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The currently available reconciliation methods for nonbinary gene trees are computationally expensive for genome-scale applications. We present ... Keywords: tree reconciliation, Gene duplication history 2 February 2017 Information and Computation: Volume 252 Issue C, February 2017 Publisher: Academic Press, Inc. Bibliometrics: Citation Count: 0 In studies of molecular evolution, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For the purpose of validating evolutionary models, biologists check whether or not a phylogenetic tree ... Keywords: Cluster containment problem, Reticulation-visibility, Phylogenetic networks, Galled networks, Tree containment problem 3 May 2014 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 11 Issue 3, May/June 2014 Publisher: IEEE Computer Society Press Bibliometrics: Citation Count: 0 Downloads (6 Weeks): 0,   Downloads (12 Months): 7,   Downloads (Overall): 30 Full text available: PDF In the tree reconciliation approach to infer the duplication history of a gene family, the gene (family) tree is compared to the corresponding species tree. Incomplete lineage sorting (ILS) gives rise to stochastic variation in the topology of a gene tree and hence likely introduces false duplication events when a ... Keywords: gene tree and species tree reconciliation, gene duplication, incomplete lineage sorting 4 April 2014 RECOMB 2014: Proceedings of the 18th Annual International Conference on Research in Computational Molecular Biology - Volume 8394 Publisher: Springer-Verlag New York, Inc. Bibliometrics: Citation Count: 1 By reconciling the phylogenetic tree of a gene family with the corresponding species tree, it is possible to infer lineage-specific duplications and losses with high confidence and hence annotate orthologs and paralogs. However, the currently available reconciliation methods for non-binary gene trees are computationally expensive for being applied on a ... 5 April 2013 RECOMB'13: Proceedings of the 17th international conference on Research in Computational Molecular Biology Publisher: Springer-Verlag Bibliometrics: Citation Count: 0 Small over-represented motifs in biological networks are believed to represent essential functional units of biological processes. A natural question is to gauge whether a motif occurs abundantly or rarely in a biological network. Given that high-throughput biotechnology is only able to interrogate a portion of the entire biological network with ... 6 October 2012 BCB '12: Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine Publisher: ACM Bibliometrics: Citation Count: 0 Downloads (6 Weeks): 0,   Downloads (12 Months): 7,   Downloads (Overall): 51 Full text available: PDF Large-scale genomic pairwise aligners usually start with a seeding procedure, which scans two sequences to obtain base matches (called hits ) that follow a certain pattern (called a seed). The seed pattern and size determine the sensitivity and specificity of the seeding procedure and greatly affect the alignment accuracy and ... Keywords: model, genomic sequence, seeding, alignment, matches 7 May 2012 ISBRA'12: Proceedings of the 8th international conference on Bioinformatics Research and Applications Publisher: Springer-Verlag Bibliometrics: Citation Count: 1 Genome-wide protein-protein interaction (PPI) data are readily available thanks to recent breakthroughs in biotechnology. However, PPI networks of extant organisms are only snapshots of the network evolution. How to infer the whole evolution history becomes a challenging problem in computational biology. In this paper, we present a likelihood-based approach to ... 8 November 2011 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 8 Issue 6, November 2011 Publisher: IEEE Computer Society Press Bibliometrics: Citation Count: 11 Downloads (6 Weeks): 0,   Downloads (12 Months): 8,   Downloads (Overall): 107 Full text available: PDF When gene copies are sampled from various species, the resulting gene tree might disagree with the containing species tree. The primary causes of gene tree and species tree discord include incomplete lineage sorting, horizontal gene transfer, and gene duplication and loss. Each of these events yields a different parsimony criterion ... Keywords: Gene tree and species tree reconciliation, deep coalescence, gene duplication and loss, the parsimony principle, NP-hardness. 9 May 2011 ISBRA'11: Proceedings of the 7th international conference on Bioinformatics research and applications Publisher: Springer-Verlag Bibliometrics: Citation Count: 2 The exemplar breakpoint distance problem is NP-hard. Assume two genomes have at most n genes from m gene families. We develop an O (2 m n O (1) ) time algorithm to compute the exemplar breakpoint distance if one of them has no repetition. We develop an O (2 m ... Keywords: examplar breakpoint distance, genome rearrangement 10 May 2011 Journal of Combinatorial Optimization: Volume 21 Issue 4, May 2011 Publisher: Springer-Verlag New York, Inc. Bibliometrics: Citation Count: 1 The marginal maximum likelihood method is a widely-used method for ancestral state reconstruction. Given an evolution model (a phylogeny tree and the edge mutation rates) and the extant states (states on leaves), the method computes efficiently the most likely ancestral state on the root. However, when the extant states are ... Keywords: Maximum likelihood method, Polynomial time approximation, Ancestral state reconstruction, Reconstruction accuracy 11 February 2011 ICCABS '11: Proceedings of the 2011 IEEE 1st International Conference on Computational Advances in Bio and Medical Sciences Publisher: IEEE Computer Society Bibliometrics: Citation Count: 2 Background: Horizontal gene transfer and gene duplication are two significant forces behind genome evolution. As more and more well-supported examples of HGTs are being revealed, there is a growing awareness that HGT is more widespread than previously thought, occurring often not only within bacteria, but also between species remotely related ... 