Oliver Eulenstein

108 papers A 2B 2C 3Misc 8Journal 57Unranked 34
YearRankTypeTitle / Venue / Authors
2026 J jnl
Healthcare robotics across home and hospital settings: innovations, challenges, and future prospects.
PeerJ Comput. Sci.
Fulayjan Alanazi, Ashraf Gaffar, Oliver Eulenstein
2025 — conf
Beyond Single Parsers: An Empirical Analysis of Dependency Parse Tree Aggregation.
PAKDD (Workshops)
Adithya Kulkarni, Mohna Chakraborty, Oliver Eulenstein, Qi Li
2025 J jnl
Computing generalized cophenetic distances under all Lp norms: A near-linear time algorithmic framework.
PLoS Comput. Biol.
Pawel Górecki, Alexey Markin, Sriram Vijendran, Oliver Eulenstein
2025 J jnl
Phylo-rs: an extensible phylogenetic analysis library in rust.
BMC Bioinform.
Sriram Vijendran, Tavis K. Anderson, Alexey Markin, Oliver Eulenstein
2024 J jnl
Asymmetric Cluster-Based Measures for Comparative Phylogenetics.
J. Comput. Biol.
Sanket Wagle, Alexey Markin, Pawel Górecki, Tavis K. Anderson, Oliver Eulenstein
2024 J jnl
Empirical Analysis for Unsupervised Universal Dependency Parse Tree Aggregation.
CoRR
Adithya Kulkarni, Oliver Eulenstein, Qi Li
2024 C conf
Using Conceptual Blending to Teach Software Design Principles to Undergraduates.
FIE
Ashraf Gaffar, Mohamed Y. Selim, Oliver Eulenstein
2023 J jnl
Phylogenetic diversity statistics for all clades in a phylogeny.
Bioinform.
Siddhant Grover, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein
2023 — conf
The Asymmetric Cluster Affinity Cost.
RECOMB-CG
Sanket Wagle, Alexey Markin, Pawel Górecki, Tavis K. Anderson, Oliver Eulenstein
2022 A conf
CPTAM: Constituency Parse Tree Aggregation Method.
SDM
Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li
2022 J jnl
CPTAM: Constituency Parse Tree Aggregation Method.
CoRR
Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li
2022 J jnl
RF-Net 2: fast inference of virus reassortment and hybridization networks.
Bioinform.
Alexey Markin, Sanket Wagle, Tavis K. Anderson, Oliver Eulenstein
2022 — conf
Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics.
IPDPS Workshops
Alvin Chon, Pawel Górecki, Oliver Eulenstein, Xiaoqiu Huang, Ali Jannesari
2021 J jnl
Consensus of All Solutions for Intractable Phylogenetic Tree Inference.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Tabaszewski, Pawel Górecki, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein
2021 J jnl
Introduction to the JBCB Special Issue on Selected Papers from BICOB-2020.
J. Bioinform. Comput. Biol.
Oliver Eulenstein, Qin Ding, Hisham Al-Mubaid
2021 — conf
Novel genomic duplication models through integer linear programming.
BCB
Jaroslaw Paszek, Oliver Eulenstein, Pawel Górecki
2021 J jnl
Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model.
Bioinform.
Alexey Markin, Oliver Eulenstein
2021 J jnl
Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming.
J. Comput. Biol.
Jaroslaw Paszek, Alexey Markin, Pawel Górecki, Oliver Eulenstein
2021 J jnl
The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Górecki, Oliver Eulenstein, Jerzy Tiuryn
2020 J jnl
Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.
Bioinform.
Huy N. Nguyen, Alexey Markin, Iddo Friedberg, Oliver Eulenstein
2020 — conf
Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model.
ISBRA
Javad Ansarifar, Alexey Markin, Pawel Górecki, Oliver Eulenstein
2019 J jnl
Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alexey Markin, Oliver Eulenstein
2019 C conf
Consensus Clusters in Robinson-Foulds Reticulation Networks.
