Edward Charles Holmes

ViroChart maps host responses from virome RNA-seq data to identify phenotypic profiles of viruses, revealing host response patterns in animal infections.

The paper uses metatranscriptomic sequencing to identify co- and incidental infections in marine turtles, revealing complex disease aetiologies involving multiple pathogens.

The paper identifies two novel pegiviruses and two orthohepaciviruses in Australian birds, revealing recombination events and co-infections among avian hepaciviruses.

The paper reports a new bat betacoronavirus from Brazil with a functional furin cleavage site in its spike protein, highlighting its phylogenetic distinctiveness and potential zoonotic risk.

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

The paper analyzes RNA viromes of ctenophores and placozoans to explore virus-host relationships, identifying novel viruses and their evolutionary patterns.

The paper reports the cryo-EM structure of piscine orthoreovirus, showing structural conservation with mammalian orthoreoviruses despite low sequence identity.

RVPSD provides a web database of 154,716 AlphaFold2-predicted RNA viral protein structures from 5,263 species, enabling structural and functional analysis of RNA viral proteomes.

The paper identifies ten new sarthrovirus species from diverse hosts in Australia, expanding the family to 11 species and seven genera, and suggests alternative replication strategies and helper virus associations.

This paper identifies novel kolmioviruses in vertebrates, showing multiple lineages co-circulated through vertebrate evolution, with HDV-HBV association emerging recently.

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

The paper detects a novel hantavirus in Australian dolphins and places it within the Mobatvirus genus, indicating hantaviruses can infect non-terrestrial mammals.

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.

The paper develops a host-response-based framework to detect viral infections by analyzing ISG expression in RNA-seq data from diverse species, revealing hidden infections missed by conventional methods.

This study identifies new RNA viruses in invasive camelids in Australia, revealing convergent evolution of upstream ORFs across divergent picornaviruses.

This study identifies 1,475 novel RNA viruses in Australian soils and demonstrates that snap-freezing is a viable storage method for at least three months.

The paper identifies a new lineage of chuviruses in Australian microbats and reveals high viral diversity and connectivity among microbat species.

The paper maps the geographic distribution and host associations of MaRNAV-1, a virus linked to Plasmodium vivax, using metatranscriptomic data.

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

The paper isolates a new jingchuvirus, TDCV, from Tasmanian devil tumor cells, showing it infects these cells but not mosquito cells, and suggests it belongs to a novel virus family.

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.

This study characterizes the RNA virome of endangered Christmas Island flying foxes, finding limited diversity dominated by dietary viruses and identifying novel viruses related to mainland Australia and invertebrates.

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

The paper investigates microbial transmission among reef fishes in the Great Barrier Reef, finding limited cross-species transmission despite ecological interactions.

This paper reports the first detection of Alphamesonivirus-1 in mammals, specifically horses with acute respiratory syndrome, challenging the belief that mesoniviruses are insect-specific.

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.

This paper detects RMV and novel tobamoviruses in Australia using metatranscriptomic sequencing of animal gut content, revealing new viral threats to horticultural systems.

This study examines genome size variation in animal RNA viruses and finds that phylogenetic constraints, not host type or genome segmentation, primarily influence genome size across viral orders.