12 September 2010 WABI'10: Proceedings of the 10th international conference on Algorithms in bioinformatics Publisher: Springer-Verlag Bibliometrics: Citation Count: 1 DNA-based species assignment and delimitation are two important problems in systematic biology. In a recent work of O'Meara, species delimitation is investigated through coupling it with species tree inference in the framework of gene tree and species tree reconciliation. We present a polynomial time algorithm for splitting individuals into species ... Keywords: DNA barcoding, deep coalescence, gene tree and species tree reconciliation, species delimitation, dene duplication and loss 13 September 2009 RECOMB-CG '09: Proceedings of the International Workshop on Comparative Genomics Publisher: Springer-Verlag Bibliometrics: Citation Count: 0 Much important evolutionary activity occurs in gene clusters, where a copy of a gene may be free to evolve new functions. Computational methods to extract evolutionary information from sequence data for such clusters are currently imperfect, in part because accurate sequence data are often lacking in these genomic regions, making ... 14 June 2009 ISAAC '01: Proceedings of the 12th International Symposium on Algorithms and Computation Publisher: Springer-Verlag Bibliometrics: Citation Count: 3 The complexity issues of two clustering problems are studied. We prove that the Smooth Clustering and Biclustering problems are NP-hard; we also propose an 0.5 approximation algorithm and 0.8 inapproximability for a simplified clutering problem. 15 June 2009 FAW '09: Proceedings of the 3d International Workshop on Frontiers in Algorithmics Publisher: Springer-Verlag Bibliometrics: Citation Count: 1 As a generalization of the spanning star forest problem, the spanning k -tree forest problem is to find a maximum-edge-weight spanning forest in which each tree has a central node and other nodes in the tree are at most k -distance away from the central node. In this paper, we ... Keywords: star, Spanning forest, k-tree, approximation algorithm 16 June 2008 SIAM Journal on Computing: Volume 38 Issue 3, June 2008 Publisher: Society for Industrial and Applied Mathematics Bibliometrics: Citation Count: 8 This paper studies the algorithmic issues of the spanning star forest problem. We prove the following results: (1) There is a polynomial-time approximation scheme for planar graphs; (2) there is a polynomial-time $\frac{3}{5}$-approximation algorithm for graphs; (3) it is NP-hard to approximate the problem within ratio $\frac{259}{260} + \epsilon$ for ... Keywords: genomic sequence alignment, approximation algorithm, dominating set, spanning star forest 17 September 2007 RECOMB-CG'07: Proceedings of the 2007 international conference on Comparative genomics Publisher: Springer-Verlag Bibliometrics: Citation Count: 1 Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor ... Keywords: duplication, contiguous ancestral region, gene order reconstruction 18 September 2007 RECOMB-CG'07: Proceedings of the 2007 international conference on Comparative genomics Publisher: Springer-Verlag Bibliometrics: Citation Count: 1 It is often impossible to sequence all descendent genomes to reconstruct an ancestral genome. In addition, more genomes do not necessarily give a higher accuracy for the reconstruction of ancestral character states. These facts lead to studying the genome selection for reconstruction problem. In this work, two greedy algorithms for ... 19 July 2007 Algorithmica: Volume 48 Issue 3, July 2007 Publisher: Springer-Verlag New York, Inc. Bibliometrics: Citation Count: 8 A 0-1 matrix has the Consecutive Ones Property (C1P) if there is a permutation of its columns that leaves the 1's consecutive in each row. The Consecutive Ones Submatrix (C1S) problem is, given a 0-1 matrix A, to find the largest number of columns of A that form a submatrix ... 20 July 2007 IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB): Volume 4 Issue 3, July 2007 Publisher: IEEE Computer Society Press Bibliometrics: Citation Count: 2 Downloads (6 Weeks): 0,   Downloads (12 Months): 4,   Downloads (Overall): 190 Full text available: PDF The small parsimony problem is studied for reconstructing recombination networks from sequence data. The small parsimony problem is polynomial-time solvable for phylogenetic trees. However, the problem is proved NP-hard even for galled recombination networks. A dynamic programming algorithm is also developed to solve the small parsimony problem. It takes $O(dn2^{3h})$ ... Keywords: combination network, phylogenetic network, parsimony method, NP-hardness, approximability, dynamic programming