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ORCIDPaola Bonizzoni
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- affiliation: University of Milano-Bicocca, Milan, Italy
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2020 – today
- 2024
[j81]Jorge Avila Cartes, Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Luca Denti:
PangeBlocks: customized construction of pangenome graphs via maximal blocks. BMC Bioinform. 25(1): 344 (2024)- [c56]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Yuri Pirola:
Solving the Minimal Positional Substring Cover Problem in Sublinear Space. CPM 2024: 12:1-12:16 - [c55]Paola Bonizzoni, Clelia De Felice, Brian Riccardi
, Rocco Zaccagnino, Rosalba Zizza:
Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property. MFCS 2024: 31:1-31:14 - [i26]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
From the Lyndon factorization to the Canonical Inverse Lyndon factorization: back and forth. CoRR abs/2404.17969 (2024) - [i25]Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, Rosalba Zizza:
Unveiling the connection between the Lyndon factorization and the Canonical Inverse Lyndon factorization via a border property. CoRR abs/2406.18473 (2024) - 2023
- [j80]Davide Cozzi, Massimiliano Rossi, Simone Rubinacci, Travis Gagie, Dominik Köppl, Christina Boucher, Paola Bonizzoni:
μ- PBWT: a lightweight r-indexing of the PBWT for storing and querying UK Biobank data. Bioinform. 39(9) (2023) - [c54]Davide Cozzi, Paola Bonizzoni, Luca Denti:
ESGq: Alternative Splicing Events Quantification across Conditions based on Event Splicing Graphs. ITAT 2023: 242-249 - [c53]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Mattia Sgrò:
Multiallelic Maximal Perfect Haplotype Blocks with Wildcards via PBWT. IWBBIO (1) 2023: 62-76 - [c52]Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, Dominik Köppl, Massimiliano Rossi:
Data Structures for SMEM-Finding in the PBWT. SPIRE 2023: 89-101 - 2022
- [j79]Paola Bonizzoni, Matteo Costantini, Clelia de Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza:
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. Inf. Sci. 607: 458-476 (2022) - [j78]Massimiliano Rossi, Marco Oliva, Paola Bonizzoni, Ben Langmead, Travis Gagie, Christina Boucher:
Finding Maximal Exact Matches Using the r-Index. J. Comput. Biol. 29(2): 188-194 (2022) - [j77]Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén:
Computational graph pangenomics: a tutorial on data structures and their applications. Nat. Comput. 21(1): 81-108 (2022) - [c51]Paola Bonizzoni, Clelia De Felice, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza:
Can Formal Languages Help Pangenomics to Represent and Analyze Multiple Genomes? DLT 2022: 3-12 - [c50]Paola Bonizzoni, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Rocco Zaccagnino, Rosalba Zizza:
KFinger: Capturing Overlaps Between Long Reads by Using Lyndon Fingerprints. IWBBIO (2) 2022: 436-449 - [i24]Paola Bonizzoni, Matteo Costantini, Clelia De Felice, Alessia Petescia, Yuri Pirola, Marco Previtali, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza:
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches. CoRR abs/2202.13884 (2022) - 2021
- [j76]Simone Ciccolella, Giulia Bernardini, Luca Denti, Paola Bonizzoni, Marco Previtali, Gianluca Della Vedova:
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels. Bioinform. 37(2): 178-184 (2021) - [j75]Simone Ciccolella, Camir Ricketts, Mauricio Soto Gomez, Murray Patterson, Dana Silverbush, Paola Bonizzoni, Iman Hajirasouliha, Gianluca Della Vedova:
Inferring cancer progression from Single-Cell Sequencing while allowing mutation losses. Bioinform. 37(3): 326-333 (2021) - [j74]Luca Denti, Yuri Pirola, Marco Previtali, Tamara Ceccato, Gianluca Della Vedova, Raffaella Rizzi, Paola Bonizzoni:
