Pawel Górecki

Natalia Rutecka

J. Comb. Optim., July, 2024

Asymmetric Cluster-Based Measures for Comparative Phylogenetics.

[BibT_eX]

[DOI]

J. Comput. Biol., 2024

Robinson-Foulds distance between phylogenetic networks and gene trees.

[BibT_eX]

[DOI]

Proceedings of the 15th ACM International Conference on Bioinformatics, 2024

2023

Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings.

[BibT_eX]

[DOI]

Proceedings of the 23rd International Workshop on Algorithms in Bioinformatics, 2023

The Asymmetric Cluster Affinity Cost.

[BibT_eX]

[DOI]

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

2022

Embedding gene trees into phylogenetic networks by conflict resolution algorithms.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2022

Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

Rooting Gene Trees via Phylogenetic Networks.

[BibT_eX]

[DOI]

Natalia Rutecka

Proceedings of the Computing and Combinatorics - 28th International Conference, 2022

2021

Consensus of All Solutions for Intractable Phylogenetic Tree Inference.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2021

Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming.

[BibT_eX]

[DOI]

J. Comput. Biol., 2021

Conflict Resolution Algorithms for Deep Coalescence Phylogenetic Networks.

[BibT_eX]

[DOI]

Proceedings of the 21st International Workshop on Algorithms in Bioinformatics, 2021

Novel genomic duplication models through integer linear programming.

[BibT_eX]

[DOI]

Proceedings of the BCB '21: 12th ACM International Conference on Bioinformatics, 2021

2020

Minimizing genomic duplication episodes.

[BibT_eX]

[DOI]

Comput. Biol. Chem., 2020

Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model.

[BibT_eX]

[DOI]

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

2019

Credibility of Evolutionary Events in Gene Trees.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2019

Mathematical properties of the gene duplication cost.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2019

Feasibility Algorithms for the Duplication-Loss Cost.

[BibT_eX]

[DOI]

Alexey Markin

Proceedings of the Computing and Combinatorics - 25th International Conference, 2019

2018

Efficient Algorithms for Genomic Duplication Models.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Inferring Gene-Species Assignments in the Presence of Horizontal Gene Transfer.

[BibT_eX]

[DOI]

Pawel Szczesny

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Bijective Diameters of Gene Tree Parsimony Costs.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2018

Minimizing the deep coalescence cost.

[BibT_eX]

[DOI]

Dawid Dabkowski

Pawel Tabaszewski

J. Bioinform. Comput. Biol., 2018

Locus-aware decomposition of gene trees with respect to polytomous species trees.

[BibT_eX]

[DOI]

Michal Aleksander Ciach

Anna Muszewska

Algorithms Mol. Biol., 2018

Cophenetic Distances: A Near-Linear Time Algorithmic Framework.

[BibT_eX]

[DOI]

Alexey Markin

Proceedings of the Computing and Combinatorics - 24th International Conference, 2018

Inferring time-consistent and well-supported horizontal gene transfers.

[BibT_eX]

[DOI]

Anna Muszewska

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2018

Phylogenetic Consensus for Exact Median Trees.

[BibT_eX]

[DOI]

Pawel Tabaszewski

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

Unconstrained Diameters for Deep Coalescence.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Detecting Locus Acquisition Events in Gene Trees.

[BibT_eX]

[DOI]

Michal Aleksander Ciach

Anna Muszewska

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

New Algorithms for the Genomic Duplication Problem.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 13th International Symposium, 2017

2016

Genomic duplication problems for unrooted gene trees.

[BibT_eX]

[DOI]

BMC Genom., 2016

Mean Values of Gene Duplication and Loss Cost Functions.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 12th International Symposium, 2016

Bootstrapping Algorithms for Gene Duplication and Speciation Events.

[BibT_eX]

[DOI]

Proceedings of the Algorithms for Computational Biology - Third International Conference, 2016

2015

Gene Tree Diameter for Deep Coalescence.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2015

Fast Algorithms for Inferring Gene-Species Associations.

[BibT_eX]

[DOI]

Arkadiusz Betkier

Pawel Szczesny

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014

Maximizing Deep Coalescence Cost.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

DrML: Probabilistic Modeling of Gene Duplications.

[BibT_eX]

[DOI]

J. Comput. Biol., 2014

Refining discordant gene trees.

[BibT_eX]

[DOI]

BMC Bioinform., 2014

Duplication Cost Diameters.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 10th International Symposium, 2014

Unconstrained gene tree diameters for deep coalescence.

[BibT_eX]

[DOI]

Proceedings of the 5th ACM Conference on Bioinformatics, 2014

2013

Unrooted Tree Reconciliation: A Unified Approach.

[BibT_eX]

[DOI]

IEEE ACM Trans. Comput. Biol. Bioinform., 2013

Exact solutions for species Tree Inference from discordant gene Trees.

[BibT_eX]

[DOI]

Wen-Chieh Chang

J. Bioinform. Comput. Biol., 2013

2012

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees.

[BibT_eX]

[DOI]

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

GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches.

[BibT_eX]

[DOI]

J. Gordon Burleigh

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

Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms.

[BibT_eX]

[DOI]

Proceedings of the Computing and Combinatorics - 18th Annual International Conference, 2012

Inferring Evolutionary Scenarios in the Duplication, Loss and Horizontal Gene Transfer Model.

[BibT_eX]

[DOI]

Proceedings of the Logic and Program Semantics, 2012

2011

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.

[BibT_eX]

[DOI]

J. Gordon Burleigh

BMC Bioinform., 2011

A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 7th International Symposium, 2011

2010

H-trees: a Model of Evolutionary Scenarios with Horizontal Gene Transfer.

[BibT_eX]

[DOI]

Fundam. Informaticae, 2010

2007

URec: a system for unrooted reconciliation.

[BibT_eX]

[DOI]

Bioinform., 2007

Inferring phylogeny from whole genomes.

[BibT_eX]

[DOI]

Bioinform., 2007

2006

DLS-trees: A model of evolutionary scenarios.

[BibT_eX]

[DOI]

Theor. Comput. Sci., 2006

2004

On the Structure of Reconciliations.

[BibT_eX]

[DOI]

Proceedings of the Comparative Genomics, 2004

Reconciliation problems for duplication, loss and horizontal gene transfer.

[BibT_eX]

[DOI]