9 citations · 18 across the 5 of their papers we have counts for
7 papers
Granular thermostat implementation within the soft-sphere Discrete Element Method (DEM) framework, considerations and limitations
Marco Previtali, Herbert Eric Huppert, Sergio Andres Galindo Torres
Dense granular flows are commonly investigated using the soft-sphere Discrete Element Method (DEM), whereas large-scale applications generally require continuum models. Granular te…
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…
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…
Fully Dynamic de Bruijn Graphs
Djamal Belazzougui, Travis Gagie, Veli Mäkinen +1
We present a space- and time-efficient fully dynamic implementation de Bruijn graphs, which can also support fixed-length jumbled pattern matching.
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…