Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees. - Oliver Eulenstein; Boris G. Mirkin; Martin Vingron (Mathematical Hierarchies and Biology, 1996)

Towards detection of sequence orthologs. - Yan P. Yuan; Oliver Eulenstein; Martin Vingron; Peer Bork (German Conference on Bioinformatics, 1997)

Towards detection of orthologues in sequence databases. - Yan P. Yuan; Oliver Eulenstein; Martin Vingron; Peer Bork (Bioinform., 1998)

On the Equivalence of Two Tree Mapping Measures. - Oliver Eulenstein; Martin Vingron (Discret. Appl. Math., 1998)

Duplication-Based Measures of Difference Between Gene and Species Trees. - Oliver Eulenstein; Boris G. Mirkin; Martin Vingron (J. Comput. Biol., 1998)

Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. - Oliver Eulenstein (GMD, 1999)

Flipping: A supertree construction method. - Duhong Chen; Lixia Diao; Oliver Eulenstein; David Fernández-Baca; Michael J. Sanderson (Bioconsensus, 2001)

Supertrees by Flipping. - Duhong Chen; Oliver Eulenstein; David Fernández-Baca; Michael J. Sanderson (COCOON, 2002)

Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem. - J. Schonfeld; Oliver Eulenstein; Kent Vander Velden; Gavin J. P. Naylor (Pacific Symposium on Biocomputing, 2002)

Rainbow: a toolbox for phylogenetic supertree construction and analysis. - Duhong Chen; Oliver Eulenstein; David Fernández-Baca (Bioinform., 2004)

Reconciling Gene Trees with Apparent Polytomies. - Wen-Chieh Chang 002; Oliver Eulenstein (COCOON, 2006)

Minimum-Flip Supertrees: Complexity and Algorithms. - Duhong Chen; Oliver Eulenstein; David Fernández-Baca; Michael J. Sanderson (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search. - Mukul S. Bansal; J. Gordon Burleigh; Oliver Eulenstein; André Wehe (RECOMB, 2007)

An Omega(n2/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. - Mukul S. Bansal; Oliver Eulenstein (WABI, 2007)

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches. - Mukul S. Bansal; Oliver Eulenstein (ISBRA, 2008)

The multiple gene duplication problem revisited. - Mukul S. Bansal; Oliver Eulenstein (ISMB, 2008)

Locating Multiple Gene Duplications through Reconciled Trees. - J. Gordon Burleigh; Mukul S. Bansal; André Wehe; Oliver Eulenstein (RECOMB, 2008)

DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. - André Wehe; Mukul S. Bansal; J. Gordon Burleigh; Oliver Eulenstein (Bioinform., 2008)

An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. - Mukul S. Bansal; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Generalized Binary Tanglegrams: Algorithms and Applications. - Mukul S. Bansal; Wen-Chieh Chang 002; Oliver Eulenstein; David Fernández-Baca (BICoB, 2009)

Triplet supertree heuristics for the tree of life. - Harris T. Lin; J. Gordon Burleigh; Oliver Eulenstein (BMC Bioinform., 2009)

Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants. - John Gordon Burleigh; Mukul S. Bansal; André Wehe; Oliver Eulenstein (J. Comput. Biol., 2009)

The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches. - Mukul S. Bansal; Oliver Eulenstein; André Wehe (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Inferring species trees from gene duplication episodes. - J. Gordon Burleigh; Mukul S. Bansal; Oliver Eulenstein; Todd J. Vision (BCB, 2010)

Triplet-Supertrees constructed from Minimum Triplet Presentations. - Max Homilius; John Gordon Burleigh; Oliver Eulenstein (BICoB, 2010)

Inferring Evolutionary Scenarios for Protein Domain Compositions. - John Wiedenhoeft; Roland Krause; Oliver Eulenstein (ISBRA, 2010)

Robinson-Foulds Supertrees. - Mukul S. Bansal; J. Gordon Burleigh; Oliver Eulenstein; David Fernández-Baca (Algorithms Mol. Biol., 2010)

Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. - Mukul S. Bansal; J. Gordon Burleigh; Oliver Eulenstein (BMC Bioinform., 2010)

iGTP: A software package for large-scale gene tree parsimony analysis. - Ruchi Chaudhary; Mukul S. Bansal; André Wehe; David Fernández-Baca; Oliver Eulenstein (BMC Bioinform., 2010)

A scalable parallelization of the gene duplication problem. - André Wehe; Wen-Chieh Chang 002; Oliver Eulenstein; Srinivas Aluru (J. Parallel Distributed Comput., 2010)

Invited: Reconciled gene trees and their applications. - Oliver Eulenstein (ICCABS, 2011)

Mining Biological Interaction Networks Using Weighted Quasi-Bicliques. - Wen-Chieh Chang 002; Sudheer Vakati; Roland Krause; Oliver Eulenstein (ISBRA, 2011)

Algorithms for Rapid Error Correction for the Gene Duplication Problem. - Ruchi Chaudhary; J. Gordon Burleigh; Oliver Eulenstein (ISBRA, 2011)

A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees. - Pawel Górecki 001; Oliver Eulenstein (ISBRA, 2011)

The Deep Coalescence Consensus Tree Problem is Pareto on Clusters. - Harris T. Lin; J. Gordon Burleigh; Oliver Eulenstein (ISBRA, 2011)

An ILP solution for the gene duplication problem. - Wen-Chieh Chang 002; J. Gordon Burleigh; David Fernández-Baca; Oliver Eulenstein (BMC Bioinform., 2011)

Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. - Pawel Górecki 001; J. Gordon Burleigh; Oliver Eulenstein (BMC Bioinform., 2011)

The Plexus Model for the Inference of Ancestral Multidomain Proteins. - John Wiedenhoeft; Roland Krause; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms. - Pawel Górecki 001; Oliver Eulenstein (COCOON, 2012)

GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches. - Pawel Górecki 001; J. Gordon Burleigh; Oliver Eulenstein (ISBRA, 2012)

A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees. - Pawel Górecki 001; Oliver Eulenstein (ISBRA, 2012)

Algorithms for Knowledge-Enhanced Supertrees. - André Wehe; J. Gordon Burleigh; Oliver Eulenstein (ISBRA, 2012)

Exploring biological interaction networks with tailored weighted quasi-bicliques. - Wen-Chieh Chang 002; Sudheer Vakati; Roland Krause; Oliver Eulenstein (BMC Bioinform., 2012)

Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. - Ruchi Chaudhary; J. Gordon Burleigh; Oliver Eulenstein (BMC Bioinform., 2012)

Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. - Pawel Górecki 001; Oliver Eulenstein (BMC Bioinform., 2012)

Consensus properties for the deep coalescence problem and their application for scalable tree search. - Harris T. Lin; J. Gordon Burleigh; Oliver Eulenstein (BMC Bioinform., 2012)

Exact solutions for species Tree Inference from discordant gene Trees. - Wen-Chieh Chang 002; Pawel Górecki 001; Oliver Eulenstein (J. Bioinform. Comput. Biol., 2013)

Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony. - Mukul S. Bansal; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Unrooted Tree Reconciliation: A Unified Approach. - Pawel Górecki 001; Oliver Eulenstein; Jerzy Tiuryn (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems. - André Wehe; J. Gordon Burleigh; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Unconstrained gene tree diameters for deep coalescence. - Pawel Górecki 001; Jaroslaw Paszek; Oliver Eulenstein (BCB, 2014)

Duplication Cost Diameters. - Pawel Górecki 001; Jaroslaw Paszek; Oliver Eulenstein (ISBRA, 2014)

Big Guys and Big Data: Mining Shareholder Interaction Networks of Transnational MediaCompanies with Weighted Quasi-Bicliques. - Sabine Baumann; Oliver Eulenstein (MKWI, 2014)

