Yuri Pirola – Publications

(A preprint version of the following papers and articles is available upon request)

Journal Articles (with peer-review)

P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali, and R. Rizzi.
An External-Memory Algorithm for String Graph Construction.
Algorithmica (in press). [url]

P. Bonizzoni, R. Dondi, G. W. Klau, Y. Pirola, N. Pisanti, and S. Zaccaria.
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes.
Journal of Computational Biology (in press). [url]

R. Palorini, G. Votta, Y. Pirola, H. De Vitto, S. De Palma, C. Airoldi, M. Vasso, F. Ricciardiello, P. P. Lombardi, C. Cirulli, R. Rizzi, F. Nicotra, K. Hiller, C. Gelfi, L. Alberghina, and F. Chiaradonna.
Protein Kinase A Activation Promotes Cancer Cell Resistance to Glucose Starvation and Anoikis.
PLoS Genetics 12.3 (2016), 1–41. [url]

P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali, and R. Rizzi.
LSG: An External-Memory Tool to Compute String Graphs for NGS Data Assembly.
Journal of Computational Biology 23.3 (2016), 137–149. [url]

Y. Pirola, S. Zaccaria, R. Dondi, G. W. Klau, N. Pisanti, and P. Bonizzoni.
HapCol: Accurate and Memory-Efficient Haplotype Assembly from Long Reads.
Bioinformatics 32.11 (2016), 1610–1617. [url]

N. Beerenwinkel, S. Beretta, P. Bonizzoni, R. Dondi, and Y. Pirola.
Covering Pairs in Directed Acyclic Graphs.
The Computer Journal 58.7 (2015), 1673–1686. [url]

C. Batini, P. Bonizzoni, M. Comerio, R. Dondi, Y. Pirola, and F. Salandra.
A Clustering Algorithm for Planning the Integration Process of a Large Number of Conceptual Schemas.
Journal of Computer Science and Technology 30.1 (2015), 214–224. [url]

S. Beretta, P. Bonizzoni, G. Della Vedova, Y. Pirola, and R. Rizzi.
Modeling alternative splicing variants from RNA-Seq data with isoform graphs.
Journal of Computational Biology 21.1 (2014), 16-40. [url]

P. Bonizzoni, G. Della Vedova, R. Dondi, and Y. Pirola.
Parameterized complexity of k-anonymity: hardness and tractability.
Journal of Combinatorial Optimization 26.1 (2013), 19-43. [url]

P. Bonizzoni, R. Dondi, and Y. Pirola.
Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability.
Algorithms 6.1 (2013), 1-11. [url]

Y. Pirola, G. Della Vedova, S. Biffani, A. Stella, and P. Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 9.6 (2012), 1582-1594. [url]

Y. Pirola, R. Rizzi, E. Picardi, G. Pesole, G. Della Vedova, and P. 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.S5 (2012). [url]

Y. Pirola, P. Bonizzoni, and T. Jiang.
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 9.1 (2012), 9-25. [url]

L. Vanneschi, Y. Pirola, G. Mauri, M. Tomassini, P. Collard, and S. Verel.
A study of the neutrality of Boolean function landscapes in genetic programming.
Theoretical Computer Science 425 (2012), 34-57. [url]

P. Bonizzoni, G. Della Vedova, R. Dondi, and Y. Pirola.
Variants of constrained longest common subsequence.
Information Processing Letters 110.20 (2010), 877-881. [arXiv version] [url]

P. Bonizzoni, G. Della Vedova, R. Dondi, Y. Pirola, and R. Rizzi.
Pure Parsimony Xor Haplotyping.
IEEE/ACM Transactions on Computational Biology and Bioinformatics 7.4 (2010), 598-610. [url]

G. Della Vedova, R. Dondi, T. Jiang, G. Pavesi, Y. Pirola, and L. Wang.
Beyond Evolutionary Trees.
Natural Computing 9.2 (2009), 421-435. [url]

P. Bonizzoni, G. Mauri, G. Pesole, E. Picardi, Y. Pirola, and R. Rizzi.
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach.
Journal of Computational Biology 16.1 (2009), 43-66. [url]

In Proceedings (with peer-review)

P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali, and R. Rizzi.
FSG: Fast String Graph Construction for De Novo Assembly of reads data.
In: Bioinformatics Research and Applications, 12th International Symposium, ISBRA 2016, Minsk, Belarus, June 5-8, 2016, Proceedings Vol. 9683. LNCS. Springer, 2016, 27–39. [url]

P. Bonizzoni, R. Dondi, G. W. Klau, Y. Pirola, N. Pisanti, and S. Zaccaria.
On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction problem.
In: Proc. of the 26th Annual Symp. on Combinatorial Pattern Matching, CPM 2015, Ischia Island, IT, June 29–July 1, 2015. Vol. 9133. LNCS. Springer, 2015, 100–113. [url]

