Li Deng

The paper reanalyzes published metagenomic sequences of phage cocktails to identify temperate phages and bacterial DNA contamination, highlighting risks for horizontal gene transfer.

Replidec identifies three phage replication cycles from metagenomic data using a Naive Bayes classifier and alignment-based methods, achieving high accuracy in both isolated genomes and simulated sequences.

The paper develops a pipeline to detect microbial and viral reads in human RNA-seq data and creates the MetaMap resource for disease-related microbiome analysis.