Shark: fishing relevant reads in an RNA-Seq sample. Bioinform. 37(4): 464-472 (2021) - [j73]Simone Ciccolella, Luca Denti, Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali:
MALVIRUS: an integrated application for viral variant analysis. BMC Bioinform. 22-S(15): 625 (2021) - [j72]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
On the longest common prefix of suffixes in an inverse Lyndon factorization and other properties. Theor. Comput. Sci. 862: 24-41 (2021) - [j71]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Computing the multi-string BWT and LCP array in external memory. Theor. Comput. Sci. 862: 42-58 (2021) - [j70]Paola Bonizzoni, Lila Kari, Ion Petre, Grzegorz Rozenberg:
Building bridges - Honoring Nataša Jonoska on the occasion of her 60th birthday. Theor. Comput. Sci. 894: 1-2 (2021) - [j69]Simone Ciccolella, Murray Patterson, Paola Bonizzoni, Gianluca Della Vedova:
Effective Clustering for Single Cell Sequencing Cancer Data. IEEE J. Biomed. Health Informatics 25(11): 4068-4078 (2021) - [c49]Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza:
Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. AlCoB 2021: 16-28 - [c48]Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski:
Incomplete Directed Perfect Phylogeny in Linear Time. WADS 2021: 172-185 - 2020
- [j68]Andrea Calabria, Stefano Beretta, Ivan Merelli, Giulio Spinozzi, Stefano Brasca, Yuri Pirola, Fabrizio Benedicenti, Erika Tenderini, Paola Bonizzoni, Luciano Milanesi, Eugenio Montini:
γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. Bioinform. 36(5): 1622-1624 (2020) - [j67]Simone Ciccolella, Mauricio Soto Gomez, Murray D. Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni:
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. BMC Bioinform. 21-S(1): 413 (2020) - [j66]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
Unavoidable Sets, Prefix Graphs and Regularity of Circular Splicing Languages. Fundam. Informaticae 171(1-4): 81-95 (2020) - [c47]Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski:
On Two Measures of Distance Between Fully-Labelled Trees. CPM 2020: 6:1-6:16 - [c46]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
Lyndon Words versus Inverse Lyndon Words: Queries on Suffixes and Bordered Words. LATA 2020: 385-396 - [i23]Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski:
On Two Measures of Distance between Fully-Labelled Trees. CoRR abs/2002.05600 (2020) - [i22]Giulia Bernardini, Paola Bonizzoni, Pawel Gawrychowski:
Incomplete Directed Perfect Phylogeny in Linear Time. CoRR abs/2010.05644 (2020)
2010 – 2019
- 2019
- [j65]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Multithread Multistring Burrows-Wheeler Transform and Longest Common Prefix Array. J. Comput. Biol. 26(9): 948-961 (2019) - [j64]Raffaella Rizzi, Stefano Beretta, Murray Patterson, Yuri Pirola, Marco Previtali, Gianluca Della Vedova, Paola Bonizzoni:
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era. Quant. Biol. 7(4): 278-292 (2019) - [j63]Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez:
Does Relaxing the Infinite Sites Assumption Give Better Tumor Phylogenies? An ILP-Based Comparative Approach. IEEE ACM Trans. Comput. Biol. Bioinform. 16(5): 1410-1423 (2019) - [c45]Simone Ciccolella, Murray D. Patterson, Paola Bonizzoni, Gianluca Della Vedova:
Effective Clustering for Single Cell Sequencing Cancer Data. BCB 2019: 437-446 - [c44]Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson:
A Rearrangement Distance for Fully-Labelled Trees. CPM 2019: 28:1-28:15 - [i21]Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, Murray Patterson:
A rearrangement distance for fully-labelled trees. CoRR abs/1904.01321 (2019) - [i20]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