P. Bonizzoni, G. Della Vedova, Y. Pirola, M. Previtali, and R. Rizzi.
Constructing String Graphs in External Memory.
In: Proc. of the 14th Int. Workshop on Algorithms in Bioinformatics, WABI 2014, Wrocław, PL, Sept. 8–10, 2014. Vol. 8701. LNCS. Springer, 2014, 311–325. [url]

N. Beerenwinkel, S. Beretta, P. Bonizzoni, R. Dondi, and Y. Pirola.
Covering pairs in directed acyclic graphs.
In Language and Automata Theory and Applications, 8th Int. Conference, LATA 2014, Madrid, Spain, March 10-14, Proceedings. Springer. Vol. 8370 pp. 126-137 (2014). [url]

Y. Pirola, G. Della Vedova, P. Bonizzoni, A. Stella, and F. Biscarini.
Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes.
In Bioinformatics, Computational Biology, and Biomedical Informatics, 4th ACM Int. Conference, ACM BCB 2013, Washington DC, USA, Sept. 22-25. ACM. pp. 33-41 (2013). [url]

Y. Pirola, G. Della Vedova, S. Biffani, A. Stella, and P. Bonizzoni.
A fast and practical approach to genotype phasing and imputation on a pedigree with erroneous and incomplete information.
In Computational Advances in Bio and medical Sciences, 2nd IEEE Int. Conference, ICCABS 2012, Las Vegas NV, USA, Feb. 23-25, Proceedings. IEEE. (2012). [url]

P. Bonizzoni, G. Della Vedova, R. Dondi, and Y. Pirola.
Parameterized Complexity of k-Anonymity: Hardness and Tractability.
In Combinatorial Algorithms, 21st Int. Workshop, IWOCA 2010, London UK, Jul 26-28, Revised selected papers. C. Iliopoulos and W. Smyth (Ed.). Springer. Vol. 6460 pp. 242-255 (2011). [url]

P. Bonizzoni, G. Della Vedova, Y. Pirola, and R. Rizzi.
PIntron: a fast method for gene structure prediction via maximal pairings of a pattern and a text.
In Computational Advances in Bio and medical Sciences, 1st IEEE Int. Conference, ICCABS 2011, Orlando FL, USA, Feb 3-5, 2011. IEEE. pp. 33-39 (2011). [url]

Y. Pirola, P. Bonizzoni, and Tao Jiang.
Haplotype Inference on Pedigrees with Recombinations and Mutations.
In Algorithms in Bioinformatics, 10th Int. Workshop, WABI 2010, Liverpool UK, Sep 6-8, 2010, Proceedings. V. Moulton and M. Singh (Ed.). Springer. Vol. 6293 pp. 148-161 (2010). [url]

P. Bonizzoni, G. Della Vedova, R. Dondi, Y. Pirola, and R. Rizzi.
Minimum Factorization Agreement of Spliced ESTs.
In Algorithms in Bioinformatics, 9th Int. Workshop, WABI 2009, Philadelphia PA, USA, Sep 12-13, 2009, Proceedings. Springer. Vol. 5724 pp. 1-12 (Sep, 2009). [url]

P. Bonizzoni, G. Della Vedova, R. Dondi, Y. Pirola, and Romeo Rizzi.
Pure Parsimony Xor Haplotyping.
In Bioinformatics Research and Applications, 5th Int. Symposium, ISBRA 2009, Fort Lauderdale FL, USA, May 13-16, 2009, Proceedings. Ion I. Mandoiu and Giri Narasimhan and Yanqing Zhang (Ed.). Springer. Vol. 5542 pp. 186-197 (May, 2009). [url]

Leonardo Vanneschi, Marco Tomassini, Philippe Collard, Sebastien Verel, Y. Pirola, and Giancarlo Mauri.
A Comprehensive View of Fitness Landscapes with Neutrality and Fitness Clouds.
In Genetic Programming, 10th European Conference, Proceedings. Marc Ebner et al. (Ed.). Springer. Vol. 4445 pp. 241-250 (2007). [url]

Leonardo Vanneschi, Y. Pirola, and Philippe Collard.
A quantitative study of neutrality in GP boolean landscapes.
In Genetic and Evolutionary Computation, 8th Annual Conference, GECCO 2006, Proceedings. ACM Press. pp. 895-902 (2006). [url]

Phd Thesis

Y. Pirola.
Combinatorial Problems in Studies of Genetic Variations: Haplotyping and Transcript Analysis.
Univ. degli Studi di Milano-Bicocca, Milan, Italy. (2010). [url]

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