Dellen, B.; Scharr, H.; Torras, C. IEEE-ACM transactions on computational biology and bioinformatics Vol. 12, num. 6, p. 1470-1478 DOI: 10.1109/TCBB.2015.2404810 Data de publicació: 2015 Article en revista
Plant growth is a dynamic process, and the precise course of events during early plant development is of major interest for plant research. In this work, we investigate the growth of rosette plants by processing time-lapse videos of growing plants, where we use Nicotiana tabacum (tobacco) as a model plant. In each frame of the video sequences, potential leaves are detected using a leaf-shape model. These detections are prone to errors due to the complex shape of plants and their changing appearance in the image, depending on leaf movement, leaf growth, and illumination conditions. To cope with this problem, we employ a novel graph-based tracking algorithm which can bridge gaps in the sequence by linking leaf detections across a range of neighboring frames. We use the overlap of fitted leaf models as a pairwise similarity measure, and forbid graph edges that would link leaf detections within a single frame. We tested the method on a set of tobacco-plant growth sequences, and could track the first leaves of the plant, including partially or temporarily occluded ones, along complete sequences, demonstrating the applicability of the method to automatic plant growth analysis. All seedlings displayed approximately the same growth behavior, and a characteristic growth signature was found.
Cardona, G.; Llabrés, J.; Rossello, F.; Valiente, G. IEEE-ACM transactions on computational biology and bioinformatics Vol. 8, num. 2, p. 410-427 DOI: 10.1109/TCBB.2010.60 Data de publicació: 2010-07-26 Article en revista
Cardona, G.; Rosselló, F.; Valiente, G. IEEE-ACM transactions on computational biology and bioinformatics Vol. 6, num. 4, p. 552-569 DOI: 10.1109/TCBB.2007.70270 Data de publicació: 2009-11-03 Article en revista
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 been made to find practical
algorithms for reconstructing a phylogenetic network from a set of sequences, all attempts to endorse a class of phylogenetic networks (strictly extending the class of phylogenetic trees) with a well-founded distance measure have, to the best of our knowledge and with the only exception of the bipartition distance on regular networks, failed so far. In this paper, we present and study a new meaningful class of phylogenetic networks, called tree-child phylogenetic networks, and we provide an injective representation of these networks
as multisets of vectors of natural numbers, their path multiplicity vectors. We then use this representation to define a distance on this class that extends the well-known Robinson-Foulds distance for phylogenetic trees and to give an alignment method for pairs of networks in this class. Simple polynomial algorithms for reconstructing a tree-child phylogenetic network from its path multiplicity vectors, for computing the distance between two tree-child phylogenetic networks and for aligning a pair of tree-child phylogenetic networks, are provided. They have been implemented as a Perl package and a Java applet, which can be found at http://bioinfo.uib.es/~recerca/phylonetworks/mudistance/.
Cardona, G.; Llabrés, M.; Rosselló, F.; Valiente, G. IEEE-ACM transactions on computational biology and bioinformatics Vol. 6, num. 4, p. 629-638 DOI: 10.1109/TCBB.2009.33. Data de publicació: 2009-11 Article en revista
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 phylogenetic trees. We also prove that it separates distinguishable phylogenetic networks. In this way, it becomes the strongest dissimilarity measure for phylogenetic networks available so far. Furthermore, we propose a generalization of that metric that separates arbitrary phylogenetic networks.
Treangen, T.; Darling, A.; Achaz, G.; Ragan, M.; Messeguer, X.; Rocha, E. IEEE-ACM transactions on computational biology and bioinformatics Vol. 6, num. 2, p. 180-189 Data de publicació: 2009-06 Article en revista
Cardona, G.; Llabrés, M.; Rosselló, F.; Valiente, G. IEEE-ACM transactions on computational biology and bioinformatics Vol. 6, num. 1, p. 46-61 DOI: 10.1109/TCBB.2008.70 Data de publicació: 2009-01 Article en revista
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 tripartitions distance and the $\mu$-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.
Lozano, A.; Pinter, R.; Rokhlenko, O.; Valiente, G.; Ziv-Ukelson, M. IEEE-ACM transactions on computational biology and bioinformatics Vol. 5, num. 4, p. 503-513 DOI: 10.1109/TCBB.2008.59 Data de publicació: 2008-10 Article en revista
The optimal transformation of one tree into another by means of elementary edit operations is an important algorithmic problem that has several interesting applications to computational biology. Here we introduce a constrained form of this problem in which a partial mapping of a set of nodes (the "seeds") in one tree to a corresponding set of nodes in the other tree is given, and present efficient algorithms for both ordered and unordered trees. Whereas ordered tree matching based on seeded nodes has applications in pattern matching of RNA structures, unordered tree matching based on seeded nodes has applications in co-speciation and phylogeny reconciliation. The latter involves the solution of the planar tanglegram layout problem, for which a polynomial-time algorithm is given here.