37 citations · 68 across the 8 of their papers we have counts for
10 papers
Numeric Lyndon-based feature embedding of sequencing reads for machine learning approaches
Paola Bonizzoni, Matteo Costantini, Clelia De Felice +7
Feature embedding methods have been proposed in literature to represent sequences as numeric vectors to be used in some bioinformatics investigations, such as family classification…
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…
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…
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…
Covering Pairs in Directed Acyclic Graphs
Niko Beerenwinkel, Stefano Beretta, Paola Bonizzoni +2
The Minimum Path Cover problem on directed acyclic graphs (DAGs) is a classical problem that provides a clear and simple mathematical formulation for several applications in differ…
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…