Publication List for Gabriel Valiente

This document contains a list of the publications of Gabriel Valiente in refereed journals and conference proceedings. Abstracts are available in HTML format by clicking on the titles. The full text of some of the publications is also available in PDF format.

Alternatively, ask Scopus, DBLP Bibliography Server, Google Scholar, or search IEEE Xplore or PubMed, or check the Scientific production pages.

Books

G. Valiente. Combinatorial Pattern Matching Algorithms in Computational Biology using Perl and R. Taylor & Francis/CRC Press (2009). Source code
M. Lewenstein, G. Valiente (Eds.), Proc. 17th Annual Symposium on Combinatorial Pattern Matching, Lecture Notes in Computer Science 4009 (2006).
X. Messeguer, G. Valiente (Eds.) Proc. 5th Annual Spanish Bioinformatics Conference. Technical University of Catalonia, Barcelona (2004).
G. Valiente. Algorithms on Trees and Graphs. Springer-Verlag (2002).

Book Chapters

G. Valiente. Efficient Algorithms on Trees and Graphs with Unique Node Labels. In A. Kendel, H. Bunke, M. Last (Ed.), Applied Graph Theory in Computer Vision and Pattern Recognition, volume 52 of Studies in Computational Intelligence, Springer-Verlag (2007), pp. 137-149.
D. Gilbert, F. Rosselló, G. Valiente, M. Veeramalai. Alignment-Free Comparison of TOPS Strings. In J. Daykin, M. Mohamed, K. Steinhöfel (Ed.), London Algorithmics and Stringology, volume 8 of Texts in Algorithmics, College Publications (2007), ch. 11, pp. 177-197.
T. Asano, P. Evans, R. Uehara, G. Valiente. Site Consistency in Phylogenetic Networks with Recombination. In C. S. Iliopoulos, K. Park, K. Steinhöfel (Ed.), Algorithms in Bioinformatics, volume 6 of Texts in Algorithmics, College Publications (2006), ch. 2, pp. 15-26.
F. Rosselló, G. Valiente. Graph Transformation in Molecular Biology. In H.-J. Kreowski, U. Montanari, F. Orejas, G. Rozenberg, G. Taentzer (Ed.), Formal Methods in Software and System Modeling, Lecture Notes in Computer Science 3393 (2005), pp. 116-133.
A. Lozano, G. Valiente. On the Maximum Common Embedded Subtree Problem for Ordered Trees. In C. S. Iliopoulos, T. Lecroq (Ed.), String Algorithmics, volume 2 of Texts in Algorithms, College Publications (2004), ch. 7, pp. 155-169.

