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Displaying 1-13 out of 13 total
Unrooted Tree Reconciliation: A Unified Approach
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Pawel Gorecki,Oliver Eulenstein,Jerzy Tiuryn
Issue Date:March 2013
pp. 522-536
Tree comparison functions are widely used in phylogenetics for comparing evolutionary trees. Unrooted trees can be compared with rooted trees by identifying all rootings of the unrooted tree that minimize some provided comparison function between two roote...
 
Maximizing Deep Coalescence Cost
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Pawel Gorecki,Oliver Eulenstein
Issue Date:January 2014
pp. 231-242
The minimizing deep coalescence (MDC) problem seeks a species tree that reconciles the given gene trees with the minimum number of deep coalescence events, called deep coalescence (DC) cost. To better assess MDC species trees we investigate into a basic ma...
 
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Andre Wehe,J. Gordon Burleigh,Oliver Eulenstein
Issue Date:November 2013
pp. 1432-1441
Phylogenetic inference is a computationally difficult problem, and constructing high-quality phylogenies that can build upon existing phylogenetic knowledge and synthesize insights from new data remains a major challenge. We introduce knowledge-enhanced ph...
 
Algorithms for Genome-Scale Phylogenetics Using Gene Tree Parsimony
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Mukul S. Bansal,Oliver Eulenstein
Issue Date:July 2013
pp. 939-956
The use of genomic data sets for phylogenetics is complicated by the fact that evolutionary processes such as gene duplication and loss, or incomplete lineage sorting (deep coalescence) cause incongruence among gene trees. One well-known approach that deal...
 
Invited: Reconciled gene trees and their applications
Found in: Computational Advances in Bio and Medical Sciences, IEEE International Conference on
By Oliver Eulenstein
Issue Date:February 2011
pp. 6
Phylogenetic trees describe the evolutionary history among various organisms. Studies on such trees have provided us with many valuable insights into a host of issues in biology, ecology, and medicine, and promise even more. As we enter the second decade o...
 
The Plexus Model for the Inference of Ancestral Multidomain Proteins
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By John Wiedenhoeft, Roland Krause, Oliver Eulenstein
Issue Date:July 2011
pp. 890-901
Interactions of protein domains control essential cellular processes. Thus, inferring the evolutionary histories of multidomain proteins in the context of their families can provide rewarding insights into protein function. However, methods to infer these ...
 
The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Mukul S. Bansal, Oliver Eulenstein, André Wehe
Issue Date:April 2009
pp. 221-231
The gene-duplication problem is to infer a species supertree from a collection of gene trees that are confounded by complex histories of gene-duplication events. This problem is NP-complete and thus requires efficient and effective heuristics. Existing heu...
 
An Ω(n^2/ log n) Speed-Up of TBR Heuristics for the Gene-Duplication Problem
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Mukul S. Bansal, Oliver Eulenstein
Issue Date:October 2008
pp. 514-524
The gene-duplication problem is to infer a species supertree from gene trees that are confounded by complex histories of gene duplications. This problem is NP-hard and thus requires efficient and effective heuristics. Existing heuristics perform a stepwise...
 
Minimum-Flip Supertrees: Complexity and Algorithms
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Duhong Chen, Oliver Eulenstein, David Fernández-Baca, Michael Sanderson
Issue Date:April 2006
pp. 165-173
The input to a supertree problem is a collection of phylogenetic trees that intersect pairwise in their leaf sets; the goal is to construct a single tree that retains as much as possible of the information in the input. This task is complicated by inconsis...
 
Guest Editors Introduction to the Special Section on Bioinformatics Research and Applications
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics
By Zhipeng Cai,Oliver Eulenstein,Cynthia Gibas
Issue Date:May 2014
pp. 453-454
No summary available.
 
Efficient Algorithms for Knowledge-Enhanced Supertree and Supermatrix Phylogenetic Problems
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Andre Wehe, J. Gordon Burleigh, Oliver Eulenstein
Issue Date:November 2013
pp. 1432-1441
Phylogenetic inference is a computationally difficult problem, and constructing high-quality phylogenies that can build upon existing phylogenetic knowledge and synthesize insights from new data remains a major challenge. We introduce knowledge-enhanced ph...
     
Unrooted Tree Reconciliation: A Unified Approach
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By Jerzy Tiuryn, Oliver Eulenstein, Pawel Gorecki
Issue Date:March 2013
pp. 522-536
Tree comparison functions are widely used in phylogenetics for comparing evolutionary trees. Unrooted trees can be compared with rooted trees by identifying all rootings of the unrooted tree that minimize some provided comparison function between two roote...
     
The Plexus Model for the Inference of Ancestral Multidomain Proteins
Found in: IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
By John Wiedenhoeft, Oliver Eulenstein, Roland Krause
Issue Date:July 2011
pp. 890-901
Interactions of protein domains control essential cellular processes. Thus, inferring the evolutionary histories of multidomain proteins in the context of their families can provide rewarding insights into protein function. However, methods to infer these ...
     
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