With the rapid increase in sequencing data, human host status inference (e.g. healthy or sick) from microbiome data has become an important issue. Existing studies are mostly based on single-point microbiome composition, while it is rare that the hos...
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those l...
We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a 'cost' of transforming one ...
MOTIVATION: Metagenomic approaches hold the potential to characterize microbial communities and unravel the intricate link between the microbiome and biological processes. Assembly is one of the most critical steps in metagenomics experiments. It con...
Journal of visualized experiments : JoVE
Sep 25, 2021
A variety of biological sequence classification tasks, such as species classification, gene function classification and viral host classification, are expected processes in many metagenomic data analyses. Since metagenomic data contain a large number...
BACKGROUND: Prokaryotic viruses referred to as phages can be divided into virulent and temperate phages. Distinguishing virulent and temperate phage-derived sequences in metavirome data is important for elucidating their different roles in interactio...
BACKGROUND: The increasing use of whole metagenome sequencing has spurred the need to improve de novo assemblers to facilitate the discovery of unknown species and the analysis of their genomic functions. MetaVelvet-SL is a short-read de novo metagen...
Studies in health technology and informatics
May 27, 2021
In recent years, microbiota has become an increasingly relevant factor for the understanding and potential treatment of diseases. In this work, based on the data reported by the largest study of microbioma in the world, a classification model has bee...
The fast accumulation of viral metagenomic data has contributed significantly to new RNA virus discovery. However, the short read size, complex composition, and large data size can all make taxonomic analysis difficult. In particular, commonly used a...