1,721,036 research outputs found
Haplotyping as perfect phylogeny
No full textWe consider the following problem: Given n genotypes, does there exist a set H of haplotypes such that each genotype is generated by a pair from this set, and this det can be derived on a perfect phylogeny. Recently, Gusfield, 2002, presented a polynomial time algorithm to solve this problem that uses established results from matroid and graph theory. In this work, we present an O(nm2) algorithm for this problem using elementary techniques. We also describe a linear space representation for representing all possible solutions, and provide a formula for counting the number of possible solutions
Practical Algorithms and Fixed-Parameter Tractability of the Single Individual Haplotyping Problem
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Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting
No full textKaltenbach H-M, Böcker S, Rahmann S. Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting. In: Ideker T, Bafna V, eds. Systems Biology and Computational Proteomics. RSB 2006, RCP 2006. Lecture Notes in Computer Science. Vol 4532. Berlin, Heidelberg: Springer; 2006: 129
SNPs Problems, Complexity, and Algorithms
No full textSingle nucleotide polymorphisms (SNPs) are the most frequent form of human genetic variation. They are of fundamental importance for a variety of applications including medical diagnostic and drug design. They also provide the highest–resolution genomic fingerprint for tracking disease genes. This paper is devoted to algorithmic problems related to computational SNPs validation based on genome assembly of diploid organisms. In diploid genomes, there are two copies of each chromosome. A description of the SNPs sequence information from one of the two chromosomes is called SNPs haplotype. The basic problem addressed here is the Haplotyping, i.e., given a set of SNPs prospects inferred from the assembly alignment of a genomic region of a chromosome, find the maximally consistent pair of SNPs haplotypes by removing data "errors" related to DNA sequencing errors, repeats, and paralogous recruitment. In this paper, we introduce several versions of the problem from a computational point of view. We show that the general SNPs Haplotyping Problem is NP–hard for mate–pairs assembly data, and design polynomial time algorithms for fragment assembly data. We give a network–flow based polynomial algorithm for the Minimum Fragment Removal Problem, and we show that the Minimum SNPs Removal problem amounts to finding the largest independent set in a weakly triangulated graph
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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