Publications

---2023---
Phylogenetic diversity statistics for all clades in a phylogeny

Grover, Siddhant; Markin, Alexey; Anderson, Tavis K; Eulenstein, Oliver;

Bioinformatics, 39, Supplement 1, i177--i184, 2023

The Asymmetric Cluster Affinity Cost

Wagle, Sanket; Markin, Alexey; Górecki, Pawel; Anderson, Tavis K; Eulenstein, Oliver;

Comparative Genomics, , , 131--145, 2023

---2022---
RF-Net 2: fast inference of virus reassortment and hybridization networks

Markin, Alexey; Wagle, Sanket; Anderson, Tavis K; Eulenstein, Oliver;

Bioinformatics, 38, 8, 2144--2152, 2022

Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics

Alvin Chon, Huang Xiaoqiu, Oliver Eulenstein, Ali Jannesari.;

21st IEEE International Workshop on High Performance Computational Biology, 2022

CPTAM: Constituency Parse Tree Aggregation Method

Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li;

SIAM International Conference on Data Mining (SDM 2022), 2022

---2021---
Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming

Paszek, Jarosław; Alexey Markin; Górecki, Paweł; Eulenstein, Oliver;

Journal of Computational Biology, 28, 8, 758--773, 2021

Novel genomic duplication models through integer linear programming

Paszek, Jarosław; Eulenstein, Oliver; Górecki, Paweł;

Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2021

---2020---
Quartet-based inference methods are statistically consistent under the unified duplication-loss-coalescence model

Markin, Alexey; Eulenstein, Oliver;

Bioinformatics, 37, 22, 4064--4074, 2020

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

Nguyen, Huy N; Markin, Alexey; Friedberg, Iddo; Eulenstein, Oliver;

Bioinformatics, 36, Supplement_2, i668--i674, 2020

Exact median-tree inference for unrooted reconciliation costs

Górecki, Paweł; Markin, Alexey; Eulenstein, Oliver;

BMC Evolutionary Biology, 20, 1, 1--15, 2020

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

Ansarifar, Javad; Markin, Alexey; Górecki, Paweł; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2020

---2019---
The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost

Górecki, Paweł; Eulenstein, Oliver; Tiuryn, Jerzy;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 18, 6, 2125--2135, 2019

Consensus of all Solutions for Intractable Phylogenetic Tree Inference

Tabaszewski, Pawel; Górecki, Pawel; Markin, Alexey; Anderson, T; Eulenstein, Oliver;

IEEE/ACM transactions on computational biology and bioinformatics, 18, 1, 149--161, 2019

Tracing the ancestry of operons in bacteria

Nguyen, Huy N; Jain, Ashish; Eulenstein, Oliver; Friedberg, Iddo;

Bioinformatics, 35, 17, 2998--3004, 2019

Robinson-foulds reticulation networks

Markin, Alexey; Anderson, Tavis K; Vadali, Venkata Sai Krishna Teja; Eulenstein, Oliver;

Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, 2019

Consensus clusters in robinson-foulds reticulation networks

Markin, Alexey; Eulenstein, Oliver;

19th International Workshop on Algorithms in Bioinformatics (WABI 2019), 2019

Feasibility Algorithms for the Duplication-Loss Cost

Górecki, Paweł; Markin, Alexey; Eulenstein, Oliver;

International Computing and Combinatorics Conference, 2019

The Cluster Affinity Distance for Phylogenies

Moon, Jucheol; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2019

---2018---
Cophenetic median trees

Markin, Alexey; Eulenstein, Oliver;

IEEE/ACM transactions on computational biology and bioinformatics, 16, 5, 1459--1470, 2018

Phylogenetic consensus for exact median trees

Tabaszewski, Pawel; Górecki, Pawel; Eulenstein, Oliver;

Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2018

Cophenetic distances: A near-linear time algorithmic framework

Górecki, Paweł; Markin, Alexey; Eulenstein, Oliver;