Lyndon words versus inverse Lyndon words: queries on suffixes and bordered words. CoRR abs/1911.01851 (2019) - 2018
- [j62]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
Inverse Lyndon words and inverse Lyndon factorizations of words. Adv. Appl. Math. 101: 281-319 (2018) - [j61]Stefano Beretta, Murray Patterson, Simone Zaccaria, Gianluca Della Vedova, Paola Bonizzoni:
HapCHAT: adaptive haplotype assembly for efficiently leveraging high coverage in long reads. BMC Bioinform. 19(1): 252:1-252:19 (2018) - [j60]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 Bioinform. 19(1): 444:1-444:21 (2018) - [c43]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 - [c42]Simone Ciccolella, Mauricio Soto Gomez, Murray Patterson, Gianluca Della Vedova, Iman Hajirasouliha, Paola Bonizzoni:
gpps: an ILP-based approach for inferring cancer progression with mutation losses from single cell data. ICCABS 2018: 1 - 2017
- [j59]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) - [j58]Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Raffaella Rizzi, Gabriella Trucco:
Species-Driven Persistent Phylogeny. Fundam. Informaticae 154(1-4): 47-63 (2017) - [j57]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
FSG: Fast String Graph Construction for De Novo Assembly. J. Comput. Biol. 24(10): 953-968 (2017) - [j56]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) - [c41]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 - [c40]Paola Bonizzoni, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez:
Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. BCB 2017: 1-10 - [i19]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) - [i18]Paola Bonizzoni, Clelia De Felice, Rocco Zaccagnino, Rosalba Zizza:
Inverse Lyndon words and Inverse Lyndon factorizations of words. CoRR abs/1705.10277 (2017) - 2016
- [j55]Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, Paola Bonizzoni:
HapCol: accurate and memory-efficient haplotype assembly from long reads. Bioinform. 32(11): 1610-1617 (2016) - [j54]Vasco Brattka, Paola Bonizzoni, Olivier Bournez, Elvira Mayordomo:
Editorial. Comput. 5(1): 1 (2016) - [j53]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) - [j52]Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria:
On the Minimum Error Correction Problem for Haplotype Assembly in Diploid and Polyploid Genomes. J. Comput. Biol. 23(9): 718-736 (2016) - [c39]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 - [i17]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) - [i16]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) - [i15]Paola Bonizzoni, Gianluca Della Vedova, Gabriella Trucco:
Solving the Persistent Phylogeny Problem in polynomial time. CoRR abs/1611.01017 (2016) - 2015
- [j51]Paola Bonizzoni, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis:
Restricted and Swap Common Superstring: A Multivariate Algorithmic Perspective. Algorithmica 72(4): 914-939 (2015) - [j50]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. Comput. J. 58(7): 1673-1686 (2015) - [j49]Paola Bonizzoni, Natasa Jonoska:
Existence of constants in regular splicing languages. Inf. Comput. 242: 340-353 (2015) - [j48]Carlo Batini, Paola Bonizzoni, Marco Comerio, Riccardo Dondi, Yuri Pirola, Francesco Salandra:
A Clustering Algorithm for Planning the Integration Process of a Large Number of Conceptual Schemas. J. Comput. Sci. Technol. 30(1): 214-224 (2015) - [c38]Paola Bonizzoni, Riccardo Dondi, Gunnar W. Klau, Yuri Pirola, Nadia Pisanti, Simone Zaccaria:
On the Fixed Parameter Tractability and Approximability of the Minimum Error Correction Problem. CPM 2015: 100-113 - [i14]Luc Boasson, Paola Bonizzoni, Clelia De Felice, Isabelle Fagnot, Gabriele Fici, Rocco Zaccagnino, Rosalba Zizza:
Splicing Systems from Past to Future: Old and New Challenges. CoRR abs/1510.01574 (2015) - 2014
- [j47]Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta, Paola Bonizzoni, Macha Nikolski, Gabriel Valiente:
Further Steps in TANGO: improved taxonomic assignment in metagenomics. Bioinform. 30(1): 17-23 (2014) - [j46]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) - [j45]Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi, Florian Sikora:
Complexity insights of the Minimum Duplication problem. Theor. Comput. Sci. 530: 66-79 (2014) - [c37]Luc Boasson, Paola Bonizzoni, Clelia De Felice, Isabelle Fagnot, Gabriele Fici, Rocco Zaccagnino, Rosalba Zizza:
Splicing Systems from Past to Future: Old and New Challenges. Discrete Mathematics and Computer Science 2014: 51-76 - [c36]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. LATA 2014: 126-137 - [c35]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. WABI 2014: 311-325 - [p3]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 - [i13]Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova, Gabriella Trucco:
Algorithms for the Constrained Perfect Phylogeny with Persistent Characters. CoRR abs/1405.7497 (2014) - [i12]Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola, Marco Previtali, Raffaella Rizzi:
Constructing String Graphs in External Memory. CoRR abs/1405.7520 (2014) - 2013
- [j44]Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Maximum Disjoint Paths on Edge-Colored Graphs: Approximability and Tractability. Algorithms 6(1): 1-11 (2013) - [j43]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) - [c34]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 - [e1]Paola Bonizzoni, Vasco Brattka, Benedikt Löwe:
The Nature of Computation. Logic, Algorithms, Applications - 9th Conference on Computability in Europe, CiE 2013, Milan, Italy, July 1-5, 2013. Proceedings. Lecture Notes in Computer Science 7921, Springer 2013, ISBN 978-3-642-39052-4 [contents] - [i11]Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni, Riccardo Dondi, Yuri Pirola:
Covering Pairs in Directed Acyclic Graphs. CoRR abs/1310.5037 (2013) - 2012
- [j42]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) - [j41]Vasco Brattka, Paola Bonizzoni, S. Barry Cooper, Benedikt Löwe, Elvira Mayordomo:
Editorial. Comput. 1(1): 1-2 (2012) - [j40]Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Florian Sikora:
On the parameterized complexity of the repetition free longest common subsequence problem. Inf. Process. Lett. 112(7): 272-276 (2012) - [j39]Yuri Pirola, Paola Bonizzoni, Tao Jiang:
An Efficient Algorithm for Haplotype Inference on Pedigrees with Recombinations and Mutations. IEEE ACM Trans. Comput. Biol. Bioinform. 9(1): 12-25 (2012) - [j38]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) - [j37]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) - [j36]Paola Bonizzoni, Chiara Braghin, Riccardo Dondi, Gabriella Trucco:
The binary perfect phylogeny with persistent characters. Theor. Comput. Sci. 454: 51-63 (2012) - [c33]Stefano Beretta, Paola Bonizzoni, Raffaella Rizzi, Gianluca Della Vedova:
Reconstructing isoform graphs from RNA-Seq data. BIBM 2012: 1-4 - [c32]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 - [c31]Paola Bonizzoni, Riccardo Dondi, Giancarlo Mauri, Italo Zoppis:
Restricted and Swap Common Superstring: A Parameterized View. IPEC 2012: 49-60 - [c30]Guillaume Blin, Paola Bonizzoni, Riccardo Dondi, Romeo Rizzi, Florian Sikora:
Complexity Insights of the Minimum Duplication Problem. SOFSEM 2012: 153-164 - [c29]Paola Bonizzoni:
The Holy Grail: Finding the Genetic Bases of Phenotypic Characters. UCNC 2012: 1 - [i10]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
- [j35]Paola Bonizzoni, Claudio Ferretti, Anthonath Roslin Sagaya Mary, Giancarlo Mauri:
