1,720,957 research outputs found
pATsi: Paralogs and singleton genes from Arabidopsis thaliana
No full textArabidopsis thaliana is widely accepted as a model species in plant
biology. Its genome, due to its small size and diploidy, was the first
to be sequenced among plants, making this species also a reference for
plant comparative genomics. Nevertheless, the evolutionary mechanisms
that shaped the Arabidopsis genome are still controversial. Indeed,
duplications, translocations, inversions, and gene loss events that
contributed to the current organization are difficult to be traced. A
reliable identification of paralogs and single-copy genes is essential
to understand these mechanisms. Therefore, we implemented a dedicated
pipeline to identify paralog genes and classify single-copy genes into
opportune categories. PATsi, a web-accessible database, was organized to
allow the straightforward access to the paralogs organized into networks
and to the classification of single-copy genes. This permits to
efficiently explore the gene collection of Arabidopsis for evolutionary
investigations and comparative genomics
MODELING MOLECULAR PATHWAYS BASED ON GENE EXPRESSION AND SOCIAL NETWORK ANALYSES: AN EXAMPLE FROM ARABIDOPSIS THALIANA
Full text linkAlthough the functional complexity of biological systems still requires suitable platforms and dedicated analyses to unravel details on the involved components and on mechanisms for their regulation and control, the design of synthetic bio-models able to reproduce useful functionalities is now becoming concrete. To this end, however, exploiting resources from complex organisms is still a challenge. As an example, the whole genome sequence of Arabidopsis thaliana in 2000 revealed that, despite the suitability of this organism as a model for plant biology, its small diploid genome showed an unexpected complexity in terms of intragenome duplications. This may complicate the identification of key genes involved in a functional network among the many variants the whole genome encodes. Moreover, although the role of Arabidopsis as a reference in plant biology and its manifold related resources, the lack of a fulfilled gene annotation and of exhaustive technological platforms still weakens the identification of all the partners in a molecular pathway.
We considered the gene expression values from microarray results on Arabidopsis tissues collected in the AtGenExpress Project Atlas at the NASC website (http://affymetrix.arabidopsis.info/narrays/experimentbrowse.pl), filtering out the experiments in physiological conditions. Pearson correlation tests permitted to define global gene correlations highlighting that i) about 83% of the genes have at least one correlation with another gene and that ii) inverse correlations are less frequent than direct ones.
In order to identify among correlated genes those depicting specific functional networks we applied a novel approach. This latter, based on social network analyses, investigates on relationships among genes in terms of the network theory. Gene networks can be filtered out on the base of the number of direct correlations shared among genes that belong to a cluster of correlated ones. Suitable thresholds in the applied methodology, together with gene family analyses and annotation clues, highlighted upscale gene associations, which provide further insights to improve the accuracy of network descriptions.
Our preliminary results underline the strong need of these approaches to identify the effective components of a functional pathway
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
Integrated bioinformatics: a key step towards the annotation of metabolic pathways. An example for ascorbic acid in tomato.
No full textVariations 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
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
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
- …
