. BIBM 2012: 1-4 - 2011
- [j6]Pier Luigi Martelli, Mattia D'Antonio, Paola Bonizzoni, Tiziana Castrignanò, Anna Maria D'Erchia, Paolo D'Onorio De Meo, Piero Fariselli, Michele Finelli, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, Raffaella Rizzi, Ivan Rossi, Alessio Valletti, Andrea Zauli, Federico Zambelli, Rita Casadio, Graziano Pesole:
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing. Nucleic Acids Research 39(Database-Issue): 80-85 (2011) - [c3]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi:
PIntron: A fast method for gene structure prediction via maximal pairings of a pattern and a text. ICCABS 2011: 33-39 - [i1]Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Raffaella Rizzi:
Predicting Variants of Alternative Splicing from NGS data without the Genome. CoRR abs/1108.0047 (2011)
2000 – 2009
- 2009
- [j5]Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi:
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. Journal of Computational Biology 16(1): 43-66 (2009) - [c2]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi:
Minimum Factorization Agreement of Spliced ESTs. WABI 2009: 1-12 - 2008
- [j4]Tiziana Castrignanò, Mattia D'Antonio, Anna Anselmo, Danilo Carrabino, A. D'Onorio De Meo, Anna Maria D'Erchia, Flavio Licciulli, Marina Mangiulli, Flavio Mignone, Giulio Pavesi, Ernesto Picardi, Alberto Riva, Raffaella Rizzi, Paola Bonizzoni, Graziano Pesole:
ASPicDB: A database resource for alternative splicing analysis. Bioinformatics 24(10): 1300-1304 (2008) - 2007
- [j3]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette:
Exemplar Longest Common Subsequence. IEEE/ACM Trans. Comput. Biology Bioinform. 4(4): 535-543 (2007) - 2006
- [j2]Tiziana Castrignanò, Raffaella Rizzi, Ivano Giuseppe Talamo, Paolo D'Onorio De Meo, Anna Anselmo, Paola Bonizzoni, Graziano Pesole:
ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization. Nucleic Acids Research 34(Web-Server-Issue): 440-443 (2006) - 2005
- [j1]Paola Bonizzoni, Raffaella Rizzi, Graziano Pesole:
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics 6: 244 (2005) - 2003
- [c1]Paola Bonizzoni, Graziano Pesole, Raffaella Rizzi:
A Method to Detect Gene Structure and Alternative Splice Sites by Agreeing ESTs to a Genomic Sequence. WABI 2003: 63-77
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