Search results for "Biological data"
showing 10 items of 53 documents
Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication.
2015
Mitochondrial DNA sequences, often in combination with nuclear markers and morphological data, are frequently used to unravel the phylogenetic relationships, population dynamics and biogeographic histories of a plethora of organisms. The information provided by examining complete mitochondrial genomes also enables investigation of other evolutionary events such as gene rearrangements, gene duplication and gene loss. Despite efforts to generate information to represent most of the currently recognized groups, some taxa are underrepresented in mitochondrial genomic databases. One such group is leeches (Annelida: Hirudinea: Clitellata). Herein, we expand our knowledge concerning leech mitochon…
Machine learning predictions of trophic status indicators and plankton dynamic in coastal lagoons
2018
Abstract Multivariate trophic indices provide an efficient way to assess and classify the eutrophication level and ecological status of a given water body, but their computation requires the availability of experimental information on many parameters, including biological data, that might not always be available. Here we show that machine learning techniques – once trained against a full data set – can be used to infer plankton biomass information from chemical and physical parameter only, so that trophic index can then be computed without using additional biological data. More specifically, we reconstruct plankton information from chemical and physical data, and this information together w…
Empirical Bayes improves assessments of diversity and similarity when overdispersion prevails in taxonomic counts with no covariates
2019
Abstract The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the proportions computed from sampling multivariate counts. In this work we present a novel method to estimate the taxonomic composition able to work even with a single sample and no covariates, when data are affected by overdispersion. The presence of overdispersion in taxonomic counts may be the result of significant environmental factors which are often unobservable but influence communities. Following the empirical Bayes approach, we combine a Bayesian mo…
Vegetation of Middle Asia – the project state of art after ten years of survey and future perspectives
2017
Middle Asia is one of the most diverse regions on earth with high endemism of vascular plants and remarkable habitat richness, mainly due to the considerable altitudinal range (300-7,500 m a.s.l.). The region is considered as one of the 34 global biodiversity hotspots. This paper presents the Vegetation of Middle Asia database (VMA; GIVD ID: AS-00-003; http://www.givd.info/ID/AS-00-003) which is the regional database that covers the area of Tajikistan, Kyrgyzstan and Uzbekistan. The database contains phytosociological relevés collected between the years 2006 and 2016 in different vegetation types with the use of the Braun-Blanquet method. The covered vegetation types include: deciduous fore…
iSEE: Interactive SummarizedExperiment Explorer
2018
Data exploration is critical to the comprehension of large biological data sets generated by high-throughput assays such as sequencing. However, most existing tools for interactive visualisation are limited to specific assays or analyses. Here, we present the iSEE (Interactive SummarizedExperiment Explorer) software package, which provides a general visual interface for exploring data in a SummarizedExperiment object. iSEE is directly compatible with many existing R/Bioconductor packages for analysing high-throughput biological data, and provides useful features such as simultaneous examination of (meta)data and analysis results, dynamic linking between plots and code tracking for reproduci…
Exceptional Pattern Discovery
2017
This chapter is devoted to a discussion on exceptional pattern discovery, namely on scenarios, contexts, and techniques concerning the mining of patterns which are so rare or so frequent to be considered as exceptional and, then, of interest for an expert to shed lights on the domain. Frequent patterns have found broad applications in areas like association rule mining, indexing, and clustering [1, 20, 23]. The application of frequent patterns in classification also achieved some success in the classification of relational data [6, 13, 14, 19, 25], text [15], and graphs [7]. The part is organized as follows. First, the frequent pattern mining on classical datasets is presented. This is not …
Reactome graph database: Efficient access to complex pathway data
2018
Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its qu…
MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs.
2016
Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions …
Genetic Diversity of O-Antigens in Hafnia alvei and the Development of a Suspension Array for Serotype Detection.
2016
Hafnia alvei is a facultative and rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. Although it has been more than 50 years since the genus was identified, very little is known about variations among Hafnia species. Diversity in O-antigens (O-polysaccharide, OPS) is thought to be a major factor in bacterial adaptation to different hosts and situations and variability in the environment. Antigenic variation is also an important factor in pathogenicity that has been used to define clones within a number of species. The genes that are required to synthesize OPS are always clustered within the bacterial chromosome. A serotyping scheme including 39 O-serotypes has…
Identification of factors involved in dimorphism and pathogenicity of Zymoseptoria tritici
2017
A forward genetics approach was applied in order to investigate the molecular basis of morphological transition in the wheat pathogenic fungus Zymoseptoria tritici. Z. tritici is a dimorphic plant pathogen displaying environmentally regulated morphogenetic transition between yeast-like and hyphal growth. Considering the infection mode of Z. tritici, the switching to hyphal growth is essential for pathogenicity allowing the fungus the host invasion through natural openings like stomata. We exploited a previously developed Agrobacterium tumefaciens-mediated transformation (ATMT) to generate a mutant library by insertional mutagenesis including more than 10,000 random mutants. To identify gene…