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Showing papers by "Wing-Kin Sung published in 2016"


Journal ArticleDOI
01 Jun 2016-Methods
TL;DR: Different components in the SV calling pipeline are described, the techniques used by existing SV callers are reviewed and it is demonstrated that library properties, especially insert size, greatly impact the sensitivity of different SV caller.

133 citations


01 Jan 2016
TL;DR: It is proved that the problem of determining whether a given set of rooted triplets can be merged without conflicts into a galled phylogenetic network, and if so, constructing such a network, is NP-hard if extended to non-dense inputs.

54 citations


Journal ArticleDOI
TL;DR: New deterministic algorithms for constructing consensus trees that are faster than all the previously known ones are presented, and are optimal since the input size is Ω(nk).
Abstract: A consensus tree is a single phylogenetic tree that summarizes the branching structure in a given set of conflicting phylogenetic trees. Many different types of consensus trees have been proposed in the literature; three of the most well-known and widely used ones are the majority rule consensus tree, the loose consensus tree, and the greedy consensus tree. This article presents new deterministic algorithms for constructing them that are faster than all the previously known ones. Given k phylogenetic trees with n leaves each and with identical leaf label sets, our algorithms run in O(nk) time (majority rule consensus tree), O(nk) time (loose consensus tree), and O(n2k) time (greedy consensus tree). Our algorithms for the majority rule consensus and the loose consensus trees are optimal since the input size is Ω(nk). Experimental results show that the algorithms are fast in practice.

21 citations


Proceedings ArticleDOI
01 Aug 2016
TL;DR: It is proved that constructing a phylogenetic tree consistent with R that contains the minimum number of additional rooted triplets is also NP-hard, and exact, exponential-time algorithms for both problems are developed.
Abstract: The problem of constructing a minimally resolved phylogenetic supertree (i.e., having the smallest possible number of internal nodes) that contains all of the rooted triplets from a consistent set R is known to be NP-hard. In this paper, we prove that constructing a phylogenetic tree consistent with R that contains the minimum number of additional rooted triplets is also NP-hard, and develop exact, exponential-time algorithms for both problems. The new algorithms are applied to construct two variants of the local consensus tree; for any set S of phylogenetic trees over some leaf label set L, this gives a minimal phylogenetic tree over L that contains every rooted triplet present in all trees in S, where ``minimal'' means either having the smallest possible number of internal nodes or the smallest possible number of rooted triplets. The second variant generalizes the RV-II tree, introduced by Kannan, Warnow, and Yooseph in 1998.

3 citations


Journal ArticleDOI
TL;DR: This paper shows how to compute the R* consensus tree of k rooted phylogenetic trees with n leaves each and identical leaf label sets in O(n2) time for unbounded k.
Abstract: The fastest known algorithms for computing the R* consensus tree of k rooted phylogenetic trees with n leaves each and identical leaf label sets run in $$O(n^{2} \sqrt{\log n})$$O(n2logn) time when $$k = 2$$k=2 (Jansson and Sung in Algorithmica 66(2):329---345, 2013) and $$O(k n^{3})$$O(kn3) time when $$k \ge 3$$kź3 (Bryant in Bioconsensus, volume 61 of DIMACS series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, pp 163---184, 2003). This paper shows how to compute it in $$O(n^{2})$$O(n2) time for $$k = 2, O(n^{2} \log ^{4/3} n)$$k=2,O(n2log4/3n) time for $$k = 3$$k=3, and $$O(n^{2} \log ^{k+2} n)$$O(n2logk+2n) time for unbounded k.

2 citations


Journal ArticleDOI
01 Jun 2016-Methods
TL;DR: This issue will discuss methods for analyzing and integrating omics datasets, and discusses recent methods for integrated analysis of protein-protein interaction data, metabolomics data, genomics and transcriptomics data.

1 citations



Journal ArticleDOI
TL;DR: In this article, the authors evaluate sequence data from the PathChip high-density hybridization array for epidemiological interpretation of detected pathogens and derive similar relative outbreak clustering in phylogenetic trees from PathChip-derived compared to classical Sanger-derived sequences.