Ara es mostren els items 25-43 de 43

    • MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data 

      Fosso, Bruno; Santamaria, Monica; D'Antonio, M.; Lovero, D.; Corrado, G.; Vizza, E.; Passaro, N.; Garbuglia, A.R.; Capobianchi, M.R.; Crescenzi, M.; Valiente Feruglio, Gabriel Alejandro; Pesole, Graziano (2017-06-01)
      Article
      Accés obert
      Shotgun metagenomics by high-throughput sequencing may allow deep and accurate characterization of host-associated total microbiomes, including bacteria, viruses, protists and fungi. However, the analysis of such sequencing ...
    • On Nakhleh's metric for reduced phylogenetic networks 

      Cardona, Gabriel; Llabrés, Mercè; Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro (2009-11)
      Article
      Accés obert
      We prove that Nakhleh’s metric for reduced phylogenetic networks is also a metric on the classes of tree-child phylogenetic networks, semibinary tree-sibling time consistent phylogenetic networks, and multilabeled ...
    • On the ancestral compatibility of two phylogenetic trees with nested taxa 

      Llabrés Segura, Mercè; Rocha, Jairo; Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro (2005-05)
      Report de recerca
      Accés obert
      Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees ...
    • On the maximum common embedded subtree problem for ordered trees 

      Valiente Feruglio, Gabriel Alejandro (2003-03)
      Report de recerca
      Accés obert
      The maximum common embedded subtree problem, which generalizes the subtree homeomorphism problem, is reduced for ordered trees to a variant of the longest common subsequence problem, called the longest common balanced ...
    • Redundancy and subsumption in high-level replacement systems 

      Valiente Feruglio, Gabriel Alejandro; Kreowski, H.-J. (1999-07)
      Report de recerca
      Accés obert
      System verification in the broadest sense deals with those semantic properties that can be decided or deduced by analyzing a syntactical description of the system. Hence, one may consider the notions of redundancy ...
    • Reference databases for taxonomic assignment in metagenomics 

      Santamaria, Monica; Fosso, Bruno; Consiglio, Arianna; De Caro, Giorigio; Grillo, Giorgio; Licciulli, Flavio; Liuni, Sabino; Marzano, Marinella; Alonso-Alemany, Daniel; Valiente Feruglio, Gabriel Alejandro; Pesole, Graziano (2012-11)
      Article
      Accés restringit per política de l'editorial
      Metagenomics is providing an unprecedented access to the environmental microbial diversity. The amplicon-based metagenomics approach involves the PCR-targeted sequencing of a genetic locus fitting different features. Namely, ...
    • Rewriting in categories of spans 

      Monserrat, Miquel; Rosselló, Francesc; Torrens, Joan; Valiente Feruglio, Gabriel Alejandro (1996-03)
      Report de recerca
      Accés obert
      Single-pushout transformation in a category of spans, in some sense a generalization of the usual notion of partial morphism, is studied in this paper. Contrary to the usual notion of partial morphism, spans are single ...
    • Simple and efficient tree comparison 

      Valiente Feruglio, Gabriel Alejandro (2001-01-08)
      Report de recerca
      Accés obert
      A new distance metric for rooted trees is presented which is based on the largest common forest of two rooted trees. The new measure is superior to previous measures based on tree edit distance, because no particular ...
    • Simple and efficient tree pattern matching 

      Valiente Feruglio, Gabriel Alejandro (2000-12)
      Report de recerca
      Accés obert
      A simple and efficient algorithm for an extension of the subtree isomorphism problem is presented that computes a certificate for each rooted subtree of a given forest, thereby partitioning the set of rooted subtrees ...
    • Single-pushout hypergraph rewriting through free completions 

      Alberich, Ricardo; Francesc, Rosselló; Valiente Feruglio, Gabriel Alejandro (1997-02)
      Report de recerca
      Accés obert
      Different relationships between single-pushout rewriting of total and partial unary algebras are studied in this paper. In general, given a single-pushout transformation rule r of total algebras, a corresponding ...
    • Single-pushout rewriting in categories of spans I: the general setting 

      Montserrat, Miquel; Francesc, Rosselló; Torrens, Joan; Valiente Feruglio, Gabriel Alejandro (1997-05)
      Report de recerca
      Accés obert
      A unifying view of all constructions of pushouts of partial morphisms considered so far in the literature of single-pushout transformation is given in this paper. Pushouts of partial morphisms are studied in an abstract ...
    • Taxonomic assignment in metagenomics with TANGO 

      Alonso-Alemany, Daniel; Clemente, José C.; Jansson, Jesper; Valiente Feruglio, Gabriel Alejandro (2011-12-01)
      Article
      Accés obert
      One of the main computational challenges facing metagenomic analysis is the taxonomic identification of short DNA fragments. The combination of sequence alignment methods with taxonomic assignment based on consensus can ...
    • The generalized Robinson-Foulds distance for phylogenetic trees 

      Llabrés Segura, Mercè; Rosselló Llompart, Francesc A.; Valiente Feruglio, Gabriel Alejandro (Mary Ann Liebert, Inc. Publishers, 2021-12-01)
      Article
      Accés obert
      The Robinson-Foulds (RF) distance, one of the most widely used metrics for comparing phylogenetic trees, has the advantage of being intuitive, with a natural interpretation in terms of common splits, and it can be computed ...
    • The K-Robinson Foulds measures for labeled trees 

      Khayatian, Elahe; Valiente Feruglio, Gabriel Alejandro; Zhang, Louxin (Springer, 2023)
      Text en actes de congrés
      Accés restringit per política de l'editorial
      Investigating the mutational history of tumor cells is important for understanding the underlying mechanisms of cancer and its evolution. Now that the evolution of tumor cells is modeled using labeled trees, researchers ...
    • The k-Robinson–Foulds dissimilarity measures for comparison of labeled treesd 

      Khayatian, Elahe; Valiente Feruglio, Gabriel Alejandro; Zhang, Louxin (2024-01-25)
      Article
      Accés obert
      Understanding the mutational history of tumor cells is a critical endeavor in unraveling the mechanisms that drive the onset and progression of cancer. Modeling tumor cell evolution with labeled trees motivates researchers ...
    • The landscape of virus-host protein–protein interaction databases 

      Valiente Feruglio, Gabriel Alejandro (Frontiers Media SA, 2022-07-15)
      Article
      Accés obert
      Knowledge of virus-host interactomes has advanced exponentially in the last decade by the use of high-throughput screening technologies to obtain a more comprehensive landscape of virus-host protein–protein interactions. ...
    • Tree edit distance and common subtrees 

      Valiente Feruglio, Gabriel Alejandro (2002-02)
      Report de recerca
      Accés obert
      The relationship between tree edit distance and maximum common subtrees is established, showing that a tree edit distance constrained by insertion and deletions on leaves only and by a simple condition on the cost of ...
    • Unbiased taxonomic annotation of metagenomic samples 

      Fosso, Bruno; Pesole, Graziano; Rosselló Llompart, Francesc A.; Valiente Feruglio, Gabriel Alejandro (2018-03)
      Article
      Accés obert
      The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then classifying each read at a node under the lowest common ...
    • Unbiased taxonomic annotation of metagenomic samples 

      Fosso, Bruno; Pesole, Graziano; Rosselló, Francesc; Valiente Feruglio, Gabriel Alejandro (Springer, 2017)
      Text en actes de congrés
      Accés obert
      The classification of reads from a metagenomic sample using a reference taxonomy is usually based on first mapping the reads to the reference sequences and then, classifying each read at a node under the lowest common ...