RNA-seq data of pig placenta and endometrium during late gestation.

Limiting the level of piglet losses before weaning is a growing demand from producers and society to improve the welfare and health of sows and piglets. In particular, perinatal mortality, which can be defined as the complete development allowing survival at birth, is mostly due to reduced piglet maturity that occurs at the end of gestation. Fetal growth and maturation depend on a fine balance between the nutrient requirements for optimal fetal growth and the maternal nutrient requirements.

BEST4 cells in the intestinal epithelium.

The recent development of single-cell transcriptomics highlighted the existence of a new lineage of mature absorptive cells in the human intestinal epithelium. This subpopulation is characterized by the specific expression of Bestrophin 4 (BEST4) and of other marker genes including , and . BEST4 cells appear early in development and are present in all regions of the small and large intestine at a low abundance (<5% of all epithelial cells).

Should we really use graph neural networks for transcriptomic prediction?

The recent development of deep learning methods have undoubtedly led to great improvement in various machine learning tasks, especially in prediction tasks. This type of methods have also been adapted to answer various problems in bioinformatics, including automatic genome annotation, artificial genome generation or phenotype prediction. In particular, a specific type of deep learning method, called graph neural network (GNN) has repeatedly been reported as a good candidate to predict phenotypes from gene expression because its ability to embed information on gene regulation or co-expression through the use of a gene network.

Asterics: a simple tool for the ExploRation and Integration of omiCS data.

Background: 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 obtain relevant biological information. Here, we present ASTERICS (version 2.5), a publicly available web interface for the analyses of omics datasets.

Plasma H-NMR metabolic and amino acid profiles of newborn piglets from two lines divergently selected for residual feed intake.

Together with environmental factors, physiological maturity at birth is a major determinant for neonatal survival and postnatal development in mammalian species. Maturity at birth is the outcome of complex mechanisms of intra-uterine development and maturation during the end of gestation. In pig production, piglet preweaning mortality averages 20% of the litter and thus, maturity is a major welfare and economic concern.

Feature selection for kernel methods in systems biology.

The substantial development of high-throughput biotechnologies has rendered large-scale multi-omics datasets increasingly available. New challenges have emerged to process and integrate this large volume of information, often obtained from widely heterogeneous sources. Kernel methods have proven successful to handle the analysis of different types of datasets obtained on the same individuals.

Major Reorganization of Chromosome Conformation During Muscle Development in Pig.

The spatial organization of the genome in the nucleus plays a crucial role in eukaryotic cell functions, yet little is known about chromatin structure variations during late fetal development in mammals. We performed high-throughput chromosome conformation capture (Hi-C) sequencing of DNA from muscle samples of pig fetuses at two late stages of gestation. Comparative analysis of the resulting Hi-C interaction matrices between both groups showed widespread differences of different types.

Network Analyses Reveal Negative Link Between Changes in Adipose Tissue GDF15 and BMI During Dietary-induced Weight Loss.

Context: Adipose tissue (AT) transcriptome studies provide holistic pictures of adaptation to weight and related bioclinical settings changes.

Objective: To implement AT gene expression profiling and investigate the link between changes in bioclinical parameters and AT gene expression during 3 steps of a 2-phase dietary intervention (DI).

Methods: AT transcriptome profiling was obtained from sequencing 1051 samples, corresponding to 556 distinct individuals enrolled in a weight loss intervention (8-week low-calorie diet (LCD) at 800 kcal/day) followed with a 6-month ad libitum randomized DI.

Joint Automatic Metabolite Identification and Quantification of a Set of H NMR Spectra.

Metabolomics is a promising approach to characterize phenotypes or to identify biomarkers. It is also easily accessible through NMR, which can provide a comprehensive understanding of the metabolome of any living organisms. However, the analysis of H NMR spectrum remains difficult, mainly due to the different problems encountered to perform automatic identification and quantification of metabolites in a reproducible way.

The maturity in fetal pigs using a multi-fluid metabolomic approach.

In mammalian species, the first days after birth are an important period for survival and the mortality rate is high before weaning. In pigs, perinatal deaths average 20% of the litter, with important economic and societal consequences. Maturity is one of the most important factors that influence piglet survival at birth.

Multi-species annotation of transcriptome and chromatin structure in domesticated animals.

Background: Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells).

Results: RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs.

Adjacency-constrained hierarchical clustering of a band similarity matrix with application to genomics.

Background: Genomic data analyses such as Genome-Wide Association Studies (GWAS) or Hi-C studies are often faced with the problem of partitioning chromosomes into successive regions based on a similarity matrix of high-resolution, locus-level measurements. An intuitive way of doing this is to perform a modified Hierarchical Agglomerative Clustering (HAC), where only adjacent clusters (according to the ordering of positions within a chromosome) are allowed to be merged. But a major practical drawback of this method is its quadratic time and space complexity in the number of loci, which is typically of the order of to for each chromosome.

ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra.

Motivation: In metabolomics, the detection of new biomarkers from Nuclear Magnetic Resonance (NMR) spectra is a promising approach. However, this analysis remains difficult due to the lack of a whole workflow that handles spectra pre-processing, automatic identification and quantification of metabolites and statistical analyses, in a reproducible way.

Results: We present ASICS, an R package that contains a complete workflow to analyse spectra from NMR experiments.