1,720,962 research outputs found
Next-generation sequencing algorithms - from read mapping to variant detection
No full textNext-Generation-Sequencing (NGS) has brought on a revolution in sequence analysis with its broad spectrum of applications ranging from genome resequencing to transcriptomics or metagenomics, and from fundamental research to diagnostics. The tremendous amounts of data necessitate highly efficient computational analysis tools for the wide variety of NGS applications. This thesis addresses a broad range of key computational aspects of resequencing applications, where a reference genome sequence is known and heavily used for interpretation of the newly sequenced sample. It presents tools for read mapping and benchmarking, for partial read mapping of small RNA reads and for structural variant/indel detection, and finally tools for detecting and genotyping SNVs and short indels. Our tools efficiently scale to large NGS data sets and are well-suited for advances in sequencing technology, since their generic algorithm design allows handling of arbitrary read lengths and variable error rates. Furthermore, they are implemented within the robust C++ library SeqAn, making them open-source, easily available, and potentially adaptable for the bioinformatics community. Among other applications, our tools have been integrated into a large-scale analysis pipeline and have been applied to large datasets, leading to interesting discoveries of human retrocopy variants and insights into the genetic causes of X-linked intellectual disabilities
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
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe 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
von Read Mapping zur Detektion von genomischen Variationen
Get PDFNext-Generation-Sequencing (NGS) has brought on a revolution in sequence
analysis with its broad spectrum of applications ranging from genome
resequencing to transcriptomics or metagenomics, and from fundamental research
to diagnostics. The tremendous amounts of data necessitate highly efficient
computational analysis tools for the wide variety of NGS applications. This
thesis addresses a broad range of key computational aspects of resequencing
applications, where a reference genome sequence is known and heavily used for
interpretation of the newly sequenced sample. It presents tools for read
mapping and benchmarking, for partial read mapping of small RNA reads and for
structural variant/indel detection, and finally tools for detecting and
genotyping SNVs and short indels. Our tools efficiently scale to large NGS
data sets and are well-suited for advances in sequencing technology, since
their generic algorithm design allows handling of arbitrary read lengths and
variable error rates. Furthermore, they are implemented within the robust C++
library SeqAn, making them open-source, easily available, and potentially
adaptable for the bioinformatics community. Among other applications, our
tools have been integrated into a large-scale analysis pipeline and have been
applied to large datasets, leading to interesting discoveries of human
retrocopy variants and insights into the genetic causes of X-linked
intellectual disabilities.Neuste DNA-Sequenzieungstechnologien (kurz genannt NGS Technologien)
ermöglichen revolutionäre neue Anwendungen, die sowohl von
Genomresequenzierung über Transkriptomsequenzierung zu Metagenomik als auch
von Grundlagenforschung zu Diagnostik reichen. Problematisch ist dabei die
Flut an Daten, die eine grosse Herausforderung für die Bionformatik darstellt.
Hocheffiziente Analysesoftware ist von enormer Wichtigkeit für das breite
Spektrum von NGS Anwendungen. Diese Arbeit adressiert mehrere Schlüsselaspekte
der Analyse von Resequenzierungsdaten, bei der ein bereits sequenziertes
Referenzgenom als Grundlage für die Interpretation eines neu sequenzierten
Datensatzes dient. Es werden Algorithmen und Programme präsentiert für das
sogenannte Read Mapping Problem und für die Auswertung der Güte seiner Lösung,
für partielles Read Mapping, welches in miRNA Studien und bei der Suche nach
strukturellen Variationen Anwendung findet, sowie letztlich zum Auffinden und
Genotypisieren von Basenmutationen und kurzen Insertionen/Deletionen im Genom.
Die vorgestellten Algorithmen sind effizient und so gestaltet, dass sie auch
bei Fortschritten in Sequenzierungstechnologien weiterhin anwendbar und
skalierbar bleiben. Zudem sind sie in der robusten C++ Bibliothek SeqAn
implementiert, was sie leicht zugänglich und adaptierbar macht. Unter anderem
wurden unsere Tools in eine Hochdurchsatz-Analysepipeline integriert und auf
grosse Datensaetze angewendet, wodurch interessante biologische Erkenntnisse
(vorallem im Zusammenhang X-Chromosom gebundener geistiger Behinderung)
gewonnen werden konnten
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe 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
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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