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1

Cophenetic Median Trees

Markin, Alexey, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2018

Language:

english

File:

PDF, 542 KB

english, 2018

2

Identifying optimal incomplete phylogenetic data sets from sequence databases

Changhui Yan, J. Gordon Burleigh, Oliver Eulenstein

Journal:

Molecular Phylogenetics and Evolution

Year:

2005

Language:

english

File:

PDF, 262 KB

english, 2005

3

An ILP solution for the gene duplication problem

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

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 248 KB

english, 2011

4

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

Pawel Górecki, Gordon J Burleigh, Oliver Eulenstein

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 395 KB

english, 2011

5

Robinson-Foulds Supertrees

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

Journal:

Algorithms for Molecular Biology

Year:

2010

Language:

english

File:

PDF, 394 KB

english, 2010

6

Groves of Phylogenetic Trees

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

Journal:

Annals of Combinatorics

Year:

2009

Language:

english

File:

PDF, 436 KB

english, 2009

7

A scalable parallelization of the gene duplication problem

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

Journal:

Journal of Parallel and Distributed Computing

Year:

2010

Language:

english

File:

PDF, 2.67 MB

english, 2010

8

Triplet supertree heuristics for the tree of life

Harris T Lin, J Gordon Burleigh, Oliver Eulenstein

Journal:

BMC Bioinformatics

Year:

2009

Language:

english

File:

PDF, 839 KB

english, 2009

9

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

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

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 417 KB

english, 2010

10

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

Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 279 KB

english, 2010

11

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

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

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 445 KB

english, 2012

12

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

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

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.14 MB

english, 2012

13

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

Górecki, Pawel, Eulenstein, Oliver

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 1.52 MB

english, 2012

14

Exploring biological interaction networks with tailored weighted quasi-bicliques

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

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 333 KB

english, 2012

15

[ACM Press the First ACM International Conference - Niagara Falls, New York (2010.08.02-2010.08.04)] Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10 - Inferring species trees from gene duplication episodes

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

Year:

2010

Language:

english

File:

PDF, 1.17 MB

english, 2010

16

[Lecture Notes in Computer Science] Bioinformatics Research and Applications Volume 7875 || Identifying Critical Transitions of Biological Processes by Dynamical Network Biomarkers

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

Year:

2013

Language:

english

File:

PDF, 48 KB

english, 2013

17

[Lecture Notes in Computer Science] Bioinformatics Research and Applications Volume 7875 || A Context-Driven Gene Prioritization Method for Web-Based Functional Genomics

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

Year:

2013

Language:

english

File:

PDF, 274 KB

english, 2013

18

[Lecture Notes in Computer Science] Bioinformatics Research and Applications Volume 7875 ||

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

Year:

2013

Language:

english

File:

PDF, 9.08 MB

english, 2013

19

Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems

Wehe, Andre, Burleigh, J. Gordon, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 367 KB

english, 2013

20

DrML: Probabilistic Modeling of Gene Duplications

Górecki, Paweł, Eulenstein, Oliver

Journal:

Journal of Computational Biology

Year:

2014

Language:

english

File:

PDF, 596 KB

english, 2014

21

[Lecture Notes in Computer Science] Bioinformatics Research and Applications Volume 7875 || Reconstructing Ancestral Genomic Orders Using Binary Encoding and Probabilistic Models

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

Year:

2013

Language:

english

File:

PDF, 246 KB

english, 2013

22

Maximizing Deep Coalescence Cost

Gorecki, Pawel, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.58 MB

english, 2014

23

[IEEE 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Orlando, FL, USA (2011.02.3-2011.02.5)] 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) - Invited: Reconciled gene trees and their applications

Eulenstein, Oliver

Year:

2011

Language:

english

File:

PDF, 40 KB

english, 2011

24

Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony

Bansal, Mukul S., Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2013

Language:

english

File:

PDF, 544 KB

english, 2013

25

EXACT SOLUTIONS FOR SPECIES TREE INFERENCE FROM DISCORDANT GENE TREES

CHANG, WEN-CHIEH, GÓRECKI, PAWEŁ, EULENSTEIN, OLIVER

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2013

Language:

english

File:

PDF, 365 KB

english, 2013

26

The Shape of Supertrees to Come: Tree Shape Related Properties of Fourteen Supertree Methods

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

Journal:

Systematic Biology

Year:

2005

Language:

english

File:

PDF, 436 KB

english, 2005

27

Performance of Flip Supertree Construction with a Heuristic Algorithm

EULENSTEIN, OLIVER, CHEN, DUHONG, BURLEIGH, J., FERNÁNDEZ-BACA, DAVID, SANDERSON, MICHAEL

Journal:

Systematic Biology

Year:

2004

Language:

english

File:

PDF, 569 KB

english, 2004

28

[ACM Press the 5th ACM Conference - Newport Beach, California (2014.09.20-2014.09.23)] Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '14 - Unconstrained gene tree diameters for deep coalescence

Górecki, Paweł, Paszek, Jarosław, Eulenstein, Oliver

Year:

