1,720,958 research outputs found
Modèles et méthodes pour la métagénomique à résolution génomique
No full textThe reconstruction of individual genomes from metagenomic data, also called MAGs has constituted a major milestone in the study of microbial communities. However, the recovery of MAGs still suffers several limitations, including the mosaic and population nature of these MAGs, the inherent difficulties to assemble pangenomes, and the recovery of strain-level variations for a given species. In this thesis, a declarative programming framework was designed and used to resolve the genome binning problem through a constrained clustering approach, with the goal to explore several optimal binning solutions, informing us about the organization dynamics of naturally occurring genomes. A novel genome binning model integrating compositional and abundance information as well as constraints on single-copy core genes was designed and implemented using the ASP language. With the goal to further enhance the recovery of MAGs, we focused on optimizing the assembly process, a key genome binning pre-processing step. We developed an automated approach to guide the co-assembly process, combining metagenomic compositional distances with an optimal clustering method. These developments were implemented into a novel genome-resolved metagenomics workflow called MAGNETO, integrating complementary assembly-binning strategies.La reconstruction de génomes à partir de données métagénomiques, aussi appelés MAG) représente une étape majeure dans l’étude des communautés microbiennes. La reconstruction de MAGs souffre néanmoins de limitations, telles que la nature fragmentée de ces MAGs, les difficultés inhérentes à la reconstruction du pangénome, ou la capture des variations entre souches d’une même espèce. Dans cette thèse, le problème du binning a été appréhendé à travers un modèle de clustering suivant le paradigme de la logique déclarative, l’objectif étant de maximiser l’information sur les génomes présents grâce à l’exploration de l’ensemble des solutions de binning possible. Ce modèle de binning incluant métrique compositionnelle, mesure d’abondance et occurrence de gènes marqueurs a été implémenté en langage ASP. Nous nous sommes ensuite concentrés sur l’optimisation du processus d’assemblage, étape préliminaire clé de la classification de contigs, avec pour objectif d’encore améliorer la reconstruction de MAGs. Nous avons développé une approche automatique pour guider le processus de co-assemblage, couplant des distances métagénomiques avec une méthode d’optimisation du clustering. Cette approche a été intégrée dans un nouveau workflow de reconstruction de MAGs, MAGNETO, qui intègre également des stratégies assemblage-binning complémentaires
Modèles et méthodes pour la métagénomique à résolution génomique
No full textThe reconstruction of individual genomes from metagenomic data, also called MAGs has constituted a major milestone in the study of microbial communities. However, the recovery of MAGs still suffers several limitations, including the mosaic and population nature of these MAGs, the inherent difficulties to assemble pangenomes, and the recovery of strain-level variations for a given species. In this thesis, a declarative programming framework was designed and used to resolve the genome binning problem through a constrained clustering approach, with the goal to explore several optimal binning solutions, informing us about the organization dynamics of naturally occurring genomes. A novel genome binning model integrating compositional and abundance information as well as constraints on single-copy core genes was designed and implemented using the ASP language. With the goal to further enhance the recovery of MAGs, we focused on optimizing the assembly process, a key genome binning pre-processing step. We developed an automated approach to guide the co-assembly process, combining metagenomic compositional distances with an optimal clustering method. These developments were implemented into a novel genome-resolved metagenomics workflow called MAGNETO, integrating complementary assembly-binning strategies.La reconstruction de génomes à partir de données métagénomiques, aussi appelés MAG) représente une étape majeure dans l’étude des communautés microbiennes. La reconstruction de MAGs souffre néanmoins de limitations, telles que la nature fragmentée de ces MAGs, les difficultés inhérentes à la reconstruction du pangénome, ou la capture des variations entre souches d’une même espèce. Dans cette thèse, le problème du binning a été appréhendé à travers un modèle de clustering suivant le paradigme de la logique déclarative, l’objectif étant de maximiser l’information sur les génomes présents grâce à l’exploration de l’ensemble des solutions de binning possible. Ce modèle de binning incluant métrique compositionnelle, mesure d’abondance et occurrence de gènes marqueurs a été implémenté en langage ASP. Nous nous sommes ensuite concentrés sur l’optimisation du processus d’assemblage, étape préliminaire clé de la classification de contigs, avec pour objectif d’encore améliorer la reconstruction de MAGs. Nous avons développé une approche automatique pour guider le processus de co-assemblage, couplant des distances métagénomiques avec une méthode d’optimisation du clustering. Cette approche a été intégrée dans un nouveau workflow de reconstruction de MAGs, MAGNETO, qui intègre également des stratégies assemblage-binning complémentaires
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
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
MAGNETO supplementary materials
No full textSupplementary materials for MAGNETO: an automated workflow for genome-resolved metagenomics
Benjamin Churcheward, Maxime Millet, Audrey Bihouée, Guillaume Fertin, Samuel Chaffron
doi: https://doi.org/10.1101/2022.05.06.49099
- …