Research Articles in Journals and Conference Proceedings

T. M. Coronado, A. Mir, F. Rosselló, G. Valiente, A balance index for phylogenetic trees based on quartets.
B. Fosso, G. Pesole, F. Rosselló, G. Valiente, Unbiased taxonomic annotation of metagenomic samples. Journal of Computational Biology 25(3):348-360 (2018). Extended version of Unbiased taxonomic annotation of metagenomic samples. In Proc. 13th International Symposium on Bioinformatics Research and Applications, Lecture Notes in Bioinformatics 10330 (2017), pp. 162-173.
B. Fosso, M. Santamaria, M. D'Antonio, D. Lovero, G. Corrado, E. Vizza, N. Passero, A. R. Garbuglia, M. R. Capobianchi, M. Crescenzi, G. Valiente, G. Pesole, MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data. Bioinformatics 33(11):1730-1732 (2017).
M. Marzano, B. Fosso, C. Manzari, F. Grieco, M. Intranuovo, G. Cozzi, G. Mulè, G. Scioscia, G. Valiente, A. Tullo, E. Sbisà, G. Pesole, M. Santamaria, Complexity and Dynamics of the Winemaking Bacterial Communities in Berries, Musts, and Wines from Apulian Grape Cultivars through Time and Space. PLOS ONE 11(6):e0157383 (2016).
B. Fosso, M. Santamaria, M. Marzano, D. Alonso-Alemany, G. Valiente, G. Donvito, A. Monaco, P. Notarangelo, G. Pesole, BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS. BMC Bioinformatics 16:203 (2015).
G. Cardona, M. Llabrès, F. Rosselló G. Valiente. The comparison of tree-sibling time consistent phylogenetic networks is graph-isomorphism-complete. The Scientific World Journal 2014 (2014) 254279.
D. Alonso-Alemany, A. Barré, S. Beretta, P. Bonizzoni, M. Nikolski, G. Valiente, Further Steps in TANGO: Improved Taxonomic Assignment in Metagenomics. Bioinformatics 30(1):17-23 (2014).
M. Santamaria, B. Fosso, A. Consiglio, G. De Caro, G. Grillo, F. Licciulli, S. Liuni, M. Marzano, D. Alonso-Alemany, G. Valiente, G. Pesole. Reference Databases for Taxonomic Assignment in Metagenomics. Briefings in Bioinformatics 13(6):682-695 (2012).
T. Asano, J. Jansson, K. Sadakane, R. Uehara, G. Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. Information Sciences 197:77-90 (2012).
D. Alonso-Alemany, J. C. Clemente, J. Jansson, G. Valiente. Taxonomic Assignment in Metagenomics with TANGO. EMBnet.journal 17(2):46-50 (2011).
P. Ribeca, G. Valiente. Computational Challenges of Sequence Classification in Microbiomic Data. Briefings in Bioinformatics 12(6):614-625 (2011).
J. C. Clemente, J. Jansson, G. Valiente. Flexible Taxonomic Assignment of Ambiguous Sequencing Reads. BMC Bioinformatics 12:8 (2011).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. Comparison of Galled Trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8(2):410-427 (2011).
M. Arenas, M. Patricio, D. Posada, G. Valiente. Characterization of Phylogenetic Networks with NetTest. BMC Bioinformatics 11:268 (2010).
M. Veeramalai, D. Gilbert, G. Valiente. An Optimized TOPS+ Comparison Method for Enhanced TOPS Models. BMC Bioinformatics 11:138 (2010).
T. Asano, J. Jansson, K. Sadakane, R. Uehara, G. Valiente. Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks. In Proc. 21st Ann. Symp. Combinatorial Pattern Matching, Lecture Notes in Computer Science 6129, pp. 190-201 (2010).
J. C. Clemente, J. Jansson, G. Valiente. Accurate Taxonomic Assignment of Short Pyrosequencing Reads. Pacific Symposium on Biocomputing 15:3-9 (2010).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. Path Lengths in Tree-Child Time Consistent Hybridization Networks. Information Sciences 180(3):366-383 (2010).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. Nodal Distances for Rooted Phylogenetic Trees. Journal of Mathematical Biology 61(2):253-276 (2010).
F. Rosselló, G. Valiente. All that Glisters is not Galled. Mathematical Biosciences 221(1):54-59 (2009).
R. Alberich, G. Cardona, F. Rosselló, G. Valiente. An Algebraic Metric for Phylogenetic Trees. Applied Mathematics Letters 22(9):1320-1324 (2009).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. On Nakhleh's Metric for Reduced Phylogenetic Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(4):629-638 (2009).
J. C. Clemente, K. Ikeo, G. Valiente, T. Gojobori. Optimized Ancestral State Reconstruction using Sankoff Parsimony. BMC Bioinformatics 10:51 (2009).
G. Cardona, F. Rosselló, G. Valiente. Extended Newick: It is Time for a Standard Representation of Phylogenetic Networks. BMC Bioinformatics 9:532 (2008).
L. Félix, F. Rosselló, G. Valiente. Efficient Reconstruction of Metabolic Pathways by Bidirectional Chemical Search. Bulletin of Mathematical Biology 71(3):750-769 (2009).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(3):454-469 (2009).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(1):46-61 (2009).
