37 citations · 70 across the 13 of their papers we have counts for
15 papers
Compact Path Representation in DAGs via Colored Edge Pebbling
Paola Bonizzoni, Alessio Conte, Gianluca Della Vedova +3
Compactly representing a variation graph is a core problem in computational pangenomics that is usually attacked with techniques that have been originated on texts and adapted to g…
Computing the BWT and LCP array of a Set of Strings in External Memory
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola +2
Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Bu…
On Computing the Dollo-1 phylogeny in polynomial time
Paola Bonizzoni, Gianluca Della Vedova, Mauricio Soto Gomez +1
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny.…
A New Lightweight Algorithm to compute the BWT and the LCP array of a Set of Strings
Paola Bonizzoni, Gianluca Della Vedova, Serena Nicosia +2
Indexing of very large collections of strings such as those produced by the widespread sequencing technologies, heavily relies on multi-string generalizations of the Burrows-Wheele…
FSG: Fast String Graph Construction for De Novo Assembly of Reads Data
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola +2
The string graph for a collection of next-generation reads is a lossless data representation that is fundamental for de novo assemblers based on the overlap-layout-consensus paradi…
Algorithms for the Constrained Perfect Phylogeny with Persistent Characters
Paola Bonizzoni, Anna Paola Carrieri, Gianluca Della Vedova +1
The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referre…
An External-Memory Algorithm for String Graph Construction
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola +2
Some recent results have introduced external-memory algorithms to compute self-indexes of a set of strings, mainly via computing the Burrows-Wheeler Transform (BWT) of the input st…
A Unifying Framework to Characterize the Power of a Language to Express Relations
Paola Bonizzoni, Peter J. Cameron, Gianluca Della Vedova +2
In this extended abstract we provide a unifying framework that can be used to characterize and compare the expressive power of query languages for different data base models. The f…
Reconstructing Isoform Graphs from RNA-Seq data
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova +1
Next-generation sequencing (NGS) technologies allow new methodologies for alternative splicing (AS) analysis. Current computational methods for AS from NGS data are mainly focused…
Haplotype Inference on Pedigrees with Recombinations, Errors, and Missing Genotypes via SAT solvers
Yuri Pirola, Gianluca Della Vedova, Stefano Biffani +2
The Minimum-Recombinant Haplotype Configuration problem (MRHC) has been highly successful in providing a sound combinatorial formulation for the important problem of genotype phasi…
PIntron: a Fast Method for Gene Structure Prediction via Maximal Pairings of a Pattern and a Text
Paola Bonizzoni, Gianluca Della Vedova, Yuri Pirola +1
Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process l…
Pure Parsimony Xor Haplotyping
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi +2
The haplotype resolution from xor-genotype data has been recently formulated as a new model for genetic studies. The xor-genotype data is a cheaply obtainable type of data distingu…
Variants of Constrained Longest Common Subsequence
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi +1
In this work, we consider a variant of the classical Longest Common Subsequence problem called Doubly-Constrained Longest Common Subsequence (DC-LCS). Given two strings s1 and s2 o…
Parameterized Complexity of the k-anonymity Problem
Stefano Beretta, Paola Bonizzoni, Gianluca Della Vedova +2
The problem of publishing personal data without giving up privacy is becoming increasingly important. An interesting formalization that has been recently proposed is the -anonym…
Approximating Clustering of Fingerprint Vectors with Missing Values
Paola Bonizzoni, Gianluca Della Vedova, Riccardo Dondi
The problem of clustering fingerprint vectors is an interesting problem in Computational Biology that has been proposed in (Figureroa et al. 2004). In this paper we show some impro…