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Article
Open AccessGenomic data integration tutorial, a plant case study
The ongoing evolution of the Next Generation Sequencing (NGS) technologies has led to the production of genomic data on a massive scale. While tools for genomic data integration and analysis are becoming incre...
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Article
Open AccessHorizontal metaproteomics and CAZymes analysis of lignocellulolytic microbial consortia selectively enriched from cow rumen and termite gut
Selectively enriched microbial consortia are potentially useful for the conversion of lignocellulose (LC) into biofuels and commodity chemicals. Consortia are also of interest to elucidate the roles of individ...
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Chapter and Conference Paper
Can We Predict QPP? An Approach Based on Multivariate Outliers
Query performance prediction (QPP) aims to forecast the effectiveness of a search engine across a range of queries and documents. While state-of-the-art predictors offer a certain level of precision, their acc...
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Article
Open AccessAsterics: a simple tool for the ExploRation and Integration of omiCS data
The rapid development of omics acquisition techniques has induced the production of a large volume of heterogeneous and multi-level omics datasets, which require specific and sometimes complex analyses to obta...
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Article
Open AccessImprovement of variables interpretability in kernel PCA
Kernel methods have been proven to be a powerful tool for the integration and analysis of high-throughput technologies generated data. Kernels offer a nonlinear version of any linear algorithm solely based on ...
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Article
Open AccessIntegrative Multi-omics Analysis of Childhood Aggressive Behavior
This study introduces and illustrates the potential of an integrated multi-omics approach in investigating the underlying biology of complex traits such as childhood aggressive behavior. In 645 twins (cases = ...
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Protocol
Multivariate Analysis with the R Package mixOmics
The high-dimensional nature of proteomics data presents challenges for statistical analysis and biological interpretation. Multivariate analysis, combined with insightful visualization can help to reveal the u...
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Protocol
Multi-omics Data Integration in the Context of Plant Abiotic Stress Signaling
In order to answer new biological questions, high-throughput data generated by new biotechnologies can be very meaningful but require specific and adapted statistical treatments. Thus, in the context of abioti...
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Article
Open AccessPlasma proteomics reveals crosstalk between lipid metabolism and immunity in dairy cows receiving essential fatty acids and conjugated linoleic acid
Essential fatty acids (EFA) and conjugated linoleic acids (CLA) are unsaturated fatty acids with immune-modulatory effects, yet their synergistic effect is poorly understood in dairy cows. This study aimed at ...
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Article
Open AccessThe antibody response induced FMDV vaccines in sheep correlates with early transcriptomic responses in blood
Foot and mouth disease (FMD) is a highly contagious viral disease with high economic impact, representing a major threat for cloven-hooved mammals worldwide. Vaccines based on adjuvanted inactivated virus (iFM...
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Article
Open AccessCarbon sources and XlnR-dependent transcriptional landscape of CAZymes in the industrial fungus Talaromyces versatilis: when exception seems to be the rule
Research on filamentous fungi emphasized the remarkable redundancy in genes encoding hydrolytic enzymes, the similarities but also the large differences in their expression, especially through the role of the ...
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Chapter and Conference Paper
Studying the Variability of System Setting Effectiveness by Data Analytics and Visualization
Search engines differ from their modules and parameters; defining the optimal system setting is challenging the more because of the complexity of a retrieval stream. The main goal of this study is to determine...
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Chapter and Conference Paper
Human-Based Query Difficulty Prediction
The purpose of an automatic query difficulty predictor is to decide whether an information retrieval system is able to provide the most appropriate answer for a current query. Researchers have investigated man...
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Article
Open AccessVisualising associations between paired ‘omics’ data sets
Each omics platform is now able to generate a large amount of data. Genomics, proteomics, metabolomics, interactomics are compiled at an ever increasing pace and now form a core part of the fundamental systems...
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Article
Adaptive sequential design for regression on multi-resolution bases
This work investigates the problem of construction of designs for estimation and discrimination between competing linear models. In our framework, the unknown signal is observed with the addition of a noise an...
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Article
How many performance measures to evaluate information retrieval systems?
Evaluating effectiveness of information retrieval systems is achieved by performing on a collection of documents, a search, in which a set of test queries are performed and, for each query, the list of the rel...
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Article
Open AccessAnalysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (Open Access publication)
A large variety of methods has been proposed in the literature for microarray data analysis. The aim of this paper was to present techniques used by the EADGENE (European Animal Disease Genomics Network of Exc...
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Article
Open AccessAnalysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)
The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class predictio...