WABI
Alexey Markin, Oliver Eulenstein
2019 J jnl
Cophenetic Median Trees.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alexey Markin, Oliver Eulenstein
2019 J jnl
Efficient Local Search for Euclidean Path-Difference Median Trees.
IEEE ACM Trans. Comput. Biol. Bioinform.
Alexey Markin, Oliver Eulenstein
2019 Misc conf
Feasibility Algorithms for the Duplication-Loss Cost.
COCOON
Pawel Górecki, Alexey Markin, Oliver Eulenstein
2019 J jnl
Foreword: Special Issue for the 2019 International Conference on Bioinformatics and Computational Biology (BICOB-2019).
J. Bioinform. Comput. Biol.
Qin Ding, Oliver Eulenstein, Hisham Al-Mubaid
2019 J jnl
Mathematical properties of the gene duplication cost.
Discret. Appl. Math.
Pawel Górecki, Agnieszka Mykowiecka, Jaroslaw Paszek, Oliver Eulenstein
2019 — conf
Robinson-Foulds Reticulation Networks.
BCB
Alexey Markin, Tavis K. Anderson, Venkata Sai Krishna Teja Vadali, Oliver Eulenstein
2019 — conf
The Cluster Affinity Distance for Phylogenies.
ISBRA
Jucheol Moon, Oliver Eulenstein
2019 J jnl
Tracing the ancestry of operons in bacteria.
Bioinform.
Huy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg
2018 J jnl
Bijective Diameters of Gene Tree Parsimony Costs.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Górecki, Oliver Eulenstein
2018 — conf
Cluster Matching Distance for Rooted Phylogenetic Trees.
ISBRA
Jucheol Moon, Oliver Eulenstein
2018 Misc conf
Cophenetic Distances: A Near-Linear Time Algorithmic Framework.
COCOON
Pawel Górecki, Alexey Markin, Oliver Eulenstein
2018 J jnl
Introduction to JBCB Special Issue on BICOB-2018.
J. Bioinform. Comput. Biol.
Hisham Al-Mubaid, Qin Ding, Oliver Eulenstein
2018 — conf
Phylogenetic Consensus for Exact Median Trees.
BCB
Pawel Tabaszewski, Pawel Górecki, Oliver Eulenstein
2018 Misc conf
Solving the Gene Duplication Feasibility Problem in Linear Time.
COCOON
Alexey Markin, Venkata Sai Krishna Teja Vadali, Oliver Eulenstein
2017 — conf
Cophenetic Median Trees Under the Manhattan Distance.
BCB
Alexey Markin, Oliver Eulenstein
2017 J jnl
Foreword.
J. Bioinform. Comput. Biol.
Oliver Eulenstein, Qin Ding, Hisham Al-Mubaid
2017 — conf
Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees.
ISBRA
Pawel Górecki, Alexey Markin, Agnieszka Mykowiecka, Jaroslaw Paszek, Oliver Eulenstein
2017 — conf
Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach.
BCB
Jucheol Moon, Oliver Eulenstein
2017 J jnl
Synthesizing large-scale species trees using the strict consensus approach.
J. Bioinform. Comput. Biol.
Jucheol Moon, Oliver Eulenstein
2017 J jnl
Unconstrained Diameters for Deep Coalescence.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein
2016 J jnl
Consensus properties and their large-scale applications for the gene duplication problem.
J. Bioinform. Comput. Biol.
Jucheol Moon, Harris T. Lin, Oliver Eulenstein
2016 Misc conf
Highly Bi-Connected Subgraphs for Computational Protein Function Annotation.
COCOON
Jucheol Moon, Iddo Friedberg, Oliver Eulenstein
2016 — conf
Manhattan Path-Difference Median Trees.
BCB
Alexey Markin, Oliver Eulenstein
2016 — conf
Path-Difference Median Trees.
ISBRA
Alexey Markin, Oliver Eulenstein
2016 — conf
Robinson-Foulds Median Trees: A Clique-based Heuristic.
BCB
Jucheol Moon, Oliver Eulenstein
2015 J jnl
Gene Tree Diameter for Deep Coalescence.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Górecki, Oliver Eulenstein
2014 — conf
Big Guys and Big Data: Mining Shareholder Interaction Networks of Transnational MediaCompanies with Weighted Quasi-Bicliques.
MKWI
Sabine Baumann, Oliver Eulenstein
2014 J jnl
DrML: Probabilistic Modeling of Gene Duplications.
J. Comput. Biol.
Pawel Górecki, Oliver Eulenstein
2014 — conf
Duplication Cost Diameters.
ISBRA
Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein
2014 J jnl
Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications.
IEEE ACM Trans. Comput. Biol. Bioinform.
Zhipeng Cai, Oliver Eulenstein, Cynthia Gibas
2014 J jnl
Guest editors' introduction to the Proceedings of the 9
BMC Bioinform.
Cynthia Gibas, Zhipeng Cai, Oliver Eulenstein
2014 J jnl
Maximizing Deep Coalescence Cost.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Górecki, Oliver Eulenstein
2014 J jnl
Refining discordant gene trees.
BMC Bioinform.
Pawel Górecki, Oliver Eulenstein
2014 — conf
Unconstrained gene tree diameters for deep coalescence.
BCB
Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein
2013 J jnl
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Oliver Eulenstein
2013 — ed.
Bioinformatics Research and Applications, 9th International Symposium, ISBRA 2013, Charlotte, NC, USA, May 20-22, 2013. Proceedings
ISBRA
Zhipeng Cai, Oliver Eulenstein, Daniel Janies, Daniel Schwartz
2013 J jnl
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems.
IEEE ACM Trans. Comput. Biol. Bioinform.
André Wehe, J. Gordon Burleigh, Oliver Eulenstein
2013 J jnl
Exact solutions for species Tree Inference from discordant gene Trees.
J. Bioinform. Comput. Biol.
Wen-Chieh Chang, Pawel Górecki, Oliver Eulenstein
2013 J jnl
Unrooted Tree Reconciliation: A Unified Approach.
IEEE ACM Trans. Comput. Biol. Bioinform.
Pawel Górecki, Oliver Eulenstein, Jerzy Tiuryn
2012 — conf
A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees.
ISBRA
Pawel Górecki, Oliver Eulenstein
2012 — conf
Algorithms for Knowledge-Enhanced Supertrees.
ISBRA
André Wehe, J. Gordon Burleigh, Oliver Eulenstein
2012 J jnl
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem.
BMC Bioinform.
Pawel Górecki, Oliver Eulenstein
2012 J jnl
Consensus properties for the deep coalescence problem and their application for scalable tree search.
BMC Bioinform.
Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein
2012 Misc conf
Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms.
COCOON
Pawel Górecki, Oliver Eulenstein
2012 J jnl
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence.
BMC Bioinform.
Ruchi Chaudhary, J. Gordon Burleigh, Oliver Eulenstein
2012 J jnl
Exploring biological interaction networks with tailored weighted quasi-bicliques.
BMC Bioinform.
Wen-Chieh Chang, Sudheer Vakati, Roland Krause, Oliver Eulenstein
2012 — conf
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches.
ISBRA
Pawel Górecki, J. Gordon Burleigh, Oliver Eulenstein
2011 — conf
A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees.
ISBRA
Pawel Górecki, Oliver Eulenstein
2011 — conf
Algorithms for Rapid Error Correction for the Gene Duplication Problem.
ISBRA
Ruchi Chaudhary, J. Gordon Burleigh, Oliver Eulenstein
2011 J jnl
An ILP solution for the gene duplication problem.
BMC Bioinform.
Wen-Chieh Chang, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein
2011 — conf
Invited: Reconciled gene trees and their applications.
ICCABS
Oliver Eulenstein
2011 J jnl
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses.
BMC Bioinform.
Pawel Górecki, J. Gordon Burleigh, Oliver Eulenstein
2011 — conf
Mining Biological Interaction Networks Using Weighted Quasi-Bicliques.
ISBRA
Wen-Chieh Chang, Sudheer Vakati, Roland Krause, Oliver Eulenstein
2011 — conf
The Deep Coalescence Consensus Tree Problem is Pareto on Clusters.
