Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses

Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses

The gut microbiota is essentially a multifunctional bioreactor within a human being. The exploration of its enormous metabolic potential provides insights into the mechanisms underlying microbial ecology and interactions with the host. The data obtained using "shotgun" metagenomics capture information about the whole spectrum of microbial functions. However, each new study presenting new sequen...

Biological profiling of gene groups utilizing Gene Ontology.

Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic functional annotation provided by the Gene Ontology the information required to automate the interpretation task is now accessible. However, the determination of...

Region-specific gene expression profiling: novel evidence for biological heterogeneity of the human amnion.

The amnion plays an important role during pregnancy and parturition. Though referred to as a single structure, this fetal tissue is regionally divided into placental amnion, reflected amnion, and umbilical amnion. Histological differences between placental amnion and reflected amnion led us to hypothesize that the amnion is biologically heterogeneous. The gene expression profiles of placental a...

Metagenomes for Improving Biocatalysis: Screening of Gene-specific Amplicons

Treephyler: fast taxonomic profiling of metagenomes

SUMMARY Assessment of phylogenetic diversity is a key element to the analysis of microbial communities. Tools are needed to handle next-generation sequencing data and to cope with the computational complexity of large-scale studies. Here, we present Treephyler, a tool for fast taxonomic profiling of metagenomes. Treephyler was evaluated on real metagenome to assess its performance in comparison...