Picture Languages Generated by Assembling Tiles. Fundam. Informaticae 110(1-4): 77-93 (2011) - [j34]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
Anonymizing binary and small tables is hard to approximate. J. Comb. Optim. 22(1): 97-119 (2011) - [j33]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 Res. 39(Database-Issue): 80-85 (2011) - [c28]Paola Bonizzoni, Natasha Jonoska:
Regular Splicing Languages Must Have a Constant. Developments in Language Theory 2011: 82-92 - [c27]Paola Bonizzoni:
Invited: A novel perspective in algorithmic combinatorial methods for phasing populations in a coalescent model. ICCABS 2011: 4 - [c26]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 - [i9]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) - [i8]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) - [i7]Chiara Braghin, Riccardo Dondi, Gabriella Trucco, Paola Bonizzoni:
The Binary Perfect Phylogeny with Persistent characters. CoRR abs/1110.6739 (2011) - 2010
- [j32]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri:
Fingerprint Clustering with Bounded Number of Missing Values. Algorithmica 58(2): 282-303 (2010) - [j31]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Variants of constrained longest common subsequence. Inf. Process. Lett. 110(20): 877-881 (2010) - [j30]Paola Bonizzoni, Gheorghe Paun, Grzegorz Rozenberg, Claudio Zandron:
Preface. Nat. Comput. 9(2): 381-382 (2010) - [j29]Paola Bonizzoni, Clelia de Felice, Gabriele Fici, Rosalba Zizza:
On the regularity of circular splicing languages: a survey and new developments. Nat. Comput. 9(2): 397-420 (2010) - [j28]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. IEEE ACM Trans. Comput. Biol. Bioinform. 7(4): 598-610 (2010) - [j27]Paola Bonizzoni:
Constants and label-equivalence: A decision procedure for reflexive regular splicing languages. Theor. Comput. Sci. 411(6): 865-877 (2010) - [j26]Paola Bonizzoni, Clelia de Felice, Rosalba Zizza:
A characterization of (regular) circular languages generated by monotone complete splicing systems. Theor. Comput. Sci. 411(48): 4149-4161 (2010) - [c25]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Parameterized Complexity of k-Anonymity: Hardness and Tractability. IWOCA 2010: 242-255 - [c24]Yuri Pirola, Paola Bonizzoni, Tao Jiang:
Haplotype Inference on Pedigrees with Recombinations and Mutations. WABI 2010: 148-161 - [i6]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. CoRR abs/1001.1210 (2010)
2000 – 2009
- 2009
- [j25]Paola Bonizzoni, Giancarlo Mauri, Graziano Pesole, Ernesto Picardi, Yuri Pirola, Raffaella Rizzi:
Detecting Alternative Gene Structures from Spliced ESTs: A Computational Approach. J. Comput. Biol. 16(1): 43-66 (2009) - [j24]Paola Bonizzoni, S. Barry Cooper, Benedikt Löwe, Andrea Sorbi:
Foreword. Theor. Comput. Sci. 410(4-5): 283-284 (2009) - [c23]Paola Bonizzoni, Remco Loos:
Finite Splicing: Generative Capacity, New Models and Complexity Aspects. Algorithmic Bioprocesses 2009: 313-329 - [c22]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
The k-Anonymity Problem Is Hard. FCT 2009: 26-37 - [c21]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters. ICTCS 2009: 55-58 - [c20]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Romeo Rizzi:
Pure Parsimony Xor Haplotyping. ISBRA 2009: 186-197 - [c19]Paola Bonizzoni, Claudio Ferretti, Anthonath Roslin Sagaya Mary, Giancarlo Mauri:
Picture Languages Generated by Assembling Tiles. LATA 2009: 224-235 - [c18]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola, Raffaella Rizzi:
Minimum Factorization Agreement of Spliced ESTs. WABI 2009: 1-12 - [c17]Paola Bonizzoni, Clelia de Felice, Rosalba Zizza:
Circular Languages Generated by Complete Splicing Systems and Pure Unitary Languages. DCM 2009: 22-31 - [i5]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
