Gabriel Valiente

Orcid: 0000-0001-9194-2703

Affiliations:
  • Polytechnic University of Catalonia, Barcelona, Spain


According to our database1, Gabriel Valiente authored at least 78 papers between 1991 and 2024.

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Bibliography

2024
The <i>k</i>-Robinson-Foulds Dissimilarity Measures for Comparison of Labeled Trees.
J. Comput. Biol., 2024

Minimizing External Vertices in Hypergraph Orientations.
Proceedings of the Combinatorial Optimization - 8th International Symposium, 2024

2023
The K-Robinson Foulds Measures for Labeled Trees.
Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022
Adjacency Maps and Efficient Graph Algorithms.
Algorithms, 2022

2021
Algorithms on Trees and Graphs - With Python Code, Second Edition
Texts in Computer Science, Springer, ISBN: 978-3-030-81884-5, 2021

The Generalized Robinson-Foulds Distance for Phylogenetic Trees.
J. Comput. Biol., 2021

2020
Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks.
BMC Bioinform., 2020

AligNet: alignment of protein-protein interaction networks.
BMC Bioinform., 2020

A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and Networks.
Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

2018
Unbiased Taxonomic Annotation of Metagenomic Samples.
J. Comput. Biol., 2018

2017
MetaShot: an accurate workflow for taxon classification of host-associated microbiome from shotgun metagenomic data.
Bioinform., 2017

2015
BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.
BMC Bioinform., 2015

2014
Further Steps in TANGO: improved taxonomic assignment in metagenomics.
Bioinform., 2014

2012
Faster computation of the Robinson-Foulds distance between phylogenetic networks.
Inf. Sci., 2012

Editorial.
Briefings Bioinform., 2012

Reference databases for taxonomic assignment in metagenomics.
Briefings Bioinform., 2012

2011
Comparison of Galled Trees.
IEEE ACM Trans. Comput. Biol. Bioinform., 2011

CPM 2006.
J. Discrete Algorithms, 2011

Flexible taxonomic assignment of ambiguous sequencing reads.
BMC Bioinform., 2011

Computational challenges of sequence classification in microbiomic data.
Briefings Bioinform., 2011

2010
Path lengths in tree-child time consistent hybridization networks.
Inf. Sci., 2010

An optimized TOPS+ comparison method for enhanced TOPS models.
BMC Bioinform., 2010

Characterization of phylogenetic networks with NetTest.
BMC Bioinform., 2010

Accurate Taxonomic Assignment of Short Pyrosequencing Reads.
Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009
Comparison of Tree-Child Phylogenetic Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

On Nakhleh's Metric for Reduced Phylogenetic Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

All that Glisters is not Galled
CoRR, 2009

The comparison of tree-sibling time consistent phylogenetic networks is graph isomorphism-complete
CoRR, 2009

Optimized ancestral state reconstruction using Sankoff parsimony.
BMC Bioinform., 2009

An algebraic metric for phylogenetic trees.
Appl. Math. Lett., 2009

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R.
Chapman and Hall / CRC mathematical and computational biology series, CRC Press, ISBN: 978-1-4200-6973-0, 2009

2008
Seeded Tree Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2008

A Distance Metric for Tree-Sibling Time Consistent Phylogenetic Networks
CoRR, 2008

Nodal distances for rooted phylogenetic trees.
CoRR, 2008

Extended Newick: it is time for a standard representation of phylogenetic networks.
BMC Bioinform., 2008

A perl package and an alignment tool for phylogenetic networks.
BMC Bioinform., 2008

A distance metric for a class of tree-sibling phylogenetic networks.
Bioinform., 2008

Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs.
Proceedings of the Research in Computational Molecular Biology, 2008

2007
Efficient Algorithms on Trees and Graphs with Unique Node Labels.
Proceedings of the Applied Graph Theory in Computer Vision and Pattern Recognition, 2007

Linear structure of bipartite permutation graphs and the longest path problem.
Inf. Process. Lett., 2007

Tripartitions do not always discriminate phylogenetic networks
CoRR, 2007

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.
BMC Bioinform., 2007

Phylogenetic reconstruction from non-genomic data.
Bioinform., 2007

Seeded Tree Alignment and Planar Tanglegram Layout.
Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Reconstructing Metabolic Pathways by Bidirectional Chemical Search.
Proceedings of the Computational Methods in Systems Biology, International Conference, 2007

2006
An algebraic view of the relation between largest common subtrees and smallest common supertrees.
Theor. Comput. Sci., 2006

The transposition distance for phylogenetic trees
CoRR, 2006

2005
Constrained tree inclusion.
J. Discrete Algorithms, 2005

On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa
CoRR, 2005

An edit script for taxonomic classifications.
BMC Bioinform., 2005

A Fast Algorithmic Technique for Comparing Large Phylogenetic Trees.
Proceedings of the String Processing and Information Retrieval, 2005

Optimal Artificial Chemistries and Metabolic Pathways.
Proceedings of the Sixth Mexican International Conference on Computer Science (ENC 2005), 2005

Graph Transformation in Molecular Biology.
Proceedings of the Formal Methods in Software and Systems Modeling, 2005

2004
Trading uninitialized space for time.
Inf. Process. Lett., 2004

Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation.
Proceedings of the 2nd International Workshop on Graph-Based Tools, 2004

On Supertrees of Phylogenetic Trees.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

Artificial Chemistries and Metabolic Pathways.
Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

Analysis of Metabolic Pathways by Graph Transformation.
Proceedings of the Graph Transformations, Second International Conference, 2004

On the Algorithm of Berztiss for Tree Pattern Matching.
Proceedings of the 5th Mexican International Conference on Computer Science (ENC 2004), 2004

2003
A New Simple Algorithm for the Maximum-Weight Independent Set Problem on Circle Graphs.
Proceedings of the Algorithms and Computation, 14th International Symposium, 2003

2002
Constraint Satisfaction Algorithms for Graph Pattern Matching.
Math. Struct. Comput. Sci., 2002

Algorithms on Trees and Graphs
Springer, ISBN: 3-540-43550-6, 2002

2001
A graph distance metric combining maximum common subgraph and minimum common supergraph.
Pattern Recognit. Lett., 2001

An Efficient Bottom-Up Distance between Trees.
Proceedings of the Eighth International Symposium on String Processing and Information Retrieval, 2001

A General Method for Graph Isomorphism.
Proceedings of the Fundamentals of Computation Theory, 13th International Symposium, 2001

2000
An Image Similarity Measure Based on Graph Matching.
Proceedings of the Seventh International Symposium on String Processing and Information Retrieval, 2000

A Relational View of Subgraph Isomorphism.
Proceedings of the Participants Copies of Fifth International Seminar on Relational Methods in Computer Science, 2000

1999
Algebraic Transformation of Unary Partial Algebras II: Single-Pushout Approach.
Theor. Comput. Sci., 1999

1998
Redundancy and Subsumption in High-Level Replacement Systems.
Proceedings of the Theory and Application of Graph Transformations, 1998

1997
Algebraic Transformation of Unary Partial Algebras I: Double-Pushout Approach.
Theor. Comput. Sci., 1997

1995
Hypergraph rewriting using conformisms.
Proceedings of the Joint COMPUGRAPH/SEMAGRAPH Workshop on Graph Rewriting and Computation, 1995

1994
A Partial Algebras Approach to Graph Transformation.
Proceedings of the Graph Gramars and Their Application to Computer Science, 1994

1993
Input-Driven Control of Rule-Based Expert Systems.
Proceedings of the Methodologies for Intelligent Systems, 7th International Symposium, 1993

1992
Using Layered Support Graphs for Verifying External Adequacy in Rule-Based Expert Systems.
SIGART Bull., 1992

On Knowledge Base Redundancy Under Uncertain Reasoning.
Proceedings of the IPMU '92, 1992

1991
On Being a Machine: A Review.
AI Mag., 1991


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