Francesc Rosselló | Universitat de les Illes Balears (original) (raw)

Papers by Francesc Rosselló

Bioinformatics, Jan 1, 2008

The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylog... more The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one, and this multiplicity makes the comparison of phylogenetic networks much more difficult than the comparison of phylogenetic trees. In fact, all attempts to define a sound distance measure on the class of all phylogenetic networks have failed so far. Thus, the only practical solutions have been either the use of rough estimates of similarity (based on comparison of the trees embedded in the networks), or narrowing the class of phylogenetic networks to a certain class where such a distance is known and can be efficiently computed. The first approach has the problem that one may identify two networks as equivalent, when they are not; the second one has the drawback that there may not exist algorithms to reconstruct such networks from biological sequences. Results: We present in this article a distance measure on the class of semi-binary tree-sibling time consistent phylogenetic networks, which generalize tree-child time consistent phylogenetic networks, and thus also galled-trees. The practical interest of this distance measure is 2-fold: it can be computed in polynomial time by means of simple algorithms, and there also exist polynomial-time algorithms for reconstructing networks of this class from DNA sequence data. Availability: The Perl package Bio::PhyloNetwork, included in the BioPerl bundle, implements many algorithms on phylogenetic networks, including the computation of the distance presented in this article. Contact: gabriel.cardona@uib.es Supplementary information: Some counterexamples, proofs of the results not included in this article, and some computational experiments are available at Bioinformatics online.

Mathematical biosciences, Jan 1, 2008

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representatio... more Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the study of reconstructibility of phylogenetic networks, Moret, Nakhleh, Warnow and collaborators introduced the so-called tripartition metric for phylogenetic networks. In this paper we show that, in fact, this tripartition metric does not satisfy the separation axiom of distances (zero distance means isomorphism, or, in a more relaxed version, zero distance means indistinguishability in some specific sense) in any of the subclasses of phylogenetic networks where it is claimed to do so. We also present a subclass of phylogenetic networks whose members can be singled out by means of their sets of tripartitions (or even clusters), and hence where the latter can be used to define a meaningful metric.

Theoretical computer …, Jan 1, 1997

The single-pushout approach to graph transformation is extended to the algebraic transformation o... more The single-pushout approach to graph transformation is extended to the algebraic transformation of partial many-sorted unary algebras. Such a generalization has been motivated by the need to model the transformation of structures which are richer and more complex than graphs and hypergraphs.

Formal Methods in Software and Systems …, Jan 1, 2005

In the beginning, one of the main fields of application of graph transformation was biology, and ... more In the beginning, one of the main fields of application of graph transformation was biology, and more specifically morphology. Later, however, it was like if the biological applications had been left aside by the graph transformation community, just to be moved back into the mainstream these very last years with a new interest in molecular biology. In this paper, we review several fields of application of graph grammars in molecular biology, including: the modeling higherdimensional structures of biomolecules, the description of biochemical reactions, the analysis of metabolic pathways, and their potential use in computational systems biology.

IEEE IEEE/ACM …, Jan 1, 2008

Abstract-The assessment of phylogenetic network reconstruction methods requires the ability to co... more Abstract-The assessment of phylogenetic network reconstruction methods requires the ability to compare phylogenetic networks. This is the first in a series of papers devoted to the analysis and comparison of metrics for tree-child time-consistent phylogenetic networks on the same set of taxa. In this paper, we study three metrics that have already been introduced in the literature: the Robinson-Foulds distance, the tripartition distance, and the -distance. They generalize to networks the classical Robinson-Foulds or partition distance for phylogenetic trees. We analyze the behavior of these metrics by studying their least and largest values and when they achieve them. As a by-product of this study, we obtain tight bounds on the size of a tree-child time-consistent phylogenetic network. . His research interests are split between number theory (mainly, arithmetical properties of curves of genus 2) and computational biology (mainly, mathematical models of evolution). . Her research is centered on mathematical models in computational and systems biology.

Arxiv preprint q-bio/0603007, Jan 1, 2006

Kolmogorov complexity has inspired several alignment-free distance measures, based on the compari... more Kolmogorov complexity has inspired several alignment-free distance measures, based on the comparison of lengths of compressions, which have been applied successfully in many areas. One of these measures, the socalled Universal Similarity Metric (USM), has been used by Krasnogor and Pelta to compare simple protein contact maps, showing that it yielded good clustering on four small datasets. We report an extensive test of this metric using a much larger and representative protein dataset: the domain dataset used by Sierk and Pearson to evaluate seven protein structure comparison methods and two protein sequence comparison methods. One result is that Krasnogor-Pelta method has less domain discriminant power than any one of the methods considered by Sierk and Pearson when using these simple contact maps. In another test, we found that the USM based distance has low agreement with the CATH tree structure for the same benchmark of Sierk and Pearson. In any case, its agreement is lower than the one of a standard sequential alignment method, SSEARCH. Finally, we manually found lots of small subsets of the database that are better clustered using SSEARCH than USM, to confirm that Krasnogor-Pelta's conclusions were based on datasets that were too small.

Theory and Application of Graph Transformations, Jan 1, 2000

The double-pushout (DPO) approach to algebraic transformation, invented 25 years ago by H. Ehrig,... more The double-pushout (DPO) approach to algebraic transformation, invented 25 years ago by H. Ehrig, M. Pfender and HJ Schneider, has been developed mainly for objects that can be understood as unary (total or partial) algebras, but, from the very beginning, objects with non-unary ...

Graph Transformations, Jan 1, 2004

Biochemical pathways, such as metabolic, regulatory, and signal transduction pathways, constitute... more Biochemical pathways, such as metabolic, regulatory, and signal transduction pathways, constitute complex networks of functional and physical interactions between molecular species in the cell. They are represented in a natural way as graphs, with molecules as nodes and processes as arcs. In particular, metabolic pathways are represented as directed graphs, with the substrates, products, and enzymes as nodes and the chemical reactions catalyzed by the enzymes as arcs. In this paper, chemical reactions in a metabolic pathway are described by edge relabeling graph transformation rules, as explicit chemical reactions and also as implicit chemical reactions, in which the substrate chemical graph, together with a minimal set of edge relabeling operations, determines uniquely the product chemical graph. Further, the problem of constructing all pathways that can accomplish a given metabolic function of transforming a substrate chemical graph to a product chemical graph using a set of explicit chemical reactions, is stated as the problem of finding an appropriate set of sequences of chemical graph transformations from the substrate to the product, and the design of a graph transformation system for the analysis of metabolic pathways is described, which is based on a database of explicit chemical reactions, a database of metabolic pathways, and a chemical graph transformation system.

BMC bioinformatics, Jan 1, 2008

Background: Phylogenetic networks are a generalization of phylogenetic trees that allow for the r... more Background: Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, like recombination between genes, hybridization between lineages, and lateral gene transfer. While most phylogenetics tools implement a wide range of algorithms on phylogenetic trees, there exist only a few applications to work with phylogenetic networks, none of which are open-source libraries, and they do not allow for the comparative analysis of phylogenetic networks by computing distances between them or aligning them.

International Journal of Intelligent …, Jan 1, 2009

In this paper we define in an axiomatic way scalar and fuzzy cardinalities of finite crisp and fu... more In this paper we define in an axiomatic way scalar and fuzzy cardinalities of finite crisp and fuzzy multisets, and we obtain explicit descriptions for them.