G. Cardona, F. Rosselló, G. Valiente. Comparison of Tree-Child Phylogenetic Networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics 6(4):552-569 (2009).
M. Arenas, G. Valiente, D. Posada. Characterization of Reticulate Networks based on the Coalescent with Recombination. Molecular Biology and Evolution 25(12):2517-2520 (2008). Erratum in Molecular Biology and Evolution 26(4):951 (2009).
G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. A Distance Metric for a Class of Tree-Sibling Phylogenetic Networks. Bioinformatics 24(13):1481-1488 (2008).
A. Lozano, R. Pinter, O. Rokhlenko, G. Valiente, M. Ziv-Ukelson. Seeded Tree Alignment. IEEE/ACM Transactions on Computational Biology and Bioinformatics 5(4):503-513 (2008).
G. Cardona, F. Rosselló, G. Valiente. A Perl Package and an Alignment Tool for Phylogenetic Networks. BMC Bioinformatics 9:175 (2008).
M. Sammeth, G. Valiente, R. Guigó, Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs. In Proc. 12th Annual International Conference on Research in Computational Molecular Biology, Lecture Notes in Bioinformatics 4955 (2008), pp. 372-395.
G. Cardona, F. Rosselló, G. Valiente. Tripartitions do not always discriminate Phylogenetic Networks. Mathematical Biosciences 211(2):356-370 (2008).
P. Ferragina, R. Giancarlo, V. Greco, G. Manzini, G. Valiente. Compression-Based Classification of Biological Sequences and Structures via the Universal Similarity Metric: Experimental Assessment. BMC Bioinformatics 8:252 (2007).
L. Félix, F. Rosselló, G. Valiente, Reconstructing Metabolic Pathways by Bidirectional Chemical Search. In Proc. 5th International Conference on Computational Methods in Systems Biology, Lecture Notes in Bioinformatics 4695 (2007), pp. 217-232.
A. Lozano, R. Pinter, O. Rokhlenko, G. Valiente, M. Ziv-Ukelson. Seeded Tree Alignment and Planar Tanglegram Layout. In Proc. 7th Workshop on Algorithms in Bioinformatics, Lecture Notes in Bioinformatics 4645 (2007), pp. 98-110.
R. Uehara, G. Valiente. Linear Structure of Bipartite Permutation Graphs and the Longest Path Problem. Information Processing Letters 103(2):71-77 (2007).
L. Félix, G. Valiente. Validation of Metabolic Pathway Databases based on Chemical Substructure Search. Biomolecular Engineering 24(3):327-335 (2007).
J. C. Clemente, K. Satou, G. Valiente. Phylogenetic Reconstruction from Non-Genomic Data. Bioinformatics 23(2):e110-e115 (2007).
J. C. Clemente, K. Satou, G. Valiente. Finding Conserved and Non-Conserved Regions Using a Metabolic Pathway Alignment Algorithm. Genome Informatics 17(2):46-56 (2006).
G. Valiente. Assessing Clustering Results with Reference Taxonomies. Genome Informatics 17(2):131-140 (2006).
M. Llabrés, J. Rocha, F. Rosselló, G. Valiente. On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa. Journal of Mathematical Biology 53(3):340-364 (2006).
F. Rosselló, G. Valiente. An Algebraic View of the Relation between Largest Common Subtrees and Smallest Common Supertrees. Theoretical Computer Science 362(1-3):33-53 (2006).
J. Casasnovas, J. C. Clemente, J. Miró-Julià, F. Rosselló, K. Satou, G. Valiente. Fuzzy Clustering improves Phylogenetic Relationships Reconstruction from Metabolic Pathways. In Proc. 11th Int. Conf. Information Processing and Management of Uncertainty in Knowledge-Based Systems, Editions EDK (2006), pp. 2807-2814.
J. C. Clemente, K. Satou, G. Valiente. Reconstruction of Phylogenetic Relationships from Metabolic Pathways based on the Enzyme Hierarchy and the Gene Ontology. Genome Informatics 16(2):45-55 (2005).
T. H. Pham, D. H. Tran, T. B. Ho, K. Satou, G. Valiente. Qualitatively Predicting Acetylation and Methylation Areas in DNA Sequences. Genome Informatics 16(2):3-11 (2005).
R. D. M. Page, G. Valiente. An Edit Script for Taxonomic Classifications. BMC Bioinformatics 6:208 (2005).
G. Valiente. A Fast Algorithmic Technique for Comparing Large Phylogenetic Trees. In Proc. 12th Int. Symp. String Processing and Information Retrieval, Lecture Notes in Computer Science 3772 (2005), pp. 370-375. Errata
L. Félix, F. Rosselló, G. Valiente. Optimal Artificial Chemistries and Metabolic Pathways. In Proc. 6th Mexican Int. Conf. Computer Science, IEEE Computer Science Press (2005), pp. 298-305.
L. Félix, G. Valiente. Efficient Validation of Metabolic Pathway Databases. In Proc. 6th Int. Symp. Computational Biology and Genome Informatics, Salt Lake City, Utah, USA (2005), pp. 1209-1212.
M. Llabrés, F. Rosselló, G. Valiente. On Supertrees of Phylogenetic Trees. In Proc. 5th Annual Spanish Bioinformatics Conference, Technical University of Catalonia, Barcelona (2004), pp. 142-145.
L. Félix, F. Rosselló, G. Valiente. Artificial Chemistries and Metabolic Pathways. In Proc. 5th Annual Spanish Bioinformatics Conference, Technical University of Catalonia, Barcelona (2004), pp. 56-59.
