David Fernández-Baca

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

2021

Exact Algorithms for No-Rainbow Coloring and Phylogenetic Decisiveness.

[BibT_eX]

[DOI]

Ghazaleh Parvini

CoRR, 2021

Testing the agreement of trees with internal labels.

[BibT_eX]

[DOI]

Lei Liu

Algorithms Mol. Biol., 2021

2020

Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Checking Phylogenetic Decisiveness in Theory and in Practice.

[BibT_eX]

[DOI]

Ghazaleh Parvini

Katherine Braught

Proceedings of the Bioinformatics Research and Applications - 16th International Symposium, 2020

2019

EvoZip: Efficient Compression of Large Collections of Evolutionary Trees.

[BibT_eX]

[DOI]

CoRR, 2019

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

[BibT_eX]

[DOI]

Lei Liu

Algorithms, 2019

2018

On compatibility and incompatibility of collections of unrooted phylogenetic trees.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2018

Fast Compatibility Testing for Rooted Phylogenetic Trees.

[BibT_eX]

[DOI]

Yun Deng

Algorithmica, 2018

Sensitivity Analysis in Combinatorial Optimization.

[BibT_eX]

[DOI]

Balaji Venkatachalam

Proceedings of the Handbook of Approximation Algorithms and Metaheuristics, 2018

2017

An efficient algorithm for testing the compatibility of phylogenies with nested taxa.

[BibT_eX]

[DOI]

Yun Deng

Algorithms Mol. Biol., 2017

2016

Fast Compatibility Testing for Phylogenies with Nested Taxa.

[BibT_eX]

[DOI]

Yun Deng

Proceedings of the Algorithms in Bioinformatics - 16th International Workshop, 2016

2015

Fixed-Parameter Algorithms for Finding Agreement Supertrees.

[BibT_eX]

[DOI]

SIAM J. Comput., 2015

Compatibility, Incompatibility, Tree-Width, and Forbidden Phylogenetic Minors.

[BibT_eX]

[DOI]

Electron. Notes Discret. Math., 2015

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

[BibT_eX]

[DOI]

John Gordon Burleigh

Bioinform., 2015

Constructing and Employing Tree Alignment Graphs for Phylogenetic Synthesis.

[BibT_eX]

[DOI]

J. Gordon Burleigh

Proceedings of the Algorithms for Computational Biology, 2015

2014

EvoMiner: frequent subtree mining in phylogenetic databases.

[BibT_eX]

[DOI]

Knowl. Inf. Syst., 2014

Characterizing compatibility and agreement of unrooted trees via cuts in graphs.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2014

Enumerating all maximal frequent subtrees in collections of phylogenetic trees.

[BibT_eX]

[DOI]

Akshay Deepak

Algorithms Mol. Biol., 2014

Editorial.

[BibT_eX]

[DOI]

Algorithmica, 2014

2013

Incompatible quartets, triplets, and characters.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2013

Extracting conflict-free information from multi-labeled trees.

[BibT_eX]

[DOI]

Akshay Deepak

Michelle M. McMahon

Algorithms Mol. Biol., 2013

Inferring species trees from incongruent multi-copy gene trees using the Robinson-Foulds distance.

[BibT_eX]

[DOI]

John Gordon Burleigh

Algorithms Mol. Biol., 2013

2012

Fast Local Search for Unrooted Robinson-Foulds Supertrees.

[BibT_eX]

[DOI]

J. Gordon Burleigh

IEEE ACM Trans. Comput. Biol. Bioinform., 2012

On Two Graph-Theoretic Characterizations of Tree Compatibility

[BibT_eX]

[DOI]

CoRR, 2012

Improved Lower Bounds on the Compatibility of Multi-State Characters

[BibT_eX]

[DOI]

CoRR, 2012

Preface to CLEI 2011 Special Issue.

[BibT_eX]

[DOI]

Luciana Porcher Nedel

Oscar Pastor

CLEI Electron. J., 2012

A simple characterization of the minimal obstruction sets for three-state perfect phylogenies.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2012

Improved Lower Bounds on the Compatibility of Quartets, Triplets, and Multi-state Characters.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Identifying Rogue Taxa through Reduced Consensus: NP-Hardness and Exact Algorithms.

[BibT_eX]

[DOI]

Akshay Deepak

Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

2011

Comparing and aggregating partially resolved trees.

[BibT_eX]

[DOI]

Mukul S. Bansal

Theor. Comput. Sci., 2011

An axiomatic study of Majority-rule (+ ) and associated consensus functions on hierarchies.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2011

An ILP solution for the gene duplication problem.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

Graph triangulations and the compatibility of unrooted phylogenetic trees.

[BibT_eX]

[DOI]

Appl. Math. Lett., 2011

Constructing Large Conservative Supertrees.

[BibT_eX]

[DOI]

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2010

iGTP: A software package for large-scale gene tree parsimony analysis.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Constructing majority-rule supertrees.

[BibT_eX]

[DOI]

Fred R. McMorris

Algorithms Mol. Biol., 2010

Robinson-Foulds Supertrees.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2010

2009

Parametric analysis for ungapped Markov models of evolution.

[BibT_eX]

[DOI]

Balaji Venkatachalam

ACM Trans. Algorithms, 2009

Computing distances between partial rankings.

[BibT_eX]

[DOI]

Mukul S. Bansal

Inf. Process. Lett., 2009

Generalized Binary Tanglegrams: Algorithms and Applications.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics and Computational Biology, 2009

2007

Sensitivity Analysis in Combinatorial Optimization.

[BibT_eX]

[DOI]

Balaji Venkatachalam

Proceedings of the Handbook of Approximation Algorithms and Metaheuristics., 2007

2006

Minimum-Flip Supertrees: Complexity and Algorithms.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2006

2004

Parametric multiple sequence alignment and phylogeny construction.

[BibT_eX]

[DOI]

Timo Seppäläinen

J. Discrete Algorithms, 2004

Inverse parametric sequence alignment.

[BibT_eX]

[DOI]

Fangting Sun

Wei Yu

J. Algorithms, 2004

Rainbow: a toolbox for phylogenetic supertree construction and analysis.

[BibT_eX]

[DOI]

Duhong Chen

Oliver Eulenstein

Bioinform., 2004

2003

Decomposable multi-parameter matroid optimization problems.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2003

A Polynomial-Time Algorithm for Near-Perfect Phylogeny.

[BibT_eX]

[DOI]

Jens Lagergren

SIAM J. Comput., 2003

2002

Bounds for parametric sequence comparison.

[BibT_eX]

[DOI]

Timo Seppäläinen

Discret. Appl. Math., 2002

Supertrees by Flipping.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics, 8th Annual International Conference, 2002

2001

On Nonlinear Parametric Search.

[BibT_eX]

[DOI]

Algorithmica, 2001

Flipping: A supertree construction method.

[BibT_eX]

[DOI]

Proceedings of the Bioconsensus, 2001

2000

Multi-parameter Minimum Spanning Trees.

[BibT_eX]

[DOI]

Proceedings of the LATIN 2000: Theoretical Informatics, 2000

1998

On the Approximability of the Steiner Tree Problem in Phylogeny.

[BibT_eX]

[DOI]

Jens Lagergren

Discret. Appl. Math., 1998

Faster Non-linear Parametric Search with Applications to Optimazation and Dynamic Geometry.

[BibT_eX]

[DOI]

Proceedings of the LATIN '98: Theoretical Informatics, 1998

1997

Linear-Time Algorithms for Parametric Minimum Spanning Tree Problems on Planar Graphs.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 1997

Optimal Parametric Search on Graphs of Bounded Tree-Width.

[BibT_eX]

[DOI]

J. Algorithms, 1997

1996

Weighted Multidimensional Search and Its Application to Convex Optimization.

[BibT_eX]

[DOI]

SIAM J. Comput., 1996

Using Sparsification for Parametric Minimum Spanning Tree Problems.

[BibT_eX]

David Eppstein

Nord. J. Comput., 1996

Simple Algorithms for Perfect Phylogeny and Triangulating Colored Graphs.

[BibT_eX]

[DOI]

Int. J. Found. Comput. Sci., 1996

1995

Fast Algorithms for Inferring Evolutionary Trees.

[BibT_eX]

[DOI]

J. Comput. Biol., 1995

Weighted Search in the Plane.

[BibT_eX]

[DOI]

Inf. Process. Lett., 1995

1994

A Polynomial-Time Algorithm for the Perfect Phylogeny Problem when the Number of Character States is Fixed.

[BibT_eX]

[DOI]

SIAM J. Comput., 1994

Parametric Problems on Graphs of Bounded Tree-Width.

[BibT_eX]

[DOI]

J. Algorithms, 1994

1993

Parametric Module Allocation on Partial k-Trees.

[BibT_eX]

[DOI]

A. Medepalli

IEEE Trans. Computers, 1993

1992

Solving the Lagrangian Dual when the Number of Constraints is Fixed.

[BibT_eX]

[DOI]

Proceedings of the Foundations of Software Technology and Theoretical Computer Science, 1992

1991

Constructing the minimization diagram of a two-parameter problem.

[BibT_eX]

[DOI]

S. Srinivasan

Oper. Res. Lett., 1991

On Matroids and Hierarchical Graphs.

[BibT_eX]

[DOI]

Mark A. Williams

Inf. Process. Lett., 1991

1990

Space-Sweep Algorithms for Parametric Optimization (Extended Abstract).

[BibT_eX]

[DOI]

Proceedings of the SWAT 90, 1990

1989

Allocating Modules to Processors in a Distributed System.

[BibT_eX]

[DOI]

IEEE Trans. Software Eng., 1989

Solving Parametric Problems on Trees.

[BibT_eX]

[DOI]

J. Algorithms, 1989

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

[BibT_eX]

[DOI]

Charles U. Martel

Algorithmica, 1989

Augmentation Problems on Hierarchically Defined Graphs (Preliminary Version).

[BibT_eX]

[DOI]

Mark A. Williams

Proceedings of the Algorithms and Data Structures, 1989

1988

Nonserial Dynamic Programming Formulations of Satisfiability.

[BibT_eX]

[DOI]

Inf. Process. Lett., 1988

1987

Fast Algorithms for Bipartite Network Flow.

[BibT_eX]

[DOI]

Dan Gusfield

Charles U. Martel