Linear-Time Algorithms for the Multiple Gene Duplication Problems

Luo, Chengwei; Chen, Ming-Chiang; Chen, Yi-Ching; Yang, Roger W. L.; Liu, Hsiao-Fei; Chao, Kun-Mao

doi:10.1109/tcbb.2009.52

Cited by 15 publications

(11 citation statements)

References 13 publications

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“…This problem can be solved in linear-time and space [ 29 ]. In this article we solve the following problem.…”

Section: Resultsmentioning

confidence: 99%

“…We implemented our algorithms and the algorithms for the rooted variant of EC Problem (based on [ 29 ]). In our experiments the rooting candidates were used to compare the results for UEC with the model of mappings (for rooted gene trees) proposed in [ 28 ].…”

Section: Resultsmentioning

confidence: 99%

“…Burleigh et al [ 27 ] and Bansal and Eulenstein [ 28 ] proposed the first polynomial time solutions for two types of the multiple gene duplication problems: the episode clustering (EC) and a more general variant of clustering called minimum episodes (ME). Finally, Luo et al [ 29 ] proposed linear time and space algorithms to these problems.…”

Section: Introductionmentioning

confidence: 99%

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Genomic duplication problems for unrooted gene trees

Paszek

Górecki

2016

BMC Genomics

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BackgroundDiscovering the location of gene duplications and multiple gene duplication episodes is a fundamental issue in evolutionary molecular biology. The problem introduced by Guigó et al. in 1996 is to map gene duplication events from a collection of rooted, binary gene family trees onto theirs corresponding rooted binary species tree in such a way that the total number of multiple gene duplication episodes is minimized. There are several models in the literature that specify how gene duplications from gene families can be interpreted as one duplication episode. However, in all duplication episode problems gene trees are rooted. This restriction limits the applicability, since unrooted gene family trees are frequently inferred by phylogenetic methods.ResultsIn this article we show the first solution to the open problem of episode clustering where the input gene family trees are unrooted. In particular, by using theoretical properties of unrooted reconciliation, we show an efficient algorithm that reduces this problem into the episode clustering problems defined for rooted trees. We show theoretical properties of the reduction algorithm and evaluation of empirical datasets.ConclusionsWe provided algorithms and tools that were successfully applied to several empirical datasets. In particular, our comparative study shows that we can improve known results on genomic duplication inference from real datasets.

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“…This problem can be solved in linear-time and space [ 29 ]. In this article we solve the following problem.…”

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genomic duplication problems for unrooted gene trees

Paszek

Górecki

2016

BMC Genomics

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“…In the approach in [75], for each G j a duplication event α ( g ) is attempted closer to the root of a species tree but below α ( g ′), where g ′ is the parent of g (if g is the root, α ( g ) is attempted closer to the root). A functional is proposed that depends on { f j } and equals the sum (over all vertices s in S ) of maximal heights of subtrees in all G j (not only those that reach the leaves) mapped by f j into a vertex s .…”

Section: Reconciliation Of Gene and Species Trees: A Brief Overviewmentioning

confidence: 99%

“…A linear complexity proved algorithm to find this global minimum is proposed. Historical references to this approach are provided in [75] and in review [76]. …”

Section: Reconciliation Of Gene and Species Trees: A Brief Overviewmentioning

confidence: 99%

Reconciliation of Gene and Species Trees

Rusin

Lyubetskaya

Gorbunov

et al. 2014

BioMed Research International

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The first part of the paper briefly overviews the problem of gene and species trees reconciliation with the focus on defining and algorithmic construction of the evolutionary scenario. Basic ideas are discussed for the aspects of mapping definitions, costs of the mapping and evolutionary scenario, imposing time scales on a scenario, incorporating horizontal gene transfers, binarization and reconciliation of polytomous trees, and construction of species trees and scenarios. The review does not intend to cover the vast diversity of literature published on these subjects. Instead, the authors strived to overview the problem of the evolutionary scenario as a central concept in many areas of evolutionary research. The second part provides detailed mathematical proofs for the solutions of two problems: (i) inferring a gene evolution along a species tree accounting for various types of evolutionary events and (ii) trees reconciliation into a single species tree when only gene duplications and losses are allowed. All proposed algorithms have a cubic time complexity and are mathematically proved to find exact solutions. Solving algorithms for problem (ii) can be naturally extended to incorporate horizontal transfers, other evolutionary events, and time scales on the species tree.

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New Algorithms for the Genomic Duplication Problem

Paszek

Górecki

2017

Comparative Genomics

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Linear-Time Algorithms for the Multiple Gene Duplication Problems

Cited by 15 publications

References 13 publications

Genomic duplication problems for unrooted gene trees

Genomic duplication problems for unrooted gene trees

Reconciliation of Gene and Species Trees

New Algorithms for the Genomic Duplication Problem

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