International Computing and Combinatorics Conference, 2018

Solving the gene duplication feasibility problem in linear time

Markin, Alexey; Vadali, Venkata Sai Krishna Teja; Eulenstein, Oliver;

International Computing and Combinatorics Conference, 2018

Cluster matching distance for rooted phylogenetic trees

Moon, Jucheol; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2018

---2017---
Bijective diameters of gene tree parsimony costs

Górecki, Paweł; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 15, 5, 1723--1727, 2017

Efficient local search for Euclidean path-difference median trees

Markin, Alexey; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 4, 1374--1385, 2017

Computing Manhattan path-difference median trees: A practical local search approach

Markin, Alexey; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16, 4, 1063--1076, 2017

Synthesizing large-scale species trees using the strict consensus approach

Moon, Jucheol; Eulenstein, Oliver;

Journal of bioinformatics and computational biology, 15, 03, 1740002, 2017

Cophenetic median trees under the manhattan distance

Markin, Alexey; Eulenstein, Oliver;

Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2017

Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees

Górecki, Paweł; Markin, Alexey; Mykowiecka, Agnieszka; Paszek, Jarosław; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2017

---2016---
Unconstrained diameters for deep coalescence

Górecki, Paweł; Paszek, Jarosław; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14, 5, 1002--1012, 2016

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

Moon, Jucheol; Lin, Harris T; Eulenstein, Oliver;

Journal of bioinformatics and computational biology, 14, 03, 1642005, 2016

Manhattan path-difference median trees

Markin, Alexey; Eulenstein, Oliver;

Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2016

Robinson-Foulds Median Trees: A Clique-based Heuristic

Moon, Jucheol; Eulenstein, Oliver;

Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 2016

Highly bi-connected subgraphs for computational protein function annotation

Moon, Jucheol; Friedberg, Iddo; Eulenstein, Oliver;

International Computing and Combinatorics Conference, 2016

Path-difference median trees

Markin, Alexey; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2016

---2015---
Consensus properties of the gene duplication problem for enhanced phylogenetic inference

Lin, H; Moon, Jucheol; Eulenstein, Oliver;

Proceedings of the International Conference on Bioinformatics and Computational Biology. Curran Associates, Inc., Red Hook, New York, United States, 2015

---2014---
Duplication cost diameters

Górecki, Paweł; Paszek, Jarosław; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2014

Gene tree diameter for deep coalescence

Górecki, Paweł; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 12, 1, 155--165, 2014

Refining discordant gene trees

Górecki, Pawel; Eulenstein, Oliver;

BMC bioinformatics, 2014

DrML: probabilistic modeling of gene duplications

Górecki, Paweł; Eulenstein, Oliver;

Journal of Computational Biology, 21, 1, 89--98, 2014

Unconstrained gene tree diameters for deep coalescence

Górecki, Paweł; Paszek, Jarosław; Eulenstein, Oliver;

Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, 2014

---2013---
Maximizing deep coalescence cost

Gorecki, Pawel; Eulenstein, Oliver;

IEEE/ACM transactions on computational biology and bioinformatics, 11, 1, 231--242, 2013

Unrooted tree reconciliation: A unified approach

Górecki, Pawel; Eulenstein, Oliver; Tiuryn, Jerzy;

IEEE/ACM transactions on computational biology and bioinformatics, 10, 2, 522--536, 2013

Exact solutions for classic gene tree parsimony problems

Chang, Wen-Chieh; Wehe, André; Górecki, Paweł; Eulenstein, Oliver;

Proc. of the 5th Int. Conf. on Bioinformatics and Computational Biology, 2013

Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013, Charlotte, NC, USA, May 20-22, 2013, Proceedings

Cai, Zhipeng; Eulenstein, Oliver; Janies, Daniel; Schwartz, Daniel;

, , , , 2013

Algorithms for Unrooted Gene Trees with Polytomies

Górecki, Paweł; Eulenstein, Oliver;

