Search results for "algorithm."
showing 10 items of 4617 documents
Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds
2018
The identification of individuals’ breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. …
Postzygotic BRAF p.Lys601Asn Mutation in Phacomatosis Pigmentokeratotica with Woolly Hair Nevus and Focal Cortical Dysplasia
2016
International audience
Statistical Explorations and Univariate Timeseries Analysis on COVID-19 Datasets to Understand the Trend of Disease Spreading and Death
2020
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Assessment of Muscular Fitness as a Predictor of Flight Duty Limitation.
2018
Introduction The high acceleration (Gz) exposure among military pilots flying fighter aircraft has been associated with an increased risk for cervical and lumbar disorders. It has been suggested that an adequate level of physical performance could reduce the risk of experiencing these disorders. The Finnish Air Force has for several years used aerobic (bicycle ergometer) and muscular fitness tests (battery of five tests) in the selection process of military pilot candidates in order to evaluate their physical fitness level. The aim of the study was to determine if these selection phase tests and anthropometry measures can predispose those individuals who might be at risk of developing sever…
Comparison of CRISPR and marker based methods for the engineering of phage T7
2020
With the recent rise in interest in using lytic bacteriophages as therapeutic agents, there is an urgent requirement to understand their fundamental biology to enable the engineering of their genomes. Current methods of phage engineering rely on homologous recombination, followed by a system of selection to identify recombinant phages. For bacteriophage T7, the host genescmkortrxhave been used as a selection mechanism along with both type I and II CRISPR systems to select against wild-type phage and enrich for the desired mutant. Here we systematically compare all three systems; we show that the use of marker-based selection is the most efficient method and we use this to generate multiple …
The GATA3 X308_Splice breast cancer mutation is a hormone context-dependent oncogenic driver
2019
AbstractAs the catalogue of oncogenic driver mutations is expanding, it is becoming clear that alterations in a given gene should not be lumped into one single class, since they might have different functions. The transcription factorGATA3is a paradigm of this. Here, we address the functions of the most commonGATA3mutation (X308_Splice) which generates a neoprotein that we designate as neoGATA3, associated with good patient prognosis. Based on extensive analyses of molecular and clinical data from approximately 3000 breast cancer patients, supported by mechanistic studiesin vitro, we show that neoGATA3 interferes with the transcriptional programs controlled by estrogen and progesterone rece…
A matching task as a potential technique for descriptive profile validation
2003
If panellists can successfully match products to the corresponding descriptive profiles, then the profiles can be regarded as product-relevant and valid. This work examined the ability of a trained panel to perform a matching task between products and their descriptive profiles. A 13-member panel, trained to assess eight cheeses in terms of 19 flavour attributes, performed the task based on their individually developed profiles. The panel's ability to match products to profiles was well above that expected by chance, and chi-square statistics for each of the products were significant (P<0.05). A correspondence analysis based on the group results indicated that all the products were relative…
Low-cost scalable discretization, prediction and feature selection for complex systems
2019
The introduced data-driven tool allows simultaneous feature selection, model inference, and marked cost and quality gains.
DNA combinatorial messages and Epigenomics: The case of chromatin organization and nucleosome occupancy in eukaryotic genomes
2019
Abstract Epigenomics is the study of modifications on the genetic material of a cell that do not depend on changes in the DNA sequence, since those latter involve specific proteins around which DNA wraps. The end result is that Epigenomic changes have a fundamental role in the proper working of each cell in Eukaryotic organisms. A particularly important part of Epigenomics concentrates on the study of chromatin, that is, a fiber composed of a DNA-protein complex and very characterizing of Eukaryotes. Understanding how chromatin is assembled and how it changes is fundamental for Biology. In more than thirty years of research in this area, Mathematics and Theoretical Computer Science have gai…
Efficient Online Laplacian Eigenmap Computation for Dimensionality Reduction in Molecular Phylogeny via Optimisation on the Sphere
2019
Reconstructing the phylogeny of large groups of large divergent genomes remains a difficult problem to solve, whatever the methods considered. Methods based on distance matrices are blocked due to the calculation of these matrices that is impossible in practice, when Bayesian inference or maximum likelihood methods presuppose multiple alignment of the genomes, which is itself difficult to achieve if precision is required. In this paper, we propose to calculate new distances for randomly selected couples of species over iterations, and then to map the biological sequences in a space of small dimension based on the partial knowledge of this genome similarity matrix. This mapping is then used …