Search results for "methodologies"
showing 10 items of 2106 documents
X!TandemPipeline: a tool to manage sequence redundancy for protein inference and phosphosite identification
2017
X!TandemPipeline is a software designed to perform protein inference and to manage redundancy in the results of phosphosite identification by database search. It provides the minimal list of proteins or phosphosites that are present in a set of samples using grouping algorithms based on the principle of parsimony. Regarding proteins, a two-level classification is performed, where groups gather proteins sharing at least one peptide and subgroups gather proteins that are not distinguishable according to the identified peptides. Regarding phosphosites, an innovative approach based on the concept of phosphoisland is used to gather overlapping phosphopeptides. The graphical interface of X!Tandem…
Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource
2021
Abstract Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last 20 years. A major challenge is the integration of these disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution and population structure of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequenc…
A unified vegetation index for quantifying the terrestrial biosphere
2021
[EN] Empirical vegetation indices derived from spectral reflectance data are widely used in remote sensing of the biosphere, as they represent robust proxies for canopy structure, leaf pigment content, and, subsequently, plant photosynthetic potential. Here, we generalize the broad family of commonly used vegetation indices by exploiting all higher-order relations between the spectral channels involved. This results in a higher sensitivity to vegetation biophysical and physiological parameters. The presented nonlinear generalization of the celebrated normalized difference vegetation index (NDVI) consistently improves accuracy in monitoring key parameters, such as leaf area index, gross prim…
Conservation and people: Towards an ethical code of conduct for the use of camera traps in wildlife research
2020
International audience; Abstract 1. Camera trapping is a widely employed tool in wildlife research, used to estimate animal abundances, understand animal movement, assess species richness and understand animal behaviour. In addition to images of wild animals, research cameras often record human images, inadvertently capturing behaviours ranging from innocuous actions to potentially serious crimes. 2. With the increasing use of camera traps, there is an urgent need to reflect on how researchers should deal with human images caught on cameras. On the one hand, it is important to respect the privacy of individuals caught on cameras, while, on the other hand, there is a larger public duty to re…
Macrophyte assessment in European lakes: Diverse approaches but convergent views of ‘good’ ecological status
2018
Graphical abstract
Wild
2021
Graphical abstract
Tackling invasive alien species in Europe II: threats and opportunities until 2020
2017
2nd Freshwater Invasives - Networking for Strategy II (FINS-II) Conference -- JUL 11-14, 2016 -- Zagreb, CROATIA Skora, Michal Edward/0000-0002-9121-1318; Groom, Quentin/0000-0002-0596-5376; Lukas, Juliane/0000-0003-3336-847X; Skora, Michal/0000-0002-9121-1318; Piria, Marina/0000-0001-6324-9282; Smith, Emily/0000-0003-2767-9933; Simonovic, Predrag/0000-0002-4819-4962; Pastorino, Paolo/0000-0002-0585-1168; Koutsikos, Nicholas/0000-0003-0680-4504; Vilizzi, Lorenzo/0000-0001-8103-885X; Dobrzycka-Krahel, Aldona/0000-0002-4252-895X; Tarkan, Ali Serhan/0000-0001-8628-0514 WOS: 000412582000002 Invasive alien species (IAS) are a significant and growing problem worldwide. In Europe, some aspects of …
Seed Bank in Annuals: Competition Between Banker and Non-banker Morphs
2002
Seed bank is a plant life history strategy against the unpredictability of the biotic and the abiotic environment. We simulated competition between a seed banking and a non-banking morph of an annual plant. A constant fraction of the banker morph seeds was allocated to the seed bank, where they had a constant mortality and germination rate. All surviving seeds of the non-banker morph germinated in the next generation. The seedlings of both morphs experienced similar density-dependent mortality. Whether one of the morphs wins or the morphs coexist was evaluated from parameter space plots and statistically with logistic regression analysis. All parameters of the model had a significant, nonli…
Drosophila Evolution over Space and Time (DEST) : A New Population Genomics Resource
2021
Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a…
A segmentation algorithm for noisy images
2005
International audience; This paper presents a segmentation algorithm for gray-level images and addresses issues related to its performance on noisy images. It formulates an image segmentation problem as a partition of a weighted image neighborhood hypergraph. To overcome the computational difficulty of directly solving this problem, a multilevel hypergraph partitioning has been used. To evaluate the algorithm, we have studied how noise affects the performance of the algorithm. The alpha-stable noise is considered and its effects on the algorithm are studied. Key words : graph, hypergraph, neighborhood hypergraph, multilevel hypergraph partitioning, image segmentation and noise removal.