Guest editors' introduction to the Proceedings of the 9th International Symposium on Biomedical Research and Applications. - Cynthia Gibas; Zhipeng Cai 001; Oliver Eulenstein (BMC Bioinform., 2014)

Refining discordant gene trees. - Pawel Górecki 001; Oliver Eulenstein (BMC Bioinform., 2014)

DrML: Probabilistic Modeling of Gene Duplications. - Pawel Górecki 001; Oliver Eulenstein (J. Comput. Biol., 2014)

Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications. - Zhipeng Cai 001; Oliver Eulenstein; Cynthia Gibas (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Maximizing Deep Coalescence Cost. - Pawel Górecki 001; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Gene Tree Diameter for Deep Coalescence. - Pawel Górecki 001; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Manhattan Path-Difference Median Trees. - Alexey Markin; Oliver Eulenstein (BCB, 2016)

Robinson-Foulds Median Trees: A Clique-based Heuristic. - Jucheol Moon; Oliver Eulenstein (BCB, 2016)

Highly Bi-Connected Subgraphs for Computational Protein Function Annotation. - Jucheol Moon; Iddo Friedberg; Oliver Eulenstein (COCOON, 2016)

Path-Difference Median Trees. - Alexey Markin; Oliver Eulenstein (ISBRA, 2016)

Consensus properties and their large-scale applications for the gene duplication problem. - Jucheol Moon; Harris T. Lin; Oliver Eulenstein (J. Bioinform. Comput. Biol., 2016)

Cophenetic Median Trees Under the Manhattan Distance. - Alexey Markin; Oliver Eulenstein (BCB, 2017)

Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach. - Jucheol Moon; Oliver Eulenstein (BCB, 2017)

Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees. - Pawel Górecki 001; Alexey Markin; Agnieszka Mykowiecka 002; Jaroslaw Paszek; Oliver Eulenstein (ISBRA, 2017)

Foreword. - Oliver Eulenstein; Qin Ding 001; Hisham Al-Mubaid (J. Bioinform. Comput. Biol., 2017)

Synthesizing large-scale species trees using the strict consensus approach. - Jucheol Moon; Oliver Eulenstein (J. Bioinform. Comput. Biol., 2017)

Unconstrained Diameters for Deep Coalescence. - Pawel Górecki 001; Jaroslaw Paszek; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Phylogenetic Consensus for Exact Median Trees. - Pawel Tabaszewski; Pawel Górecki 001; Oliver Eulenstein (BCB, 2018)

Cophenetic Distances: A Near-Linear Time Algorithmic Framework. - Pawel Górecki 001; Alexey Markin; Oliver Eulenstein (COCOON, 2018)

Solving the Gene Duplication Feasibility Problem in Linear Time. - Alexey Markin; Venkata Sai Krishna Teja Vadali; Oliver Eulenstein (COCOON, 2018)

Cluster Matching Distance for Rooted Phylogenetic Trees. - Jucheol Moon; Oliver Eulenstein (ISBRA, 2018)

Introduction to JBCB Special Issue on BICOB-2018. - Hisham Al-Mubaid; Qin Ding 001; Oliver Eulenstein (J. Bioinform. Comput. Biol., 2018)

Bijective Diameters of Gene Tree Parsimony Costs. - Pawel Górecki 001; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Robinson-Foulds Reticulation Networks. - Alexey Markin; Tavis K. Anderson; Venkata Sai Krishna Teja Vadali; Oliver Eulenstein (BCB, 2019)

Feasibility Algorithms for the Duplication-Loss Cost. - Pawel Górecki 001; Alexey Markin; Oliver Eulenstein (COCOON, 2019)

The Cluster Affinity Distance for Phylogenies. - Jucheol Moon; Oliver Eulenstein (ISBRA, 2019)

Consensus Clusters in Robinson-Foulds Reticulation Networks. - Alexey Markin; Oliver Eulenstein (WABI, 2019)

Tracing the ancestry of operons in bacteria. - Huy N. Nguyen; Ashish Jain; Oliver Eulenstein; Iddo Friedberg (Bioinform., 2019)

Mathematical properties of the gene duplication cost. - Pawel Górecki 001; Agnieszka Mykowiecka 002; Jaroslaw Paszek; Oliver Eulenstein (Discret. Appl. Math., 2019)

Foreword: Special Issue for the 2019 International Conference on Bioinformatics and Computational Biology (BICOB-2019). - Qin Ding 001; Oliver Eulenstein; Hisham Al-Mubaid (J. Bioinform. Comput. Biol., 2019)

Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach. - Alexey Markin; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Efficient Local Search for Euclidean Path-Difference Median Trees. - Alexey Markin; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Cophenetic Median Trees. - Alexey Markin; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model. - Javad Ansarifar; Alexey Markin; Pawel Górecki 001; Oliver Eulenstein (ISBRA, 2020)

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it. - Huy N. Nguyen; Alexey Markin; Iddo Friedberg; Oliver Eulenstein (Bioinform., 2020)

Novel genomic duplication models through integer linear programming. - Jaroslaw Paszek; Oliver Eulenstein; Pawel Górecki 001 (BCB, 2021)

Introduction to the JBCB Special Issue on Selected Papers from BICOB-2020. - Oliver Eulenstein; Qin Ding 001; Hisham Al-Mubaid (J. Bioinform. Comput. Biol., 2021)

Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming. - Jaroslaw Paszek; Alexey Markin; Pawel Górecki 001; Oliver Eulenstein (J. Comput. Biol., 2021)

The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost. - Pawel Górecki 001; Oliver Eulenstein; Jerzy Tiuryn (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Consensus of All Solutions for Intractable Phylogenetic Tree Inference. - Pawel Tabaszewski; Pawel Górecki 001; Alexey Markin; Tavis K. Anderson; Oliver Eulenstein (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model. - Alexey Markin; Oliver Eulenstein (Bioinform., 2021)

Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics. - Alvin Chon; Pawel Górecki 001; Oliver Eulenstein; Xiaoqiu Huang 001; Ali Jannesari (IPDPS Workshops, 2022)

CPTAM: Constituency Parse Tree Aggregation Method. - Adithya Kulkarni; Nasim Sabetpour; Alexey Markin; Oliver Eulenstein; Qi Li 012 (SDM, 2022)

RF-Net 2: fast inference of virus reassortment and hybridization networks. - Alexey Markin; Sanket Wagle; Tavis K. Anderson; Oliver Eulenstein (Bioinform., 2022)

The Asymmetric Cluster Affinity Cost. - Sanket Wagle; Alexey Markin; Pawel Górecki 001; Tavis K. Anderson; Oliver Eulenstein (RECOMB-CG, 2023)

Phylogenetic diversity statistics for all clades in a phylogeny. - Siddhant Grover; Alexey Markin; Tavis K. Anderson; Oliver Eulenstein (Bioinform., 2023)

Using Conceptual Blending to Teach Software Design Principles to Undergraduates. - Ashraf Gaffar; Mohamed Y. Selim; Oliver Eulenstein (FIE, 2024)

Empirical Analysis for Unsupervised Universal Dependency Parse Tree Aggregation. - Adithya Kulkarni; Oliver Eulenstein; Qi Li 012 (CoRR, 2024)

Asymmetric Cluster-Based Measures for Comparative Phylogenetics. - Sanket Wagle; Alexey Markin; Pawel Górecki 001; Tavis K. Anderson; Oliver Eulenstein (J. Comput. Biol., 2024)

Beyond Single Parsers: An Empirical Analysis of Dependency Parse Tree Aggregation. - Adithya Kulkarni; Mohna Chakraborty; Oliver Eulenstein; Qi Li 012 (PAKDD (Workshops), 2025)

Phylo-rs: an extensible phylogenetic analysis library in rust. - Sriram Vijendran; Tavis K. Anderson; Alexey Markin; Oliver Eulenstein (BMC Bioinform., 2025)