Deep learning describes a class of machine learning algorithms that are capable of
combining raw inputs into layers of intermediate features. These algorithms have recently …

The human gut microbiota is engaged in multiple interactions affecting host health during
the host's entire life span. Microbes colonize the neonatal gut immediately following birth …

Metagenomic assembly enables new organism discovery from microbial communities, but it
can only capture few abundant organisms from most metagenomes. Here we present …

The gut microbiome has been shown to influence the response of tumors to anti–PD-1
(programmed cell death–1) immunotherapy in preclinical mouse models and observational …

Although Kraken'sk-mer-based approach provides a fast taxonomic classification of
metagenomic sequence data, its large memory requirements can be limiting for some …

Background & Aims Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-
2) infects gastrointestinal tissues, little is known about the roles of gut commensal microbes …

MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of
common data outputs generated from current microbiome studies. It enables researchers …

Anti–PD-1–based immunotherapy has had a major impact on cancer treatment but has only
benefited a subset of patients. Among the variables that could contribute to interpatient …

The human gut microbiome encodes a large variety of antimicrobial peptides (AMPs), but
the short lengths of AMPs pose a challenge for computational prediction. Here we combined …

The inflammatory bowel diseases (IBDs), which include Crohn's disease (CD) and ulcerative
colitis (UC), are multifactorial chronic conditions of the gastrointestinal tract. While IBD has …