- Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez:
Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. BCB 2017: 1-10 - Gianluca Della Vedova, Murray Patterson, Raffaella Rizzi, Mauricio Soto Gomez:
Character-Based Phylogeny Construction and Its Application to Tumor Evolution. CiE 2017: 3-13 - 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
- 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. J. Comput. Biol. 23(3): 137-149 (2016) - Jon C. Ison, Kristoffer Rapacki, Hervé Ménager, Matús Kalas, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan M. Bolser, Tim Booth, Anthony Bretaudeau, Jan Brezovsky, Rita Casadio, Gianni Cesareni, Frederik Coppens, Michael Cornell, Gianmauro Cuccuru, Kristian Davidsen, Gianluca Della Vedova, Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn A. Grüning, Manuela Helmer-Citterich, Hans Ienasescu, Vassilios Ioannidis, Martin Closter Jespersen, Rafael C. Jiménez, Nick S. Juty, Peter Juvan, Maximilian Koch, Camille Laibe, Jing-Woei Li, Luana Licata, Fabien Mareuil, Ivan Micetic, Rune Møllegaard Friborg, Sébastien Moretti, Chris Morris, Steffen Möller, Aleksandra Nenadic, Hedi Peterson, Giuseppe Profiti, Peter M. Rice, Paolo Romano, Paola Roncaglia, Rabie Saidi, Andrea Schafferhans, Veit Schwämmle, Callum Smith, Maria Maddalena Sperotto, Heinz Stockinger, Radka Svobodová Vareková, Silvio C. E. Tosatto, Victor de la Torre, Paolo Uva, Allegra Via, Guy Yachdav, Federico Zambelli, Gert Vriend, Burkhard Rost, Helen E. Parkinson, Peter Løngreen, Søren Brunak:
Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Res. 44(Database-Issue): 38-47 (2016) - 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 - 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) - 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) - Paola Bonizzoni, Gianluca Della Vedova, Gabriella Trucco:
Solving the Persistent Phylogeny Problem in polynomial time. CoRR abs/1611.01017 (2016) - 2014
- Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi:
Modeling Alternative Splicing Variants from RNA-Seq Data with Isoform Graphs. J. Comput. Biol. 21(1): 16-40 (2014) - Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. WABI 2014: 311-325 - Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Riccardo Dondi, Teresa M. Przytycka:
When and How the Perfect Phylogeny Model Explains Evolution. Discrete and Topological Models in Molecular Biology 2014: 67-83 - Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco:
Algorithms for the Constrained Perfect Phylogeny with Persistent Characters. CoRR abs/1405.7497 (2014) - Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. CoRR abs/1405.7520 (2014) - 2013
- Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Parameterized complexity of k-anonymity: hardness and tractability. J. Comb. Optim. 26(1): 19-43 (2013) - Yuri Pirola, Gianluca Della Vedova, Paola Bonizzoni, Alessandra Stella, Filippo Biscarini:
Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. BCB 2013: 33 - 2012
- 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 Bioinform. 13(S-5): S2 (2012) - Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni:
A Fast and Practical Approach to Genotype Phasing and Imputation on a Pedigree with Erroneous and Incomplete Information. IEEE ACM Trans. Comput. Biol. Bioinform. 9(6): 1582-1594 (2012) - Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
A randomized PTAS for the minimum Consensus Clustering with a fixed number of clusters. Theor. Comput. Sci. 429: 36-45 (2012) - Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova:
Reconstructing isoform graphs from RNA-Seq data. BIBM 2012: 1-4 - Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni:
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information. ICCABS 2012: 1-6 - Paola Bonizzoni, Peter J. Cameron, Gianluca Della Vedova, Alberto Leporati, Giancarlo Mauri:
A Unifying Framework to Characterize the Power of a Language to Express Relations. CoRR abs/1203.4732 (2012) - 2011
- Paul M. Ruegger, Gianluca Della Vedova, Tao Jiang, James Borneman:
Improving Probe Set Selection for Microbial Community Analysis by Leveraging Taxonomic Information of Training Sequences. BMC Bioinform. 12: 394 (2011) - Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
Anonymizing binary and small tables is hard to approximate. J. Comb. Optim. 22(1): 97-119 (2011) - 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 - Yuri Pirola, Gianluca Della Vedova, Stefano Biffani, Alessandra Stella, Paola Bonizzoni:
Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers. CoRR abs/1107.3724 (2011) - 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) - 2010
- Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri:
Fingerprint Clustering with Bounded Number of Missing Values. Algorithmica 58(2): 282-303 (2010) - Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Variants of constrained longest common subsequence. Inf. Process. Lett. 110(20): 877-881 (2010) - Gianluca Della Vedova, Riccardo Dondi, Tao Jiang, Giulio Pavesi, Yuri Pirola, Lusheng Wang:
Beyond evolutionary trees. Nat. Comput. 9(2): 421-435 (2010)