Oliver Eulenstein

Qi Li

CoRR, 2024

2023

Phylogenetic diversity statistics for all clades in a phylogeny.

[BibT_eX]

[DOI]

Bioinform., 2023

The Asymmetric Cluster Affinity Cost.

[BibT_eX]

[DOI]

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

2022

RF-Net 2: fast inference of virus reassortment and hybridization networks.

[BibT_eX]

[DOI]

Bioinform., 2022

CPTAM: Constituency Parse Tree Aggregation Method.

[BibT_eX]

[DOI]

Proceedings of the 2022 SIAM International Conference on Data Mining, 2022

Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics.

[BibT_eX]

[DOI]

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

2021

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model.

[BibT_eX]

[DOI]

Bioinform., November, 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]

Jerzy Tiuryn

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

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

[BibT_eX]

[DOI]

J. Comput. Biol., 2021

Introduction to the JBCB Special Issue on Selected Papers from BICOB-2020.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 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

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.

[BibT_eX]

[DOI]

Bioinform., 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

Cophenetic Median Trees.

[BibT_eX]

[DOI]

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

Efficient Local Search for Euclidean Path-Difference Median Trees.

[BibT_eX]

[DOI]

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

Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach.

[BibT_eX]

[DOI]

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

Foreword: Special Issue for the 2019 International Conference on Bioinformatics and Computational Biology (BICOB-2019).

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2019

Mathematical properties of the gene duplication cost.

[BibT_eX]

[DOI]

Discret. Appl. Math., 2019

Tracing the ancestry of operons in bacteria.

[BibT_eX]

[DOI]

Bioinform., 2019

Consensus Clusters in Robinson-Foulds Reticulation Networks.

[BibT_eX]

[DOI]

Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

The Cluster Affinity Distance for Phylogenies.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

Feasibility Algorithms for the Duplication-Loss Cost.

[BibT_eX]

[DOI]

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

Robinson-Foulds Reticulation Networks.

[BibT_eX]

[DOI]

Venkata Sai Krishna Teja Vadali

Tavis K. Anderson

Proceedings of the 10th ACM International Conference on Bioinformatics, 2019

2018

Bijective Diameters of Gene Tree Parsimony Costs.

[BibT_eX]

[DOI]

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

Introduction to JBCB Special Issue on BICOB-2018.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2018

Cluster Matching Distance for Rooted Phylogenetic Trees.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications - 14th International Symposium, 2018

Solving the Gene Duplication Feasibility Problem in Linear Time.

[BibT_eX]

[DOI]

Venkata Sai Krishna Teja Vadali

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

Cophenetic Distances: A Near-Linear Time Algorithmic Framework.

[BibT_eX]

[DOI]

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

Synthesizing large-scale species trees using the strict consensus approach.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2017

Foreword.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2017

Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees.

[BibT_eX]

[DOI]

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

Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach.

[BibT_eX]

[DOI]

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

Cophenetic Median Trees Under the Manhattan Distance.

[BibT_eX]

[DOI]

Proceedings of the 8th ACM International Conference on Bioinformatics, 2017

2016

Consensus properties and their large-scale applications for the gene duplication problem.

[BibT_eX]

[DOI]

J. Bioinform. Comput. Biol., 2016

Path-Difference Median Trees.

[BibT_eX]

[DOI]

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

Highly Bi-Connected Subgraphs for Computational Protein Function Annotation.

[BibT_eX]

[DOI]

Iddo Friedberg

Proceedings of the Computing and Combinatorics - 22nd International Conference, 2016

Robinson-Foulds Median Trees: A Clique-based Heuristic.

[BibT_eX]

[DOI]

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

Manhattan Path-Difference Median Trees.

[BibT_eX]

[DOI]

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

Gene Tree Diameter for Deep Coalescence.

[BibT_eX]

[DOI]

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

2014

Maximizing Deep Coalescence Cost.

[BibT_eX]

[DOI]

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

Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications.

[BibT_eX]

[DOI]

Zhipeng Cai

Cynthia Gibas

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

Guest editors' introduction to the Proceedings of the 9th International Symposium on Biomedical Research and Applications.

[BibT_eX]

[DOI]

Cynthia Gibas

Zhipeng Cai

BMC Bioinform., 2014

Big Guys and Big Data: Mining Shareholder Interaction Networks of Transnational MediaCompanies with Weighted Quasi-Bicliques.

[BibT_eX]

Sabine Baumann

Proceedings of the Multikonferenz Wirtschaftsinformatik, 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

Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems.

[BibT_eX]

[DOI]

André Wehe

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

Unrooted Tree Reconciliation: A Unified Approach.

[BibT_eX]

[DOI]

Jerzy Tiuryn

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

Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony.

[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

Consensus properties for the deep coalescence problem and their application for scalable tree search.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

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

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.

[BibT_eX]

[DOI]

Ruchi Chaudhary

BMC Bioinform., 2012

Exploring biological interaction networks with tailored weighted quasi-bicliques.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

Algorithms for Knowledge-Enhanced Supertrees.

[BibT_eX]

[DOI]

André Wehe

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

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

2011

The Plexus Model for the Inference of Ancestral Multidomain Proteins.

[BibT_eX]

[DOI]

John Wiedenhoeft

Roland Krause

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

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

[BibT_eX]

[DOI]

BMC Bioinform., 2011

An ILP solution for the gene duplication problem.

[BibT_eX]

[DOI]

BMC Bioinform., 2011

The Deep Coalescence Consensus Tree Problem is Pareto on Clusters.

[BibT_eX]

[DOI]

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

Algorithms for Rapid Error Correction for the Gene Duplication Problem.

[BibT_eX]

[DOI]

Ruchi Chaudhary

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

Mining Biological Interaction Networks Using Weighted Quasi-Bicliques.

[BibT_eX]

[DOI]

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

Invited: Reconciled gene trees and their applications.

[BibT_eX]

[DOI]

Proceedings of the IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences, 2011

2010

A scalable parallelization of the gene duplication problem.

[BibT_eX]

[DOI]

J. Parallel Distributed Comput., 2010

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

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.

[BibT_eX]

[DOI]

BMC Bioinform., 2010

Robinson-Foulds Supertrees.

[BibT_eX]

[DOI]

Algorithms Mol. Biol., 2010

Inferring Evolutionary Scenarios for Protein Domain Compositions.

[BibT_eX]

[DOI]

John Wiedenhoeft

Roland Krause

Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

Triplet-Supertrees constructed from Minimum Triplet Presentations.

[BibT_eX]

Max Homilius

John Gordon Burleigh

Proceedings of the ISCA 2nd International Conference on Bioinformatics and Computational Biology, 2010

Inferring species trees from gene duplication episodes.

[BibT_eX]

[DOI]

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2009

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches.

[BibT_eX]

[DOI]

André Wehe

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

Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants.

[BibT_eX]

[DOI]

J. Comput. Biol., 2009

Triplet supertree heuristics for the tree of life.

[BibT_eX]

[DOI]

BMC Bioinform., 2009

Generalized Binary Tanglegrams: Algorithms and Applications.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics and Computational Biology, 2009

2008

An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem.

[BibT_eX]

[DOI]

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

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

[BibT_eX]

[DOI]

Bioinform., 2008

Locating Multiple Gene Duplications through Reconciled Trees.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2008

The multiple gene duplication problem revisited.

[BibT_eX]

[DOI]

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches.

[BibT_eX]

[DOI]

Proceedings of the Bioinformatics Research and Applications, 2008

2007

An Omega(n2/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem.

[BibT_eX]

[DOI]

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

Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search.

[BibT_eX]

[DOI]

Proceedings of the Research in Computational Molecular Biology, 2007

2006

Minimum-Flip Supertrees: Complexity and Algorithms.

[BibT_eX]

[DOI]

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

Reconciling Gene Trees with Apparent Polytomies.

[BibT_eX]

[DOI]

Wen-Chieh Chang

Proceedings of the Computing and Combinatorics, 12th Annual International Conference, 2006

2004

Rainbow: a toolbox for phylogenetic supertree construction and analysis.

[BibT_eX]

[DOI]

Duhong Chen

David Fernández-Baca

Bioinform., 2004

2002

Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem.

[BibT_eX]

[DOI]

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

Supertrees by Flipping.

[BibT_eX]

[DOI]

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

2001

Flipping: A supertree construction method.

[BibT_eX]

[DOI]

Proceedings of the Bioconsensus, 2001

1999

Vorhersage von Genduplikationen und deren Entwicklung in der Evolution.

[BibT_eX]

GMD research series 20/1998, GMD, ISBN: 978-3-88457-344-0, 1999

1998

Duplication-Based Measures of Difference Between Gene and Species Trees.

[BibT_eX]

[DOI]

Boris G. Mirkin

Martin Vingron

J. Comput. Biol., 1998

On the Equivalence of Two Tree Mapping Measures.

[BibT_eX]

[DOI]

Martin Vingron

Discret. Appl. Math., 1998

Towards detection of orthologues in sequence databases.

[BibT_eX]

[DOI]

Bioinform., 1998

1997

Towards detection of sequence orthologs.

[BibT_eX]

Proceedings of the German Conference on Bioinformatics, 1997

1996

Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees.

[BibT_eX]

[DOI]