Short Abstract Proceedings of ISBRA:86-95, 2013

Mathematical Properties and Normalization of the Gene Duplication Cost

Bryan Shrader, André Wehe, Oliver Eulenstein;

Short Abstract Proceedings of ISBRA:92-96, 2013

---2012---
Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems

Wehe, André; Burleigh, J Gordon; Eulenstein, Oliver;

IEEE/ACM transactions on computational biology and bioinformatics, 10, 6, 1432--1441, 2012

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

Górecki, Pawel; Eulenstein, Oliver;

BMC bioinformatics, 2012

Exploring biological interaction networks with tailored weighted quasi-bicliques

Chang, Wen-Chieh; Vakati, Sudheer; Krause, Roland; Eulenstein, Oliver;

BMC bioinformatics, 2012

Efficient algorithms for rapid error correction for gene tree reconciliation using gene duplications, gene duplication and loss, and deep coalescence

Chaudhari, R; Burleigh, GJ; Eulenstein, O;

BMC Bioinformatics, 13, Suppl 10, S11, 2012

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

Lin, Harris T; Burleigh, J Gordon; Eulenstein, Oliver;

BMC bioinformatics, 2012

Who Pulls the Strings Behind the Scenes? Analysing Power Structures of International Media Finance Networks with Innovative Graph-Based Methods

Baumann, Sabine; Eulenstein, Oliver;

Internet, Politics, Policy: Big Data, Big Challenges 2012 pg 21--22, 2012

Algorithms for knowledge-enhanced supertrees

Wehe, André; Burleigh, J Gordon; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2012

GTP supertrees from unrooted gene trees: linear time algorithms for NNI based local searches

Górecki, Paweł; Burleigh, J Gordon; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2012

Deep coalescence reconciliation with unrooted gene trees: Linear time algorithms

Górecki, Paweł; Eulenstein, Oliver;

International Computing and Combinatorics Conference, 2012

A Robinson-Foulds measure to compare unrooted trees with rooted trees

Górecki, Paweł; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2012

---2011---
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses

Górecki, Pawel; Burleigh, Gordon J; Eulenstein, Oliver;

BMC bioinformatics, 12, 1, 1--9, 2011

An ILP solution for the gene duplication problem

Chang, Wen-Chieh; Burleigh, Gordon J; Fernández-Baca, David F; Eulenstein, Oliver;

BMC bioinformatics, 12, 1, 1--8, 2011

Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

Burleigh, J Gordon; Bansal, Mukul S; Eulenstein, Oliver; Hartmann, Stefanie; Wehe, André; Vision, Todd J;

Systematic Biology, 60, 2, 117--125, 2011

The plexus model for the inference of ancestral multidomain proteins

Wiedenhoeft, John; Krause, Roland; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8, 4, 890--901, 2011

A linear time algorithm for error-corrected reconciliation of unrooted gene trees

Górecki, Paweł; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2011

Mining biological interaction networks using weighted quasi-bicliques

Chang, Wen-Chieh; Vakati, Sudheer; Krause, Roland; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2011

Algorithms for rapid error correction for the gene duplication problem

Chaudhary, Ruchi; Burleigh, J Gordon; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2011

Life in the Fast Lane: Analysing corporate communication networks with innovative graph-based methods to prepare for crisis situations

Baumann, Sabine; Eulenstein, Oliver;

Centre for Corporate Communication (Hrsg.) Communicating Crisis in an Age of Complexity, Conference Proceedings #1 of the 2nd International Conference on Crisis Communication at the Beginning of the 21st Century, 2011

Reconciled gene trees and their applications

Eulenstein, Oliver;

2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), 2011

The deep coalescence consensus tree problem is pareto on clusters

Lin, Harris T; Burleigh, J Gordon; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2011

---2010---
iGTP: a software package for large-scale gene tree parsimony analysis

Chaudhary, Ruchi; Bansal, Mukul S; Wehe, André; Fernández-Baca, David; Eulenstein, Oliver;

BMC bioinformatics, 11, 1, 1--7, 2010

Robinson-foulds supertrees

Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver; Fernández-Baca, David;

Algorithms for molecular biology, 5, 1, 1--12, 2010

A scalable parallelization of the gene duplication problem

Wehe, André; Chang, Wen-Chieh; Eulenstein, Oliver; Aluru, Srinivas;

Journal of Parallel and Distributed Computing, 70, 3, 237--244, 2010

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

Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver;

BMC bioinformatics, 11, 1, 1--9, 2010

Inferring species trees from gene duplication episodes

Burleigh, J Gordon; Bansal, Mukul S; Eulenstein, Oliver; Vision, Todd J;

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

Triplet-Supertrees constructed from Minimum Triplet Presentations.

Homilius, Max; Burleigh, John Gordon; Eulenstein, Oliver;

BICoB, 2010

Inferring evolutionary scenarios for protein domain compositions

Wiedenhoeft, John; Krause, Roland; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2010

Reconciling phylogenetic trees

Oliver Eulenstein, S. Huzurbazar,; Liberles, David;

, , , , 2010

---2009---
The gene-duplication problem: Near-linear time algorithms for NNI-based local searches

Bansal, Mukul S; Eulenstein, Oliver; Wehe, André;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6, 2, 221--231, 2009

Triplet supertree heuristics for the tree of life

Lin, Harris T; Burleigh, J Gordon; Eulenstein, Oliver;

BMC bioinformatics, 10, 1, 1--12, 2009

Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants

Burleigh, John Gordon; Bansal, Mukul S; Wehe, André; Eulenstein, Oliver;

Journal of Computational Biology, 16, 8, 1071--1083, 2009

Groves of phylogenetic trees

Ané, Cécile; Eulenstein, Oliver; Piaggio-Talice, Raul; Sanderson, Michael J;

Annals of Combinatorics, 13, 2, 139--167, 2009

Generalized binary tanglegrams: Algorithms and applications

Bansal, Mukul S; Chang, Wen-Chieh; Eulenstein, Oliver; Fernández-Baca, David;

International Conference on Bioinformatics and Computational Biology, 2009

---2008---
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony

Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver;

Bioinformatics, 24, 13, 1540--1541, 2008

The multiple gene duplication problem revisited

Bansal, Mukul S; Eulenstein, Oliver;

Bioinformatics, 24, 13, i132--i138, 2008

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

Bansal, Mukul S; Eulenstein, Oliver;

IEEE/ACM Transactions on Computational Biology and Bioinformatics, 5, 4, 514--524, 2008

Locating multiple gene duplications through reconciled trees

Burleigh, J Gordon; Bansal, Mukul S; Wehe, Andre; Eulenstein, Oliver;

Annual International Conference on Research in Computational Molecular Biology, 2008

The gene-duplication problem: near-linear time algorithms for NNI based local searches

Bansal, Mukul S; Eulenstein, Oliver;

International Symposium on Bioinformatics Research and Applications, 2008

---2007---
An $Ømega$ (n 2/logn) Speed-Up of Heuristics for the Gene-Duplication Problem

Bansal, Mukul S; Eulenstein, Oliver;

International Workshop on Algorithms in Bioinformatics, 2007

Heuristics for the gene-duplication problem: A $Θ$ (n) speed-up for the local search

Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver; Wehe, André;

Annual International Conference on Research in Computational Molecular Biology, 2007

Fragmentation of large data sets in phylogenetic analyses

Michael J. Sanderson, Cécile Ané, Oliver Eulenstein, David Fernández-Baca, Kim Junhyong, Michelle M. McMahon,; Piaggio-Talice., Raul;

, , , , 2007

---2006---
Improved heuristics for minimum-flip supertree construction

Chen, Duhong; Eulenstein, Oliver; Fernández-Baca, David; Burleigh, J Gordon;