F. Rosselló, G. Valiente. Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation. In Proc. 2nd Int. Workshop on Graph-Based Tools, Electr. Notes Theoret. Comput. Sci. 127(1):157-166 (2005).
F. Rosselló, G. Valiente. Analysis of Metabolic Pathways by Graph Transformation. In Proc. 2nd Int. Conf. Graph Transformation, Lecture Notes in Computer Science 3256 (2004), pp. 70-82.
G. Valiente. On the Algorithm of Berztiss for Tree Pattern Matching. In Proc. 5th Mexican Int. Conf. Computer Science, IEEE Computer Science Press (2004), pp. 43-49.
G. Valiente. Trading Uninitialized Space for Time. Inform. Process. Lett. 92(1):9-13. (2004).
G. Valiente. A New Simple Algorithm for the Maximum-Weight Independent Set Problem on Circle Graphs. In Proc. 14th Ann. Int. Symp. Algorithms and Computation, Lecture Notes in Computer Science 2906 (2003), pp. 126-135.
G. Valiente. Constrained Tree Inclusion. In Proc. 14th Ann. Symp. Combinatorial Pattern Matching, Lecture Notes in Computer Science 2676 (2003), pp. 361-371. Extended version of Constrained Tree Inclusion in J. Discrete Algorithms 3(2-4):431-447. (2005).
J. Larrosa, G. Valiente. Constraint Satisfaction Algorithms for Graph Pattern Matching. Math. Struct. Comput. Sci. 12(4):403-422. (2002).
G. Valiente. Structure of Scientific Collaboration in Graph Transformation. Bull. EATCS 78(1):329-345. (2002).
G. Valiente. An Efficient Bottom-Up Distance between Trees. In Proc. 8th Int. Symp. String Processing and Information Retrieval, Laguna de San Rafael, Chile (2001), pp. 212-219. IEEE Computer Science Press.
G. Valiente. A General Method for Graph Isomorphism. In Proc. 13th Int. Symp. Fundamentals of Computation Theory, Lecture Notes in Computer Science 2138 (2001), pp. 428-431.
M.-L. Fernández, G. Valiente. A Graph Distance Metric combining Maximum Common Subgraph and Minimum Common Supergraph. Pattern. Recogn. Lett. 22(6-7):753-758. (2001).
R. Baeza-Yates, G. Valiente. An Image Similarity Measure based on Graph Matching. In Proc. 7th Int. Symp. String Processing and Information Retrieval, A Coruña, Spain (2000), pp. 28-38. IEEE Computer Science Press.
J. Cortadella, G. Valiente. A Relational View of Subgraph Isomorphism. In Proc. Fifth Int. Seminar on Relational Methods in Computer Science, Québec, Canada (2000), pp. 45-54.
H.-J. Kreowski, G. Valiente. Redundancy and Subsumption in High-Level Replacement Systems. Theory and Application of Graph Transformations, Lecture Notes in Computer Science 1764 (2000), pp. 215-227.
P. Burmeister, M. Monserrat, F. Rosselló, G. Valiente. Algebraic Transformation of Unary Partial Algebras II: Single-Pushout Approach. Theoret. Comput. Sci. 216(1-2):311-362. (1999).
G. Valiente. Grammatica: An Implementation of Algebraic Graph Transformation on Mathematica. In Proc. Sixth Int. Workshop on Theory and Application of Graph Transformations (1998), pp. 261-267. Also appeared as Grammatica: Graph transformation with Mathematica in the CD-ROM Companion to volume 2 of the Handbook of Graph Grammars and Computing by Graph Transformation (H. Ehrig, G. Engels, H.-J. Kreowski, G. Rozenberg, editors), World Scientific (1999).
P. Burmeister, F. Rosselló, J. Torrens, G. Valiente. Algebraic Transformation of Unary Partial Algebras I: Double-Pushout Approach. Theoret. Comput. Sci. 184(1-2):145-193. (1997).
C. Martínez, G. Valiente. An Algorithm for Graph Pattern-Matching. In Proc. Fourth South American Workshop on String Processing, volume 8 of International Informatics Series, Carleton University Press (1997), pp. 180-197.
R. Alberich, P. Burmeister, F. Rosselló, G. Valiente, B. Wojdylo. A Partial Algebras Approach to Graph Transformation. Graph Grammars and their Application to Computer Science, Lecture Notes in Computer Science 1073 (1996), pp. 1-15.
M. Monserrat, F. Rosselló, J. Torrens, G. Valiente. Hypergraph Rewriting using Conformisms. In Proc. Joint COMPUGRAPH and SEMAGRAPH Workshop on Graph Rewriting and Computation, Electr. Notes Theoret. Comput. Sci. 1(2):105-112 (1995).
G. Valiente. Verification of Knowledge Base Redundancy and Subsumption using Graph Transformations. Int. J. Expert Systems 6(3):341-355 (1993).
G. Valiente. Input-Driven Control of Rule-Based Expert Systems. Methodologies for Intelligent Systems, Lecture Notes in Computer Science 689 (1993), pp. 86-95.
G. Valiente. On Knowledge Base Redundancy under Uncertain Reasoning. Advanced Methods in Artificial Intelligence, Lecture Notes in Computer Science 682 (1993), pp. 321-329.
G. Valiente. Using Layered Support Graphs for Verifying External Adequacy in Rule-Based Expert Systems. ACM SIGART Bull. 3(1):20-24 (1992).

