David Fernández-Baca

According to our database1, David Fernández-Baca authored at least 74 papers between 1987 and 2021.

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Bibliography

2021
Exact Algorithms for No-Rainbow Coloring and Phylogenetic Decisiveness.
CoRR, 2021

2020
Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences.
IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Checking Phylogenetic Decisiveness in Theory and in Practice.
Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

Testing the Agreement of Trees with Internal Labels.
Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

2019
EvoZip: Efficient Compression of Large Collections of Evolutionary Trees.
CoRR, 2019

Tree Compatibility, Incomplete Directed Perfect Phylogeny, and Dynamic Graph Connectivity: An Experimental Study.
Algorithms, 2019

2018
On compatibility and incompatibility of collections of unrooted phylogenetic trees.
Discret. Appl. Math., 2018

Fast Compatibility Testing for Rooted Phylogenetic Trees.
Algorithmica, 2018

Sensitivity Analysis in Combinatorial Optimization.
Proceedings of the Handbook of Approximation Algorithms and Metaheuristics, 2018

2017
An efficient algorithm for testing the compatibility of phylogenies with nested taxa.
Algorithms Mol. Biol., 2017

2016
Fast Compatibility Testing for Phylogenies with Nested Taxa.
Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

2015
Fixed-Parameter Algorithms for Finding Agreement Supertrees.
SIAM J. Comput., 2015

Compatibility, Incompatibility, Tree-Width, and Forbidden Phylogenetic Minors.
Electron. Notes Discret. Math., 2015

MulRF: a software package for phylogenetic analysis using multi-copy gene trees.
Bioinform., 2015

Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis.
Proceedings of the Algorithms for Computational Biology, 2015

2014
EvoMiner: frequent subtree mining in phylogenetic databases.
Knowl. Inf. Syst., 2014

Characterizing compatibility and agreement of unrooted trees via cuts in graphs.
Algorithms Mol. Biol., 2014

Enumerating all maximal frequent subtrees in collections of phylogenetic trees.
Algorithms Mol. Biol., 2014

Editorial.
Algorithmica, 2014

2013
Incompatible quartets, triplets, and characters.
Algorithms Mol. Biol., 2013

Extracting conflict-free information from multi-labeled trees.
Algorithms Mol. Biol., 2013

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance.
Algorithms Mol. Biol., 2013

2012
Fast Local Search for Unrooted Robinson-Foulds Supertrees.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

On Two Graph-Theoretic Characterizations of Tree Compatibility
CoRR, 2012

Improved Lower Bounds on the Compatibility of Multi-State Characters
CoRR, 2012

Preface to CLEI 2011 Special Issue.
CLEI Electron. J., 2012

A simple characterization of the minimal obstruction sets for three-state perfect phylogenies.
Appl. Math. Lett., 2012

Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters.
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms.
Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

2011
Comparing and aggregating partially resolved trees.
Theor. Comput. Sci., 2011

An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies.
Discret. Appl. Math., 2011

An ILP solution for the gene duplication problem.
BMC Bioinform., 2011

Graph triangulations and the compatibility of unrooted phylogenetic trees.
Appl. Math. Lett., 2011

Constructing Large Conservative Supertrees.
Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2010
iGTP: A software package for large-scale gene tree parsimony analysis.
BMC Bioinform., 2010

Constructing majority-rule supertrees.
Algorithms Mol. Biol., 2010

Robinson-Foulds Supertrees.
Algorithms Mol. Biol., 2010

2009
Parametric analysis for ungapped Markov models of evolution.
ACM Trans. Algorithms, 2009

Computing distances between partial rankings.
Inf. Process. Lett., 2009

Generalized Binary Tanglegrams: Algorithms and Applications.
Proceedings of the Bioinformatics and Computational Biology, 2009

2007
Sensitivity Analysis in Combinatorial Optimization.
Proceedings of the Handbook of Approximation Algorithms and Metaheuristics., 2007

2006
Minimum-Flip Supertrees: Complexity and Algorithms.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

2004
Parametric multiple sequence alignment and phylogeny construction.
J. Discrete Algorithms, 2004

Inverse parametric sequence alignment.
J. Algorithms, 2004

Rainbow: a toolbox for phylogenetic supertree construction and analysis.
Bioinform., 2004

2003
Decomposable multi-parameter matroid optimization problems.
Theor. Comput. Sci., 2003

A Polynomial-Time Algorithm for Near-Perfect Phylogeny.
SIAM J. Comput., 2003

2002
Bounds for parametric sequence comparison.
Discret. Appl. Math., 2002

Supertrees by Flipping.
Proceedings of the Computing and Combinatorics, 8th Annual International Conference, 2002

2001
On Nonlinear Parametric Search.
Algorithmica, 2001

Flipping: A supertree construction method.
Proceedings of the Bioconsensus, 2001

2000
Multi-parameter Minimum Spanning Trees.
Proceedings of the LATIN 2000: Theoretical Informatics, 2000

1998
On the Approximability of the Steiner Tree Problem in Phylogeny.
Discret. Appl. Math., 1998

Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry.
Proceedings of the LATIN '98: Theoretical Informatics, 1998

1997
Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs.
Theor. Comput. Sci., 1997

Optimal Parametric Search on Graphs of Bounded Tree-Width.
J. Algorithms, 1997

1996
Weighted Multidimensional Search and Its Application to Convex Optimization.
SIAM J. Comput., 1996

Using Sparsification for Parametric Minimum Spanning Tree Problems.
Nord. J. Comput., 1996

Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs.
Int. J. Found. Comput. Sci., 1996

1995
Fast Algorithms for Inferring Evolutionary Trees.
J. Comput. Biol., 1995

Weighted Search in the Plane.
Inf. Process. Lett., 1995

1994
A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed.
SIAM J. Comput., 1994

Parametric Problems on Graphs of Bounded Tree-Width.
J. Algorithms, 1994

1993
Parametric Module Allocation on Partial k-Trees.
IEEE Trans. Computers, 1993

1992
Solving the Lagrangian Dual when the Number of Constraints is Fixed.
Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1992

1991
Constructing the minimization diagram of a two-parameter problem.
Oper. Res. Lett., 1991

On Matroids and Hierarchical Graphs.
Inf. Process. Lett., 1991

1990
Space-Sweep Algorithms for Parametric Optimization (Extended Abstract).
Proceedings of the SWAT 90, 1990

1989
Allocating Modules to Processors in a Distributed System.
IEEE Trans. Software Eng., 1989

Solving Parametric Problems on Trees.
J. Algorithms, 1989

On the Efficiency of Maximum-Flow Algorithms on Networks with Small Integer Capacities.
Algorithmica, 1989

Augmentation Problems on Hierarchically Defined Graphs (Preliminary Version).
Proceedings of the Algorithms and Data Structures, 1989

1988
Nonserial Dynamic Programming Formulations of Satisfiability.
Inf. Process. Lett., 1988

1987
Fast Algorithms for Bipartite Network Flow.
SIAM J. Comput., 1987


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