Gabriel Valiente

Louxin Zhang

J. Comput. Biol., 2024

Minimizing External Vertices in Hypergraph Orientations.

[BibT_eX]

[DOI]

Proceedings of the Combinatorial Optimization - 8th International Symposium, 2024

2023

The K-Robinson Foulds Measures for Labeled Trees.

[BibT_eX]

[DOI]

Elahe Khayatian

Louxin Zhang

Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022

Adjacency Maps and Efficient Graph Algorithms.

[BibT_eX]

[DOI]

Algorithms, 2022

2021

Algorithms on Trees and Graphs - With Python Code, Second Edition

[BibT_eX]

[DOI]

Texts in Computer Science, Springer, ISBN: 978-3-030-81884-5, 2021

The Generalized Robinson-Foulds Distance for Phylogenetic Trees.

[BibT_eX]

[DOI]

Mercè Llabrés

J. Comput. Biol., 2021

2020

Alignment of biological networks by integer linear programming: virus-host protein-protein interaction networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

AligNet: alignment of protein-protein interaction networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2020

A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and Networks.

[BibT_eX]

[DOI]

Mercè Llabrés

Proceedings of the BCB '20: 11th ACM International Conference on Bioinformatics, 2020

2018

Unbiased Taxonomic Annotation of Metagenomic Samples.

[BibT_eX]

[DOI]

J. Comput. Biol., 2018

2017

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

[BibT_eX]

[DOI]

Bioinform., 2017

2015

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS.

[BibT_eX]

[DOI]

Bruno Fosso

Monica Santamaria

Marinella Marzano

Daniel Alonso-Alemany

BMC Bioinform., 2015

2014

Further Steps in TANGO: improved taxonomic assignment in metagenomics.

[BibT_eX]

[DOI]

Daniel Alonso-Alemany

Bioinform., 2014

2012

Faster computation of the Robinson-Foulds distance between phylogenetic networks.

[BibT_eX]

[DOI]

Inf. Sci., 2012

Editorial.

[BibT_eX]

[DOI]

Graziano Pesole

Briefings Bioinform., 2012

Reference databases for taxonomic assignment in metagenomics.

[BibT_eX]

[DOI]

Daniel Alonso-Alemany

Graziano Pesole

Briefings Bioinform., 2012

2011

Comparison of Galled Trees.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2011

CPM 2006.

[BibT_eX]

[DOI]

Moshe Lewenstein

J. Discrete Algorithms, 2011

Flexible taxonomic assignment of ambiguous sequencing reads.

[BibT_eX]

[DOI]

José Carlos Clemente

Jesper Jansson

BMC Bioinform., 2011

Computational challenges of sequence classification in microbiomic data.

[BibT_eX]

[DOI]

Paolo Ribeca

Briefings Bioinform., 2011

2010

Path lengths in tree-child time consistent hybridization networks.

[BibT_eX]

[DOI]

Inf. Sci., 2010

An optimized TOPS+ comparison method for enhanced TOPS models.

[BibT_eX]

[DOI]

Mallika Veeramalai

David R. Gilbert

BMC Bioinform., 2010

Characterization of phylogenetic networks with NetTest.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Accurate Taxonomic Assignment of Short Pyrosequencing Reads.

[BibT_eX]

[DOI]

José Carlos Clemente

Jesper Jansson

Proceedings of the Biocomputing 2010: Proceedings of the Pacific Symposium, 2010

2009

Comparison of Tree-Child Phylogenetic Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

On Nakhleh's Metric for Reduced Phylogenetic Networks.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Metrics for Phylogenetic Networks II: Nodal and Triplets Metrics.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Metrics for Phylogenetic Networks I: Generalizations of the Robinson-Foulds Metric.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2009

All that Glisters is not Galled

[BibT_eX]

[DOI]

CoRR, 2009

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

[BibT_eX]

[DOI]

CoRR, 2009

Optimized ancestral state reconstruction using Sankoff parsimony.

[BibT_eX]

[DOI]

BMC Bioinform., 2009

An algebraic metric for phylogenetic trees.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2009

Combinatorial Pattern Matching Algorithms in Computational Biology Using Perl and R.

[BibT_eX]

Chapman and Hall / CRC mathematical and computational biology series, CRC Press, ISBN: 978-1-4200-6973-0, 2009

2008

Seeded Tree Alignment.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2008

A Distance Metric for Tree-Sibling Time Consistent Phylogenetic Networks

[BibT_eX]

[DOI]

CoRR, 2008

Nodal distances for rooted phylogenetic trees.

[BibT_eX]

[DOI]

CoRR, 2008

Extended Newick: it is time for a standard representation of phylogenetic networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

A perl package and an alignment tool for phylogenetic networks.

[BibT_eX]

[DOI]

BMC Bioinform., 2008

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

[BibT_eX]

[DOI]

Bioinform., 2008

Bubbles: Alternative Splicing Events of Arbitrary Dimension in Splicing Graphs.

[BibT_eX]

[DOI]

Michael Sammeth

Roderic Guigó

Proceedings of the Research in Computational Molecular Biology, 2008

2007

Efficient Algorithms on Trees and Graphs with Unique Node Labels.

[BibT_eX]

[DOI]

Proceedings of the Applied Graph Theory in Computer Vision and Pattern Recognition, 2007

Linear structure of bipartite permutation graphs and the longest path problem.

[BibT_eX]

[DOI]

Ryuhei Uehara

Inf. Process. Lett., 2007

Tripartitions do not always discriminate phylogenetic networks

[BibT_eX]

[DOI]

CoRR, 2007

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

[BibT_eX]

[DOI]

BMC Bioinform., 2007

Phylogenetic reconstruction from non-genomic data.

[BibT_eX]

[DOI]

José Carlos Clemente

Kenji Satou

Bioinform., 2007

Seeded Tree Alignment and Planar Tanglegram Layout.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics, 7th International Workshop, 2007

Reconstructing Metabolic Pathways by Bidirectional Chemical Search.

[BibT_eX]

[DOI]

Liliana Félix

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.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2006

The transposition distance for phylogenetic trees

[BibT_eX]

[DOI]

CoRR, 2006

2005

Constrained tree inclusion.

[BibT_eX]

[DOI]

J. Discrete Algorithms, 2005

On the Ancestral Compatibility of Two Phylogenetic Trees with Nested Taxa

[BibT_eX]

[DOI]

CoRR, 2005

An edit script for taxonomic classifications.

[BibT_eX]

[DOI]

Roderic D. M. Page

BMC Bioinform., 2005

A Fast Algorithmic Technique for Comparing Large Phylogenetic Trees.

[BibT_eX]

[DOI]

Proceedings of the String Processing and Information Retrieval, 2005

Optimal Artificial Chemistries and Metabolic Pathways.

[BibT_eX]

[DOI]

Liliana Félix

Proceedings of the Sixth Mexican International Conference on Computer Science (ENC 2005), 2005

Graph Transformation in Molecular Biology.

[BibT_eX]

[DOI]

Proceedings of the Formal Methods in Software and Systems Modeling, 2005

2004

Trading uninitialized space for time.

[BibT_eX]

[DOI]

Inf. Process. Lett., 2004

Chemical Graphs, Chemical Reaction Graphs, and Chemical Graph Transformation.

[BibT_eX]

[DOI]

Proceedings of the 2nd International Workshop on Graph-Based Tools, 2004

On Supertrees of Phylogenetic Trees.

[BibT_eX]

Mercè Llabrés

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

Artificial Chemistries and Metabolic Pathways.

[BibT_eX]

Liliana Félix

Proceedings of the 5th Annual Spanish Bioinformatics Conference, Barcelona, Catalonia, 2004

Analysis of Metabolic Pathways by Graph Transformation.

[BibT_eX]

[DOI]

Proceedings of the Graph Transformations, Second International Conference, 2004

On the Algorithm of Berztiss for Tree Pattern Matching.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Computation, 14th International Symposium, 2003

2002

Constraint Satisfaction Algorithms for Graph Pattern Matching.

[BibT_eX]

[DOI]

Javier Larrosa

Math. Struct. Comput. Sci., 2002

Algorithms on Trees and Graphs

[BibT_eX]

[DOI]

Springer, ISBN: 3-540-43550-6, 2002

2001

A graph distance metric combining maximum common subgraph and minimum common supergraph.

[BibT_eX]

[DOI]

Mirtha-Lina Fernández

Pattern Recognit. Lett., 2001

An Efficient Bottom-Up Distance between Trees.

[BibT_eX]

[DOI]

Proceedings of the Eighth International Symposium on String Processing and Information Retrieval, 2001

A General Method for Graph Isomorphism.

[BibT_eX]

[DOI]

Proceedings of the Fundamentals of Computation Theory, 13th International Symposium, 2001

2000

An Image Similarity Measure Based on Graph Matching.

[BibT_eX]

[DOI]

Ricardo A. Baeza-Yates

Proceedings of the Seventh International Symposium on String Processing and Information Retrieval, 2000

A Relational View of Subgraph Isomorphism.

[BibT_eX]

Jordi Cortadella

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.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1999

1998

Redundancy and Subsumption in High-Level Replacement Systems.

[BibT_eX]

[DOI]

Hans-Jörg Kreowski

Proceedings of the Theory and Application of Graph Transformations, 1998

1997

Algebraic Transformation of Unary Partial Algebras I: Double-Pushout Approach.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1997

1995

Hypergraph rewriting using conformisms.

[BibT_eX]

[DOI]

Proceedings of the Joint COMPUGRAPH/SEMAGRAPH Workshop on Graph Rewriting and Computation, 1995

1994

A Partial Algebras Approach to Graph Transformation.

[BibT_eX]

[DOI]

Proceedings of the Graph Gramars and Their Application to Computer Science, 1994

1993

Input-Driven Control of Rule-Based Expert Systems.

[BibT_eX]

[DOI]

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.

[BibT_eX]

[DOI]

SIGART Bull., 1992

On Knowledge Base Redundancy Under Uncertain Reasoning.

[BibT_eX]

[DOI]

Proceedings of the IPMU '92, 1992

1991

On Being a Machine: A Review.

[BibT_eX]

[DOI]