Preprints

G. Cardona, M. Llabrés, F. Rosselló, G. Valiente. The Comparison of Tree-Sibling Time Consistent Phylogenetic Networks is Graph Isomorphism-Complete.

Posters

M. Llabrés, J. Planas-Iglesias, B. Oliva, F. Rosselló, G. Valiente. Global Alignment of Protein Interaction Networks. 5th Int. Conf. Computational Methods in Systems Biology. Edinburgh, UK (2007).
F. Rosselló, G. Valiente. Alignment-Free Comparison of Metabolic Pathways. 10th Annual Int. Conf. Research in Computational Molecular Biology. Venice, Italy (2006).
T. Asano, F. Rosselló, G. Valiente. Template Matrices for Perfect Phylogeny Haplotyping and Site Consistency. 10th Annual Int. Conf. Research in Computational Molecular Biology. Venice, Italy (2006).
L. M. C. Meireles, G. Valiente, T. Akutsu. Frequent Glycan Substructures in KEGG GLYCAN Database. Joint Int. Conf. on Bioinformatics, Association of Asian Societies for Bioinformatics, and Korean Society for Bioinformatics. Busan, South Korea (2005).
M. Llabrés, F. Rosselló, G. Valiente. On Supertrees of Phylogenetic Trees. In Proc. 5th Annual Spanish Bioinformatics Conference, Barcelona (2004), pp. 142-145.