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Paola 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]