ISBRA
Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein
2011 J jnl
The Plexus Model for the Inference of Ancestral Multidomain Proteins.
IEEE ACM Trans. Comput. Biol. Bioinform.
John Wiedenhoeft, Roland Krause, Oliver Eulenstein
2010 J jnl
A scalable parallelization of the gene duplication problem.
J. Parallel Distributed Comput.
André Wehe, Wen-Chieh Chang, Oliver Eulenstein, Srinivas Aluru
2010 J jnl
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models.
BMC Bioinform.
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein
2010 — conf
Inferring Evolutionary Scenarios for Protein Domain Compositions.
ISBRA
John Wiedenhoeft, Roland Krause, Oliver Eulenstein
2010 — conf
Inferring species trees from gene duplication episodes.
BCB
J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision
2010 J jnl
Robinson-Foulds Supertrees.
Algorithms Mol. Biol.
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca
2010 — conf
Triplet-Supertrees constructed from Minimum Triplet Presentations.
BICoB
Max Homilius, John Gordon Burleigh, Oliver Eulenstein
2010 J jnl
iGTP: A software package for large-scale gene tree parsimony analysis.
BMC Bioinform.
Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein
2009 — conf
Generalized Binary Tanglegrams: Algorithms and Applications.
BICoB
Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca
2009 J jnl
Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants.
J. Comput. Biol.
John Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein
2009 J jnl
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Oliver Eulenstein, André Wehe
2009 J jnl
Triplet supertree heuristics for the tree of life.
BMC Bioinform.
Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein
2008 J jnl
An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem.
IEEE ACM Trans. Comput. Biol. Bioinform.
Mukul S. Bansal, Oliver Eulenstein
2008 J jnl
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.
Bioinform.
André Wehe, Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein
2008 B conf
Locating Multiple Gene Duplications through Reconciled Trees.
RECOMB
J. Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein
2008 — conf
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches.
ISBRA
Mukul S. Bansal, Oliver Eulenstein
2008 A conf
The multiple gene duplication problem revisited.
ISMB
Mukul S. Bansal, Oliver Eulenstein
2007 C conf
An
WABI
Mukul S. Bansal, Oliver Eulenstein
2007 B conf
Heuristics for the Gene-Duplication Problem: A
RECOMB
Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe
2006 J jnl
Minimum-Flip Supertrees: Complexity and Algorithms.
IEEE ACM Trans. Comput. Biol. Bioinform.
Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
2006 Misc conf
Reconciling Gene Trees with Apparent Polytomies.
COCOON
Wen-Chieh Chang, Oliver Eulenstein
2004 J jnl
Rainbow: a toolbox for phylogenetic supertree construction and analysis.
Bioinform.
Duhong Chen, Oliver Eulenstein, David Fernández-Baca
2002 Misc conf
Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem.
Pacific Symposium on Biocomputing
J. Schonfeld, Oliver Eulenstein, Kent Vander Velden, Gavin J. P. Naylor
2002 Misc conf
Supertrees by Flipping.
COCOON
Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
2001 — conf
Flipping: A supertree construction method.
Bioconsensus
Duhong Chen, Lixia Diao, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson
1999 — book
Vorhersage von Genduplikationen und deren Entwicklung in der Evolution.
Oliver Eulenstein
1998 J jnl
Duplication-Based Measures of Difference Between Gene and Species Trees.
J. Comput. Biol.
Oliver Eulenstein, Boris G. Mirkin, Martin Vingron
1998 J jnl
On the Equivalence of Two Tree Mapping Measures.
Discret. Appl. Math.
Oliver Eulenstein, Martin Vingron
1998 J jnl
Towards detection of orthologues in sequence databases.
Bioinform.
Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork
1997 — conf
Towards detection of sequence orthologs.
German Conference on Bioinformatics
Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork
1996 — conf
Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees.
Mathematical Hierarchies and Biology
Oliver Eulenstein, Boris G. Mirkin, Martin Vingron