A PTAS for the Minimum Consensus Clustering Problem with a Fixed Number of Clusters. CoRR abs/0907.1840 (2009) - [i4]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Parameterized Complexity of the k-anonymity Problem. CoRR abs/0910.3148 (2009) - [i3]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Yuri Pirola:
Variants of Constrained Longest Common Subsequence. CoRR abs/0912.0368 (2009) - 2008
- [j23]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. Bioinform. 24(10): 1300-1304 (2008) - [j22]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang:
On the Approximation of Correlation Clustering and Consensus Clustering. J. Comput. Syst. Sci. 74(5): 671-696 (2008) - 2007
- [j21]Paola Bonizzoni:
A Linear-Time Algorithm for the Perfect Phylogeny Haplotype Problem. Algorithmica 48(3): 267-285 (2007) - [j20]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Raffaella Rizzi, Stéphane Vialette:
Exemplar Longest Common Subsequence. IEEE ACM Trans. Comput. Biol. Bioinform. 4(4): 535-543 (2007) - [i2]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
Anonymizing Binary Tables is APX-hard. CoRR abs/0707.0421 (2007) - 2006
- [j19]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza:
Linear splicing and syntactic monoid. Discret. Appl. Math. 154(3): 452-470 (2006) - [j18]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 Res. 34(Web-Server-Issue): 440-443 (2006) - [c16]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Giancarlo Mauri:
Fingerprint Clustering with Bounded Number of Missing Values. CPM 2006: 106-116 - [c15]Paola Bonizzoni, Giancarlo Mauri:
A Decision Procedure for Reflexive Regular Splicing Languages. Developments in Language Theory 2006: 315-326 - [c14]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Guillaume Fertin, Stéphane Vialette:
Exemplar Longest Common Subsequence. International Conference on Computational Science (2) 2006: 622-629 - 2005
- [j17]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 Bioinform. 6: 244 (2005) - [j16]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza:
On the power of circular splicing. Discret. Appl. Math. 150(1-3): 51-66 (2005) - [j15]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani:
Experimental analysis of a new algorithm for partial haplotype completion. Int. J. Bioinform. Res. Appl. 1(4): 461-473 (2005) - [j14]Paola Bonizzoni, Clelia de Felice, Rosalba Zizza:
The structure of reflexive regular splicing languages via Schützenberger constants. Theor. Comput. Sci. 334(1-3): 71-98 (2005) - [j13]Paola Bonizzoni, Giancarlo Mauri:
Regular splicing languages and subclasses. Theor. Comput. Sci. 340(1): 349-363 (2005) - [j12]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
Reconciling a gene tree to a species tree under the duplication cost model. Theor. Comput. Sci. 347(1-2): 36-53 (2005) - [c13]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri:
Recombinant DNA , Gene Splicing as Generative Devices of Formal Languages. CiE 2005: 65-67 - [c12]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Lorenzo Mariani:
Experimental Analysis of a New Algorithm for Partial Haplotype Completion. International Conference on Computational Science (2) 2005: 952-959 - [c11]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Tao Jiang:
Correlation Clustering and Consensus Clustering. ISAAC 2005: 226-235 - [i1]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
Approximating Clustering of Fingerprint Vectors with Missing Values. CoRR abs/cs/0511082 (2005) - 2004
- [j11]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza:
Circular splicing and regularity. RAIRO Theor. Informatics Appl. 38(3): 189-228 (2004) - [j10]Paola Bonizzoni, Gianluca Della Vedova, Tao Jiang:
Foreword - Special Issue on Bioinformatics. J. Comput. Sci. Technol. 19(1): 1 (2004) - 2003
- [j9]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi, Jing Li:
The Haplotyping Problem: An Overview of Computational Models and Solutions. J. Comput. Sci. Technol. 18(6): 675-688 (2003) - [c10]Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi:
Reconciling Gene Trees to a Species Tree. CIAC 2003: 120-131 - [c9]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza:
Regular Languages Generated by Reflexive Finite Splicing Systems. Developments in Language Theory 2003: 134-145 - [c8]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 - 2002
- [c7]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza:
Decision Problems for Linear and Circular Splicing Systems. Developments in Language Theory 2002: 78-92 - 2001
- [j8]Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri:
Experimenting an approximation algorithm for the LCS. Discret. Appl. Math. 110(1): 13-24 (2001) - [j7]Paola Bonizzoni, Claudio Ferretti, Giancarlo Mauri, Rosalba Zizza:
Separating some splicing models. Inf. Process. Lett. 79(6): 255-259 (2001) - [j6]Paola Bonizzoni, Gianluca Della Vedova:
The complexity of multiple sequence alignment with SP-score that is a metric. Theor. Comput. Sci. 259(1-2): 63-79 (2001) - [j5]Paola Bonizzoni, Ross M. McConnell:
Nesting of prime substructures in k-ary relations. Theor. Comput. Sci. 259(1-2): 341-357 (2001) - [c6]Claudio Zandron, Giancarlo Mauri, Claudio Ferretti, Paola Bonizzoni:
Splicing systems using merge and separate operations. Where Mathematics, Computer Science, Linguistics and Biology Meet 2001: 435-446 - [c5]Paolo Barone, Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri:
An approximation algorithm for the shortest common supersequence problem: an experimental analysis. SAC 2001: 56-60 - 2000
- [j4]Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri:
Approximating the Maximum Isomorphic Agreement Subtree is Hard. Int. J. Found. Comput. Sci. 11(4): 579-590 (2000) - [c4]Paola Bonizzoni, Gianluca Della Vedova, Giancarlo Mauri:
Approximating the Maximum Isomorphic Agreement Subtree Is Hard. CPM 2000: 119-128 - [c3]Paola Bonizzoni, Clelia de Felice, Giancarlo Mauri, Rosalba Zizza:
DNA and Circular Splicing. DNA Computing 2000: 117-129
1990 – 1999
- 1999
- [j3]Paola Bonizzoni, Gianluca Della Vedova:
An Algorithm for the Modular Decomposition of Hypergraphs. J. Algorithms 32(2): 65-86 (1999) - 1995
- [c2]Paola Bonizzoni, Gianluca Della Vedova:
Modular Decomposition of Hypergraphs. WG 1995: 303-317 - 1994
- [j2]Paola Bonizzoni:
Primitive 2-structures with the (n-2)-Property. Theor. Comput. Sci. 132(2): 151-178 (1994) - [c1]Paola Bonizzoni:
A Tight Lower Bound for Primitivity in k-Structures. ICALP 1994: 556-567 - 1992
- [j1]Paola Bonizzoni, Giancarlo Mauri:
On Automata on Infinite Trees. Theor. Comput. Sci. 93(2): 227-244 (1992) - [p2]Ahmed Saoudi, Paola Bonizzoni:
Automata on infinite trees and rational control. Tree Automata and Languages 1992: 189-200 - [p1]Paola Bonizzoni, Giancarlo Mauri, Giovanni Pighizzini, Nicoletta Sabadini:
Recognizing sets of labelled acyclic graphs. Tree Automata and Languages 1992: 201-224
Coauthor Index
Clelia de Felice
aka: Clelia De Felice
aka: Clelia De Felice
[j81] [c53] [j77] [j76] [j75] [j74] [j73] [j71] [j69] [j67] [j65] [j64] [j63] [c45] [c44] [i21] [j61] [j60] [c43] [c42] [j59] [j58] [j57] [j56] [c40] [i19] [j53] [c39] [i17] [i16] [i15] [j46] [c35] [p3] [i13] [i12] [j43] [c34] [j42] [j38] [j37] [c33] [c32] [i10] [j34] [c26] [i9] [i8] [j32] [j31] [j28] [c25] [i6] [c22] [c21] [c20] [c18] [i5] [i4] [i3] [j22] [j20] [i2] [c16] [c14] [j15] [j12] [c12] [c11] [i1] [j10] [j9] [c10] [j8] [j6] [c5] [j4] [c4] [j3] [c2]
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