Mǎng Shī

The paper uses metatranscriptomics to discover liver-associated parasites in small mammals, finding diverse and widespread taxa including novel lineages and covarying viruses.

The paper analyzes 5,163 mosquito meta-transcriptomes to characterize microbial diversity and interactions, identifying pathogens and cross-kingdom associations.

LucaVirus predicts viral evolution and function using a unified nucleotide-protein language model, achieving state-of-the-art results in key virology tasks.

LucaPhylo infers phylogenetic trees from unaligned protein sequences using hyperbolic geometry and protein language models, achieving accuracy comparable to alignment-based methods for divergent RNA viruses.

This paper introduces fluProfiler, a framework using viral sequences to predict antigenic relationships and improve vaccine strain selection by reducing reliance on time-consuming HI assays.

The paper identifies RNA viruses in water shaping shrimp and fish viromes in aquaculture, showing strong correlations and shared species between water and aquatic animals.

SegFinder identifies RNA virus genome segments by analyzing co-occurrence across samples, discovering novel segments and expanding known segmented virus families.

This paper introduces LucaOne, a foundation model trained on nucleic acid and protein sequences, demonstrating understanding of biological principles and performing well on related tasks.

The paper analyzes tunicate metatranscriptomes to show that some disease-causing RNA viruses evolved before vertebrates and that recombination between viral orders shaped their evolution.

The paper analyzes the pathogen infectome of small mammals in southern China, identifying new pathogens and factors influencing their distribution and diversity.

This study identifies 742 RNA virus species in Lake Nam Co, revealing novel viral groups and evolutionary adaptations in an extreme high-altitude environment.

The paper analyzes the infectome of bat kidneys from Yunnan, China, identifying novel viruses, a protozoan parasite, and bacterial species, including henipaviruses related to Hendra and Nipah viruses.

The paper analyzes wildlife infectomes to identify zoonotic pathogens, finding 62 novel pathogens including a new coronavirus genus and highlighting high pathogen diversity in Carnivora and Rodentia.

The paper identifies 162 viral species in small mammals from Yunnan, China, including 102 novel species and 24 with potential human health risks.

VirID improves RNA virus discovery and characterization from metagenomic data by reducing false positives, accurately estimating diversity, and identifying virus-host associations.

The paper analyzes meta-transcriptomic data from companion animals to identify microbial communities and assess zoonotic risks.

The paper identifies a novel RNA virus in zoonotic Plasmodium knowlesi isolates, showing it belongs to an unclassified viral taxon called ormycoviruses.

The paper identifies a novel HDV-like agent in ducks, showing genetic divergence but structural and functional similarities to HDV, challenging current understanding of HDV origins.

This study characterizes the faecal virome of captive and wild Tasmanian devils using VLP metagenomics and meta-transcriptomics, revealing novel viruses and highlighting differences in viral diversity between populations.