Now showing items 1-20 of 39

    • A balance index for phylogenetic trees based on rooted quartets 

      Martínez Coronado, Tomás; Mir Torres, Arnau; Rosselló Llompart, Francesc A.; Valiente Feruglio, Gabriel Alejandro (2019-06-17)
      Article
      Open Access
      We define a new balance index for rooted phylogenetic trees based on the symmetry of the evolutive history of every set of 4 leaves. This index makes sense for multifurcating trees and it can be computed in time linear in ...
    • A generalized Robinson-Foulds distance for clonal trees, mutation trees, and phylogenetic trees and networks 

      Llabrés Segura, Mercè; Rosselló Llompart, Francesc A.; Valiente Feruglio, Gabriel Alejandro (Association for Computing Machinery (ACM), 2020)
      Conference report
      Open Access
      Cancer evolution is often modeled by clonal trees (whose nodes are labeled by multiple somatic mutations) or mutation trees (where nodes are labeled by single somatic mutations). Clonal trees are generated from sequence ...
    • A Graph distance metric combining maximum common subgraph and minimum common supergraph 

      Fernández, Mirtha-Lina; Valiente Feruglio, Gabriel Alejandro (2001-01)
      Research report
      Open Access
      The relationship between two important problems in pattern recognition using attributed relational graphs, the maximum common subgraph and the minimum common supergraph of two graphs, is established by means of simple ...
    • A Relational view of subgraph isomorphism 

      Cortadella, Jordi; Valiente Feruglio, Gabriel Alejandro (1999-10)
      Research report
      Open Access
      This paper presents a novel approach to the problem of finding all subgraph isomorphisms of a (pattern) graph into another (target) graph. A relational formulation of the problem, combined with a representation of relations ...
    • Adjacency maps and efficient graph algorithms 

      Valiente Feruglio, Gabriel Alejandro (Multidisciplinary Digital Publishing Institute (MDPI), 2022-02-20)
      Article
      Open Access
      Graph algorithms that test adjacencies are usually implemented with an adjacency-matrix representation because the adjacency test takes constant time with adjacency matrices, but it takes linear time in the degree of the ...
    • Algebraic transformation of unary partial algebras I: double-pushout approach 

      Burmeister, P.; Rossello, F.; Torrens, J.; Valiente Feruglio, Gabriel Alejandro (1996-01-01)
      Research report
      Open Access
      The transformation of total graph structures has been studied from the algebraic point of view over more than two decades now, and it has motivated the development of the so-called double-pushout and single-pushout ...
    • Algebraic transformation of unary partial algebras II: single-pushout approach 

      Burmeister, P; Montserrat, M; Rosselló, F; Valiente Feruglio, Gabriel Alejandro (1996-06)
      Research report
      Open Access
      The single-pushout approach to graph transformation is extended to the algebraic transformation of partial many-sorted unary algebras. The main result presented in this article is an algebraic characterization of the ...
    • AligNet: alignment of protein-protein interaction networks 

      Alcala Mena, Adrià; Alberich Martí, Ricardo; Llabrés Segura, Mercè; Rosselló Llompart, Francesc A.; Valiente Feruglio, Gabriel Alejandro (2020-11-18)
      Article
      Open Access
      Background: All molecular functions and biological processes are carried out by groups of proteins that interact with each other. Metaproteomic data continuously generates new proteins whose molecular functions and relations ...
    • Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks 

      Llabrés Segura, Mercè; Riera Roca, Gabriel; Rosselló Llompart, Francesc A.; Valiente Feruglio, Gabriel Alejandro (2020-11-18)
      Article
      Open Access
      Background: The alignment of protein-protein interaction networks was recently formulated as an integer quadratic programming problem, along with a linearization that can be solved by integer linear programming software ...
    • Alignment of virus-host protein-protein interaction networks by integer linear programming: SARS-CoV-2 

