1,721,453 research outputs found
StringMasters 2012 & 2013 special issue – volume 2
Full text linkSpecial issue on StringMasters 2012 & 2013, with papers that were developed out of one of the StringMasters meetings
Alignment-free sequence comparison using absent words
Full text linkSequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free techniques, which are based on measures referring to the composition of sequences in terms of their constituent patterns. These measures, such as q-gram distance, are usually computed in time linear with respect to the length of the sequences. In this paper, we focus on the complementary idea: how two sequences can be efficiently compared based on information that does not occur in the sequences. A word is an absent word of some sequence if it does not occur in the sequence. An absent word is minimal if all its proper factors occur in the sequence. Here we present the first linear-time and linear-space algorithm to compare two sequences by considering all their minimal absent words. In the process, we present results of combinatorial interest, and also extend the proposed techniques to compare circular sequences. We also present an algorithm that, given a word x of length n, computes the largest integer for which all factors of x of that length occur in some minimal absent word of x in time and space O(n). Finally, we show that the known asymptotic upper bound on the number of minimal absent words of a word is tight
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Full text link“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
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
On the Complexity of Sparse Exon Assembly
No full textGene structure prediction is one of the most important problems in computational molecular biology. It involves two steps: the first is finding the evidence (e.g., predicting splice sites) and the second is interpreting the evidence, that is, trying to determine the whole gene structure by assembling its pieces. In this paper, we suggest a combinatorial solution to the second step, which is also referred to as the "Exon Assembly Problem." We use a similarity-based approach that aims to produce a single gene structure based on similarities to a known homologous sequence. We target the sparse case, where filtering has been applied to the data, resulting in a set of O(n) candidate exon blocks. Our algorithm yields an O(n2√n) solution
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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