Evolutionary Bioinformatics, 2, , 117693430600200003, 2006

Minimum-flip supertrees: complexity and algorithms

Chen, Duhong; Eulenstein, Oliver; Fernandez-Baca, David; Sanderson, Michael;

IEEE/ACM transactions on computational biology and bioinformatics, 3, 2, 165--173, 2006

Reconciling gene trees with apparent polytomies

Chang, Wen-Chieh; Eulenstein, Oliver;

International Computing and Combinatorics Conference, 2006

---2005---
Identifying optimal incomplete phylogenetic data sets from sequence databases

Yan, Changhui; Burleigh, J Gordon; Eulenstein, Oliver;

Molecular phylogenetics and evolution, 35, 3, 528--535, 2005

The shape of supertrees to come: tree shape related properties of fourteen supertree methods

Wilkinson, Mark; Cotton, James A; Creevey, Chris; Eulenstein, Oliver; Harris, Simon R; Lapointe, Francois-Joseph; Levasseur, Claudine; Mcinerney, James O; Pisani, Davide; Thorley, Joseph L;

Systematic biology, 54, 3, 419--431, 2005

Consensus trees and supertrees

Eulenstein, Oliver;

, , , , 2005

---2004---
Performance of flip supertree construction with a heuristic algorithm

Eulenstein, Oliver; Chen, Duhong; Burleigh, J Gordon; Fernández-Baca, David; Sanderson, Michael J;

Systematic Biology, 53, 2, 299--308, 2004

Rainbow: a toolbox for phylogenetic supertree construction and analysis

Chen, Duhong; Eulenstein, Oliver; Fernández-Baca, David;

Bioinformatics, 20, 16, 2872--2873, 2004

MRF supertrees

J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca,; Sanderson, Michael J.;

, , , , 2004

Quartet supertrees

Raul Piaggio-Talice, J. Gordon Burleigh,; Eulenstein., Oliver;

, , , , 2004

---2003---
Obtaining maximal concatenated phylogenetic data sets from large sequence databases

Sanderson, Michael J; Driskell, Amy C; Ree, Richard H; Eulenstein, Oliver; Langley, Sasha;

Molecular biology and evolution, 20, 7, 1036--1042, 2003

Flipping: a supertree construction method

Chen, Duhong; Diao, Lixia; Eulenstein, Oliver; Fernández-Baca, David; Sanderson, M;

DIMACS series in discrete mathematics and theoretical computer science, 61, , 135--162, 2003

---2002---
Supertrees by flipping

Chen, Duhong; Eulenstein, Oliver; Fernández-Baca, David; Sanderson, Michael;

International Computing and Combinatorics Conference, 2002

---2001---
Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem

Schonfeld, J; Eulenstein, Oliver; Vander Velden, Kent; Naylor, Gavin JP;

Biocomputing 2002, 2001

---1998---
Duplication-based measures of difference between gene and species trees

Eulenstein, Oliver; Mirkin, Boris; Vingron, Martin;

Journal of Computational Biology, 5, 1, 135--148, 1998

On the equivalence of two tree mapping measures

Eulenstein, Oliver; Vingron, Martin;

Discrete Applied Mathematics, 88, 1-3, 103--128, 1998

Towards detection of orthologues in sequence databases.

Yuan, Yan P.; Eulenstein, Oliver; Vingron, Martin; Bork, Peer;

Bioinformatics (Oxford, England), 14, 3, 285--289, 1998

---1997---
Comparison of Annotating Duplication, Tree Mapping, and Copying as Methods to Compare Gene Trees with Species

Eulenstein, Oliver; Mirkin, Boris; Vingron, Martin;

Mathematical Hierarchies and Biology: DIMACS Workshop, November 13-15, 1996, 1997

---1990---
Multi-viewing of an EDIF Netlist Schema.

Eulenstein, Oliver;

Proceedings Fourth European EDIF Forum, 1990