Titlebook: Algorithms for Computational Biology; First International Adrian-Horia Dediu,Carlos Martín-Vide,Bianca Truth Conference proceedings 2014 S

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Psa617

A Greedy Algorithm for Hierarchical Complete Linkage Clusteringg a running time of . with a space requirement of . and one having a running time of . with a space requirement of Θ(..), where . is the number of points to be clustered. Both methods are not capable to handle large point sets. In this paper, we give an algorithm with a space requirement of . which

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Vester’s Sensitivity Model for Genetic Networks with Time-Discrete DynamicsThe gene expression data .. is given for various time points and the matrix . of interactions among the genes is unknown. First we formulate and solve a parameter estimation problem by linear programming in order to obtain the entries of the matrix .. We then use ideas from Vester’s ., more precisel

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Complexity and Polynomial-Time Approximation Algorithms around the Scaffolding Problem an undirected graph with no loop, and a perfect matching on this graph, find a set of cycles and paths covering every vertex of the graph, with edges alternatively in the matching and outside the matching, and satisfying a given constraint on the numbers of cycles and paths. We show that this probl

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Heuristics for the Sorting by Length-Weighted Inversions Problem on Signed Permutationser. In this work, we deal with inversion events, which occur when a segment of DNA sequence in the genome is reversed. In our model, each inversion costs the number of elements in the reversed segment. We present a new heuristic for this problem and we show that our method outperforms a previous app

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ADJ

On Optimal Read Trimming in Next Generation Sequencing and Its Complexitycally, and algorithmic work in this area has been neglected. Here, we address this topic and formulate three constrained optimization problems for block-based trimming, i.e., truncating the same low-quality positions at both ends for all reads and removing low-quality truncated reads. We find that t

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On the Implementation of Quantitative Model Refinementased models and for .-based models. In this paper, we investigate and compare this approach in three different modeling frameworks: rule-based modeling, Petri nets and guarded command languages. As case study we use a model for the eukaryotic heat shock response that we refine to include the acetyla

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HapMonster: A Statistically Unified Approach for Variant Calling and Haplotyping Based on Phase-Infoe of demographic history. One of approaches for estimating haplotypes is to use phase-informative reads, which span multiple heterozygous variant positions. Although the quality of estimated variants is crucial in haplotype phasing, accurate variant calling is still challenging due to errors on sequ

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Mapping-Free and Assembly-Free Discovery of Inversion Breakpoints from Raw NGS Readsharacterized by a fixed size topological pattern in the .. We describe precisely the possible sources of false positives and false negatives and we additionally propose a sequence-based filter giving a good trade-off between precision and recall of the method. We implemented these ideas in a prototy