2014

Language:

english

File:

PDF, 467 KB

english, 2014

29

Gene Tree Diameter for Deep Coalescence

Gorecki, Pawel, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2015

Language:

english

File:

PDF, 792 KB

english, 2015

30

Unconstrained Diameters for Deep Coalescence

Gorecki, Pawel, Paszek, Jaroslaw, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2016

Language:

english

File:

PDF, 3.52 MB

english, 2016

31

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

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

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2016

Language:

english

File:

PDF, 565 KB

english, 2016

32

Refining discordant gene trees

Górecki, Pawel, Eulenstein, Oliver

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 2.72 MB

english, 2014

33

Guest editors' introduction to the Proceedings of the 9thInternational Symposium on Biomedical Research and Applications

Gibas, Cynthia J, Cai, Zhipeng, Eulenstein, Oliver

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 226 KB

english, 2014

34

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

Cai, Zhipeng, Eulenstein, Oliver, Gibas, Cynthia

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2014

Language:

english

File:

PDF, 84 KB

english, 2014

35

Performance of Flip Supertree Construction with a Heuristic Algorithm

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

Journal:

Systematic Biology

Year:

2004

Language:

english

File:

PDF, 2.14 MB

english, 2004

36

Genome-Scale Phylogenetics: Inferring the Plant Tree of Life from 18,896 Gene Trees

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

Journal:

Systematic Biology

Year:

2011

Language:

english

File:

PDF, 1.90 MB

english, 2011

37

The Shape of Supertrees to Come: Tree Shape Related Properties of Fourteen Supertree Methods

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

Journal:

Systematic Biology

Year:

2005

Language:

english

File:

PDF, 3.00 MB

english, 2005

38

Synthesizing large-scale species trees using the strict consensus approach

Moon, Jucheol, Eulenstein, Oliver

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2017

Language:

english

File:

PDF, 747 KB

english, 2017

39

Computing Manhattan Path-Difference MedianTrees: a Practical Local Search Approach

Markin, Alexey, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 526 KB

english, 2017

40

[ACM Press the 8th ACM International Conference - Boston, Massachusetts, USA (2017.08.20-2017.08.23)] Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17 - Cophenetic Median Trees Under the Manhattan Distance

Markin, Alexey, Eulenstein, Oliver

Year:

2017

Language:

english

File:

PDF, 702 KB

english, 2017

41

Efficient Local Search for Euclidean Path-Difference Median Trees

Markin, Alexey, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 466 KB

english, 2017

42

Foreword

Eulenstein, Oliver, Ding, Qin, Al-Mubaid, Hisham

Journal:

Journal of Bioinformatics and Computational Biology

Year:

2017

Language:

english

File:

PDF, 41 KB

english, 2017

43

Improved Heuristics for Minimum-Flip Supertree Construction

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

Journal:

Evolutionary Bioinformatics

Year:

2006

Language:

english

File:

PDF, 600 KB

english, 2006

44

[ACM Press the 8th ACM International Conference - Boston, Massachusetts, USA (2017.08.20-2017.08.23)] Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics - ACM-BCB '17 - Synthesizing Species Trees from Unrooted Gene Trees

Moon, Jucheol, Eulenstein, Oliver

Year:

2017

Language:

english

File:

PDF, 2.42 MB

english, 2017

45

Bijective Diameters of Gene Tree Parsimony Costs

Gorecki, Pawel, Eulenstein, Oliver

Journal:

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 348 KB

english, 2017

46

[ACM Press the 2018 ACM International Conference - Washington, DC, USA (2018.08.29-2018.09.01)] Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '18 - Phylogenetic Consensus for Exact Median Trees

Tabaszewski, Pawel, Górecki, Pawel, Eulenstein, Oliver

Year:

2018

Language:

english

File:

PDF, 1.40 MB

english, 2018

47

Mathematical properties of the gene duplication cost

Górecki, Paweł, Mykowiecka, Agnieszka, Paszek, Jarosław, Eulenstein, Oliver

Journal:

Discrete Applied Mathematics

Year:

2018

Language:

english

File:

PDF, 393 KB

english, 2018

48

Tracing the Ancestry of Operons in Bacteria

Nguyen, Huy, Jain, Ashish, Eulenstein, Oliver, Friedberg, Iddo, Schwartz, Russell

Journal:

Year:

2019

File:

PDF, 4.18 MB

2019

49

[ACM Press the 7th ACM International Conference - Seattle, WA, USA (2016.10.02-2016.10.05)] Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16 - Manhattan Path-Difference Median Trees

Markin, Alexey, Eulenstein, Oliver

Year:

2016

Language:

english

File:

PDF, 355 KB

english, 2016

50

[ACM Press the 7th ACM International Conference - Seattle, WA, USA (2016.10.02-2016.10.05)] Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '16 - Robinson-Foulds Median Trees

Moon, Jucheol, Eulenstein, Oliver

Year:

2016

Language:

english

File:

PDF, 815 KB

english, 2016

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