A network-based integrated framework for predicting virus-prokaryote interactions.

Metagenomic sequencing has greatly enhanced the discovery of viral genomic sequences; however, it remains challenging to identify the host(s) of these new viruses. We developed VirHostMatcher-Net, a flexible, network-based, Markov random field framework for predicting virus-prokaryote interactions using multiple, integrated features: CRISPR sequences and alignment-free similarity measures ([Formula: see text] and WIsH). Evaluation of this method on a benchmark set of 1462 known virus-prokaryote pairs yielded host prediction accuracy of 59% and 86% at the genus and phylum levels, representing 16-27% and 6-10% improvement, respectively, over previous single-feature prediction approaches.

Plankton networks driving carbon export in the oligotrophic ocean.

The biological carbon pump is the process by which CO2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean.