Despite recent progress, the organization and ecological properties of the intestinal microbial ecosystem remain under-investigated. Here, using a manually curated metabolic module framework for (meta-)genomic data analysis, we studied species–function relationships in gut microbial genomes and microbiomes...
Dimensionality reduction is used to preserve significant properties of data in a low-dimensional space. In particular, data representation in a lower dimension is needed in applications, where information comes from multiple high dimensional sources. Data integration, however, is a challenge in itself.
In this contribution, we consider a general framework to perform dimensionality reduction taking into account that data are heterogeneous. We propose a novel approach, called Deep Kernel Dimensionality Reduction which is designed for learning layers of new compact data representations simultaneously. The method can be also used to learn shared representations between modalities. We show by experiments on standard and on real large-scale biomedical data sets that the proposed method embeds data in a new compact meaningful representation, and leads to a lower classification error compared to the state-of-the-art methods.
MOCAT2 is a software pipeline for metagenomic sequence assembly and gene prediction with novel features for taxonomic and functional abundance profiling. The automated generation and efficient annotation of non-redundant reference catalogs by propagating pre-computed assignments from 18 databases covering various functional categories allows for fast and comprehensive functional characterization of metagenomes.
The number of morbidly obese patients undergoing bariatric surgery (BS) has increased dramatically in recent years. Therefore, monitoring food intake and its consequences in terms of nutritional status is necessary to prevent nutritional deficiencies. The aim of this study was to analyze the effect of food restriction on nutritional parameters in the short-term (≤3 months) period after BS in morbid obesity.