      Llabrés Segura, Mercè; Valiente Feruglio, Gabriel Alejandro (Public Library of Science (PLOS), 2020-12-07)
      Article
      Open Access
      Motivation: Beside socio-economic issues, coronavirus pandemic COVID-19, the infectious disease caused by the newly discovered coronavirus SARS-CoV-2, has caused a deep impact in the scientific community, that has ...
    • An algebraic view of the relation between largest common subtrees and smallest common supertrees 

      Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro (2004-12)
      Research report
      Open Access
      The relationship between two important problems in tree pattern matching, the largest common subtree and the smallest common supertree of two trees, is established by means of simple constructions, which allow one to obtain ...
    • An Efficient representation for sparse graphs 

      Valiente Feruglio, Gabriel Alejandro (2002-02)
      Research report
      Open Access
      The design of efficient graph algorithms usually precludes the test of edge existence, because an efficient support of that operation already requires time (n^2) for the initialization of an adjacency-matrix representation. ...
    • An optimized TOPS+ comparison method for enhanced TOPS models 

      Veeramalai, Mallika; Gilbert, David; Valiente Feruglio, Gabriel Alejandro (2010-03-17)
      Article
      Open Access
      Background: Although methods based on highly abstract descriptions of protein structures, such as VAST and TOPS, can perform very fast protein structure comparison, the results can lack a high degree of biological significance. ...
    • BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS 

      Fosso, Bruno; Santamaria, Monica; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente Feruglio, Gabriel Alejandro; Donvito, Giacinto; Monaco, Alfonso; Notarangelo, Pasquale; Pesole, Graziano (2015-07-01)
      Article
      Open Access
      Background: Substantial advances in microbiology, molecular evolution and biodiversity have been carried out in recent years thanks to Metagenomics, which allows to unveil the composition and functions of mixed microbial ...
    • Characterization of phylogenetic networks with NetTest 

      Arenas, Miguel; Patricio, Mateus; Posada, David; Valiente Feruglio, Gabriel Alejandro (2010-05-20)
      Article
      Open Access
      Background: Typical evolutionary events like recombination, hybridization or gene transfer make necessary the use of phylogenetic networks to properly depict the evolution of DNA and protein sequences. Although several ...
    • Comparison of Tree-Child Phylogenetic Networks 

      Cardona, Gabriel; Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro (2009-11-03)
      Article
      Open Access
      Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of nontreelike evolutionary events, like recombination, hybridization, or lateral gene transfer. While much progress has ...
    • Complexity and dynamics of the winemaking bacterial communities in berries, musts, and wines from apulian grape cultivars through time and space 

      Marzano, Marinella; Fosso, Bruno; Manzari, Caterina; Grieco, Francesco; Intranuovo, Marianna; Cozzi, Giuseppe; Mulè, Giuseppina; Scioscia, Gaetano; Valiente Feruglio, Gabriel Alejandro; Tullo, Apollonia; Sbisa, Elisabetta; Pesole, Graziano; Santamaria, Monica (2016-06-14)
      Article
      Open Access
      Currently, there is very little information available regarding the microbiome associated with the wine production chain. Here, we used an amplicon sequencing approach based on high-throughput sequencing (HTS) to obtain a ...
    • Composició de textos científics amb LATEX 

      Valiente Feruglio, Gabriel Alejandro (Edicions UPC, 1996)
      Book
      Restricted access to the UPC academic community
      El LaTeX és un dels sistemes de tractament de textos científics de més àmplia difusió dins el món acadèmic. Es caracteritza per la gran qualitat que pot competir amb la dels treballs impresos per les principals editorials ...
    • Composición de textos científicos con LATEX 

      Valiente Feruglio, Gabriel Alejandro (Edicions UPC, 1997)
      Book
      Restricted access to the UPC academic community
      El LaTeX es uno de los sistemas de tratamiento de textos científicos de más amplia difusión dentro del mundo académico. Se caracteriza por la gran calidad del trabajo impreso, calidad que puede competir con la de los ...
    • Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment 

      Ferragina, Paolo; Giancarlo, Raffaele; Greco, Valentina; Manzini, Giovanni; Valiente Feruglio, Gabriel Alejandro (2007-07)
      Article
      Open Access
      Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic ...