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2020 – today
- 2024
[j51]Sanket Wagle
, Alexey Markin, Pawel Górecki, Tavis K. Anderson, Oliver Eulenstein:
Asymmetric Cluster-Based Measures for Comparative Phylogenetics. J. Comput. Biol. 31(4): 312-327 (2024)- [i2]Adithya Kulkarni, Oliver Eulenstein, Qi Li:
Empirical Analysis for Unsupervised Universal Dependency Parse Tree Aggregation. CoRR abs/2403.19183 (2024) - 2023
- [j50]Siddhant Grover, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein:
Phylogenetic diversity statistics for all clades in a phylogeny. Bioinform. 39(Supplement-1): 177-184 (2023) - [c47]Sanket Wagle, Alexey Markin, Pawel Górecki, Tavis K. Anderson, Oliver Eulenstein:
The Asymmetric Cluster Affinity Cost. RECOMB-CG 2023: 131-145 - 2022
- [j49]Alexey Markin, Sanket Wagle, Tavis K. Anderson, Oliver Eulenstein:
RF-Net 2: fast inference of virus reassortment and hybridization networks. Bioinform. 38(8): 2144-2152 (2022) - [c46]Alvin Chon, Pawel Górecki, Oliver Eulenstein, Xiaoqiu Huang, Ali Jannesari:
Scalable and Extensible Robinson-Foulds for Comparative Phylogenetics. IPDPS Workshops 2022: 166-175 - [c45]Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li:
CPTAM: Constituency Parse Tree Aggregation Method. SDM 2022: 630-638 - [i1]Adithya Kulkarni, Nasim Sabetpour, Alexey Markin, Oliver Eulenstein, Qi Li:
CPTAM: Constituency Parse Tree Aggregation Method. CoRR abs/2201.07905 (2022) - 2021
- [j48]Alexey Markin, Oliver Eulenstein:
Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model. Bioinform. 37(22): 4064-4074 (2021) - [j47]Oliver Eulenstein, Qin Ding, Hisham Al-Mubaid:
Introduction to the JBCB Special Issue on Selected Papers from BICOB-2020. J. Bioinform. Comput. Biol. 19(1): 2102001:1-2102001:2 (2021) - [j46]Jaroslaw Paszek, Alexey Markin, Pawel Górecki, Oliver Eulenstein:
Taming the Duplication-Loss-Coalescence Model with Integer Linear Programming. J. Comput. Biol. 28(8): 758-773 (2021) - [j45]Pawel Tabaszewski, Pawel Górecki, Alexey Markin, Tavis K. Anderson, Oliver Eulenstein:
Consensus of All Solutions for Intractable Phylogenetic Tree Inference. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 149-161 (2021) - [j44]Pawel Górecki, Oliver Eulenstein, Jerzy Tiuryn:
The Unconstrained Diameters of the Duplication-Loss Cost and the Loss Cost. IEEE ACM Trans. Comput. Biol. Bioinform. 18(6): 2125-2135 (2021) - [c44]Jaroslaw Paszek, Oliver Eulenstein, Pawel Górecki:
Novel genomic duplication models through integer linear programming. BCB 2021: 16:1-16:11 - 2020
- [c43]Javad Ansarifar, Alexey Markin, Pawel Górecki, Oliver Eulenstein:
Integer Linear Programming Formulation for the Unified Duplication-Loss-Coalescence Model. ISBRA 2020: 229-242
2010 – 2019
- 2019
- [j43]Huy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg:
Tracing the ancestry of operons in bacteria. Bioinform. 35(17): 2998-3004 (2019) - [j42]Pawel Górecki, Agnieszka Mykowiecka, Jaroslaw Paszek, Oliver Eulenstein:
Mathematical properties of the gene duplication cost. Discret. Appl. Math. 258: 114-122 (2019) - [j41]Qin Ding, Oliver Eulenstein, Hisham Al-Mubaid:
Foreword: Special Issue for the 2019 International Conference on Bioinformatics and Computational Biology (BICOB-2019). J. Bioinform. Comput. Biol. 17(6): 1902004:1-1902004:2 (2019) - [j40]Alexey Markin, Oliver Eulenstein:
Computing Manhattan Path-Difference Median Trees: A Practical Local Search Approach. IEEE ACM Trans. Comput. Biol. Bioinform. 16(4): 1063-1076 (2019) - [j39]Alexey Markin, Oliver Eulenstein:
Efficient Local Search for Euclidean Path-Difference Median Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 16(4): 1374-1385 (2019) - [j38]Alexey Markin, Oliver Eulenstein:
Cophenetic Median Trees. IEEE ACM Trans. Comput. Biol. Bioinform. 16(5): 1459-1470 (2019) - [c42]Alexey Markin, Tavis K. Anderson, Venkata Sai Krishna Teja Vadali, Oliver Eulenstein:
Robinson-Foulds Reticulation Networks. BCB 2019: 77-86 - [c41]Pawel Górecki, Alexey Markin, Oliver Eulenstein:
Feasibility Algorithms for the Duplication-Loss Cost. COCOON 2019: 206-218 - [c40]Jucheol Moon, Oliver Eulenstein:
The Cluster Affinity Distance for Phylogenies. ISBRA 2019: 52-64 - [c39]Alexey Markin, Oliver Eulenstein:
Consensus Clusters in Robinson-Foulds Reticulation Networks. WABI 2019: 12:1-12:12 - 2018
- [j37]Hisham Al-Mubaid, Qin Ding, Oliver Eulenstein:
Introduction to JBCB Special Issue on BICOB-2018. J. Bioinform. Comput. Biol. 16(5): 1802004:1-1802004:3 (2018) - [j36]Pawel Górecki, Oliver Eulenstein:
Bijective Diameters of Gene Tree Parsimony Costs. IEEE ACM Trans. Comput. Biol. Bioinform. 15(5): 1723-1727 (2018) - [c38]Pawel Tabaszewski, Pawel Górecki, Oliver Eulenstein:
Phylogenetic Consensus for Exact Median Trees. BCB 2018: 366-375 - [c37]Pawel Górecki, Alexey Markin, Oliver Eulenstein:
Cophenetic Distances: A Near-Linear Time Algorithmic Framework. COCOON 2018: 168-179 - [c36]Alexey Markin, Venkata Sai Krishna Teja Vadali, Oliver Eulenstein:
Solving the Gene Duplication Feasibility Problem in Linear Time. COCOON 2018: 378-390 - [c35]Jucheol Moon, Oliver Eulenstein:
Cluster Matching Distance for Rooted Phylogenetic Trees. ISBRA 2018: 321-332 - 2017
- [j35]Jucheol Moon, Oliver Eulenstein:
Synthesizing large-scale species trees using the strict consensus approach. J. Bioinform. Comput. Biol. 15(3): 1740002:1-1740002:17 (2017) - [j34]Oliver Eulenstein, Qin Ding, Hisham Al-Mubaid:
Foreword. J. Bioinform. Comput. Biol. 15(6): 1702004:1-1702004:2 (2017) - [j33]Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein:
Unconstrained Diameters for Deep Coalescence. IEEE ACM Trans. Comput. Biol. Bioinform. 14(5): 1002-1012 (2017) - [c34]Alexey Markin, Oliver Eulenstein:
Cophenetic Median Trees Under the Manhattan Distance. BCB 2017: 194-202 - [c33]Jucheol Moon, Oliver Eulenstein:
Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach. BCB 2017: 253-262 - [c32]Pawel Górecki, Alexey Markin, Agnieszka Mykowiecka, Jaroslaw Paszek, Oliver Eulenstein:
Phylogenetic Tree Reconciliation: Mean Values for Fixed Gene Trees. ISBRA 2017: 234-245 - 2016
- [j32]Jucheol Moon, Harris T. Lin, Oliver Eulenstein:
Consensus properties and their large-scale applications for the gene duplication problem. J. Bioinform. Comput. Biol. 14(3): 1642005:1-1642005:17 (2016) - [c31]Jucheol Moon, Oliver Eulenstein:
Robinson-Foulds Median Trees: A Clique-based Heuristic. BCB 2016: 374-383 - [c30]Alexey Markin, Oliver Eulenstein:
Manhattan Path-Difference Median Trees. BCB 2016: 404-413 - [c29]Jucheol Moon, Iddo Friedberg, Oliver Eulenstein:
Highly Bi-Connected Subgraphs for Computational Protein Function Annotation. COCOON 2016: 573-584 - [c28]Alexey Markin, Oliver Eulenstein:
Path-Difference Median Trees. ISBRA 2016: 211-223 - 2015
- [j31]Pawel Górecki, Oliver Eulenstein:
Gene Tree Diameter for Deep Coalescence. IEEE ACM Trans. Comput. Biol. Bioinform. 12(1): 155-165 (2015) - 2014
- [j30]Cynthia Gibas, Zhipeng Cai, Oliver Eulenstein:
Guest editors' introduction to the Proceedings of the 9th International Symposium on Biomedical Research and Applications. BMC Bioinform. 15(S-13): S1 (2014) - [j29]Pawel Górecki, Oliver Eulenstein:
Refining discordant gene trees. BMC Bioinform. 15(S-13): S3 (2014) - [j28]Pawel Górecki, Oliver Eulenstein:
DrML: Probabilistic Modeling of Gene Duplications. J. Comput. Biol. 21(1): 89-98 (2014) - [j27]Pawel Górecki, Oliver Eulenstein:
Maximizing Deep Coalescence Cost. IEEE ACM Trans. Comput. Biol. Bioinform. 11(1): 231-242 (2014) - [j26]Zhipeng Cai, Oliver Eulenstein, Cynthia Gibas:
Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications. IEEE ACM Trans. Comput. Biol. Bioinform. 11(3): 453-454 (2014) - [c27]Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein:
Unconstrained gene tree diameters for deep coalescence. BCB 2014: 114-121 - [c26]Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein:
Duplication Cost Diameters. ISBRA 2014: 212-223 - [c25]Sabine Baumann, Oliver Eulenstein:
Big Guys and Big Data: Mining Shareholder Interaction Networks of Transnational MediaCompanies with Weighted Quasi-Bicliques. MKWI 2014: 181-193 - 2013
- [j25]Wen-Chieh Chang, Pawel Górecki, Oliver Eulenstein:
Exact solutions for species Tree Inference from discordant gene Trees. J. Bioinform. Comput. Biol. 11(5) (2013) - [j24]Pawel Górecki, Oliver Eulenstein, Jerzy Tiuryn:
Unrooted Tree Reconciliation: A Unified Approach. IEEE ACM Trans. Comput. Biol. Bioinform. 10(2): 522-536 (2013) - [j23]Mukul S. Bansal, Oliver Eulenstein:
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony. IEEE ACM Trans. Comput. Biol. Bioinform. 10(4): 939-956 (2013) - [j22]André Wehe, J. Gordon Burleigh, Oliver Eulenstein:
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems. IEEE ACM Trans. Comput. Biol. Bioinform. 10(6): 1432-1441 (2013) - [e1]Zhipeng Cai, Oliver Eulenstein, Daniel Janies, Daniel Schwartz:
Bioinformatics Research and Applications, 9th International Symposium, ISBRA 2013, Charlotte, NC, USA, May 20-22, 2013. Proceedings. Lecture Notes in Computer Science 7875, Springer 2013, ISBN 978-3-642-38035-8 [contents] - 2012
- [j21]Ruchi Chaudhary, J. Gordon Burleigh, Oliver Eulenstein:
Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence. BMC Bioinform. 13(S-10): S11 (2012) - [j20]Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein:
Consensus properties for the deep coalescence problem and their application for scalable tree search. BMC Bioinform. 13(S-10): S12 (2012) - [j19]Pawel Górecki, Oliver Eulenstein:
Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem. BMC Bioinform. 13(S-10): S14 (2012) - [j18]Wen-Chieh Chang, Sudheer Vakati, Roland Krause, Oliver Eulenstein:
Exploring biological interaction networks with tailored weighted quasi-bicliques. BMC Bioinform. 13(S-10): S16 (2012) - [c24]Pawel Górecki, Oliver Eulenstein:
Deep Coalescence Reconciliation with Unrooted Gene Trees: Linear Time Algorithms. COCOON 2012: 531-542 - [c23]Pawel Górecki, J. Gordon Burleigh, Oliver Eulenstein:
GTP Supertrees from Unrooted Gene Trees: Linear Time Algorithms for NNI Based Local Searches. ISBRA 2012: 102-114 - [c22]Pawel Górecki, Oliver Eulenstein:
A Robinson-Foulds Measure to Compare Unrooted Trees with Rooted Trees. ISBRA 2012: 115-126 - [c21]André Wehe, J. Gordon Burleigh, Oliver Eulenstein:
Algorithms for Knowledge-Enhanced Supertrees. ISBRA 2012: 263-274 - 2011
- [j17]Wen-Chieh Chang, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein:
An ILP solution for the gene duplication problem. BMC Bioinform. 12(S-1): S14 (2011) - [j16]Pawel Górecki, J. Gordon Burleigh, Oliver Eulenstein:
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. BMC Bioinform. 12(S-1): S15 (2011) - [j15]John Wiedenhoeft, Roland Krause, Oliver Eulenstein:
The Plexus Model for the Inference of Ancestral Multidomain Proteins. IEEE ACM Trans. Comput. Biol. Bioinform. 8(4): 890-901 (2011) - [c20]Oliver Eulenstein:
Invited: Reconciled gene trees and their applications. ICCABS 2011: 6 - [c19]Pawel Górecki, Oliver Eulenstein:
A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees. ISBRA 2011: 148-159 - [c18]Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein:
The Deep Coalescence Consensus Tree Problem is Pareto on Clusters. ISBRA 2011: 172-183 - [c17]Ruchi Chaudhary, J. Gordon Burleigh, Oliver Eulenstein:
Algorithms for Rapid Error Correction for the Gene Duplication Problem. ISBRA 2011: 227-239 - [c16]Wen-Chieh Chang, Sudheer Vakati, Roland Krause, Oliver Eulenstein:
Mining Biological Interaction Networks Using Weighted Quasi-Bicliques. ISBRA 2011: 428-439 - 2010
- [j14]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca:
Robinson-Foulds Supertrees. Algorithms Mol. Biol. 5: 18 (2010) - [j13]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein:
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. BMC Bioinform. 11(S-1): 42 (2010) - [j12]Ruchi Chaudhary, Mukul S. Bansal, André Wehe, David Fernández-Baca, Oliver Eulenstein:
iGTP: A software package for large-scale gene tree parsimony analysis. BMC Bioinform. 11: 574 (2010) - [j11]André Wehe, Wen-Chieh Chang, Oliver Eulenstein, Srinivas Aluru:
A scalable parallelization of the gene duplication problem. J. Parallel Distributed Comput. 70(3): 237-244 (2010) - [c15]J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision:
Inferring species trees from gene duplication episodes. BCB 2010: 198-203 - [c14]Max Homilius, John Gordon Burleigh, Oliver Eulenstein:
Triplet-Supertrees constructed from Minimum Triplet Presentations. BICoB 2010: 127-132 - [c13]John Wiedenhoeft, Roland Krause, Oliver Eulenstein:
Inferring Evolutionary Scenarios for Protein Domain Compositions. ISBRA 2010: 179-190
2000 – 2009
- 2009
- [j10]Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein:
Triplet supertree heuristics for the tree of life. BMC Bioinform. 10(S-1) (2009) - [j9]John Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein:
Locating Large-Scale Gene Duplication Events through Reconciled Trees: Implications for Identifying Ancient Polyploidy Events in Plants. J. Comput. Biol. 16(8): 1071-1083 (2009) - [j8]Mukul S. Bansal, Oliver Eulenstein, André Wehe:
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches. IEEE ACM Trans. Comput. Biol. Bioinform. 6(2): 221-231 (2009) - [c12]Mukul S. Bansal, Wen-Chieh Chang, Oliver Eulenstein, David Fernández-Baca:
Generalized Binary Tanglegrams: Algorithms and Applications. BICoB 2009: 114-125 - 2008
- [j7]André Wehe, Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein:
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinform. 24(13): 1540-1541 (2008) - [j6]Mukul S. Bansal, Oliver Eulenstein:
An Omega(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. IEEE ACM Trans. Comput. Biol. Bioinform. 5(4): 514-524 (2008) - [c11]Mukul S. Bansal, Oliver Eulenstein:
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches. ISBRA 2008: 14-25 - [c10]Mukul S. Bansal, Oliver Eulenstein:
The multiple gene duplication problem revisited. ISMB 2008: 132-138 - [c9]J. Gordon Burleigh, Mukul S. Bansal, André Wehe, Oliver Eulenstein:
Locating Multiple Gene Duplications through Reconciled Trees. RECOMB 2008: 273-284 - 2007
- [c8]Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein, André Wehe:
Heuristics for the Gene-Duplication Problem: A Theta ( n ) Speed-Up for the Local Search. RECOMB 2007: 238-252 - [c7]Mukul S. Bansal, Oliver Eulenstein:
An Omega(n2/log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem. WABI 2007: 124-135 - 2006
- [j5]Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson:
Minimum-Flip Supertrees: Complexity and Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 165-173 (2006) - [c6]Wen-Chieh Chang, Oliver Eulenstein:
Reconciling Gene Trees with Apparent Polytomies. COCOON 2006: 235-244 - 2004
- [j4]Duhong Chen, Oliver Eulenstein, David Fernández-Baca:
Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinform. 20(16): 2872-2873 (2004) - 2002
- [c5]Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson:
Supertrees by Flipping. COCOON 2002: 391-400 - [c4]J. Schonfeld, Oliver Eulenstein, Kent Vander Velden, Gavin J. P. Naylor:
Investigating Evolutionary Lines of Least Resistance Using the Inverse Protein-Folding Problem. Pacific Symposium on Biocomputing 2002: 613-624 - 2001
- [c3]Duhong Chen, Lixia Diao, Oliver Eulenstein, David Fernández-Baca, Michael J. Sanderson:
Flipping: A supertree construction method. Bioconsensus 2001: 135-160
1990 – 1999
- 1999
- [b1]Oliver Eulenstein:
Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. GMD research series 20/1998, GMD 1999, ISBN 978-3-88457-344-0, pp. I-XII, 1-189 - 1998
- [j3]Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork:
Towards detection of orthologues in sequence databases. Bioinform. 14(3): 285-289 (1998) - [j2]Oliver Eulenstein, Martin Vingron:
On the Equivalence of Two Tree Mapping Measures. Discret. Appl. Math. 88(1-3): 103-128 (1998) - [j1]Oliver Eulenstein, Boris G. Mirkin, Martin Vingron:
Duplication-Based Measures of Difference Between Gene and Species Trees. J. Comput. Biol. 5(1): 135-148 (1998) - 1997
- [c2]Yan P. Yuan, Oliver Eulenstein, Martin Vingron, Peer Bork:
Towards detection of sequence orthologs. German Conference on Bioinformatics 1997: 25-30 - 1996
- [c1]Oliver Eulenstein, Boris G. Mirkin, Martin Vingron:
Comparison of annotating duplication, tree mapping, and copying as methods to compare gene trees with species trees. Mathematical Hierarchies and Biology 1996: 71-94
Coauthor Index
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