Author

J.-S. Eden

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 11 Evolutionary Biology· 4 Ecology· 2 Pathology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 10 Approach:experimental assay· 9 Assay:metagenomics· 8 Research Focus:host-pathogen & immune response· 7 Assay:bulk RNA-seq· 6 Research Focus:cell type annotation· 4 Organism:human· 4 Organism:mouse· 4

Frequent Co-Authors

E. C. Holmes· 15 shared M. Shi· 10 shared K. Rose· 6 shared W.-S. Chang· 5 shared D. E. Dwyer· 3 shared I. Carter· 3 shared J. H.- O. Pettersson· 3 shared J. Kok· 3 shared

Activity by Year

2018-2023 · peak 8/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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15 shared papersMicrobiology

E. C. Holmes

Mutual co-authors in cluster

Author profile →

18 papers

Recent·Most cited

Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses

Y.-f. Pan, H. Zhao, Q.-y. Gou, P.-b. Shi, J.-h. Tian, Y. Feng, K. Li, W.-h. Yang, D. Wu, G. Tang, B. Zhang, Z. Ren, S. Peng, G.-y. Luo, S.-j. Le, , M. Shi

The paper analyzes the virome of 2,438 individual mosquitoes across China to reveal viral diversity, geographic hotspots, and the impact of host phylogeny on viral composition.

bioRxiv · Aug 28, 2023 · PreprintEcology

Using artificial intelligence to document the hidden RNA virosphere

X. Hou, Y. He, P. Fang, S.-Q. Mei, Z. Xu, W.-C. Wu, J.-H. Tian, S. Zhang, Z.-Y. Zeng, Q.-Y. Gou, G.-Y. Xin, S.-J. Le, Y.-Y. Xia, Y.-L. Zhou, F.-M. Hui, , M. Shi

This study uses a deep learning algorithm to discover highly divergent RNA viruses in metatranscriptomes, identifying 161,979 potential species and 180 supergroups.

bioRxiv · Apr 18, 2023Microbiology

Extensive characterization of HIV-1 reservoirs reveals links to plasma viremia before and during analytical treatment interruption

B. Cole, L. Lambrechts, Z. Boyer, Y. Noppe, M.-A. De Scheerder, J.-S. Eden, B. Vrancken, T. Schlub, L. M. Frenkel, S. McLaughlin, S. Palmer, L. Vandekerckhove

This study characterizes HIV-1 reservoirs in four individuals during treatment interruption, identifying proviruses linked to plasma viremia and showing their role in viral rebound.

bioRxiv · Feb 4, 2021Microbiology

The spatial-temporal dynamics of respiratory syncytial virus infections across the east-west coasts of Australia during 2016-17

M. Robertson, J.-S. Eden, A. Levy, I. Carter, R. L. Tulloch, E. J. Cutmore, B. A. Horsburgh, C. T. Sikazwe, D. E. Dwyer, D. W. Smith, J. Kok

This study analyzes RSV genome sequences from eastern and western Australia to understand spatial-temporal dynamics and transmission patterns during 2016-17.

bioRxiv · Nov 6, 2020Microbiology

Meta-transcriptomic identification of divergent Amnoonviridae in fish

O. M. H. Turnbull, A. S. Ortiz-Baez, J.-S. Eden, M. Shi, J. E. Williamson, T. F. Gaston, Y.-Z. Zhang, E. C. Holmes, J. L. Geoghegan

The paper identifies two new Amnoonviridae viruses in fish and finds additional TiLV transcripts, suggesting a broad host range for the family.

bioRxiv · Oct 6, 2020Microbiology

Meta-transcriptomic analysis of virus diversity in urban wild birds with paretic disease

W.-S. Chang, J.-S. Eden, J. Hall, M. Shi, K. Rose, E. C. Holmes

The paper identifies novel viruses in urban wild birds with paresis using meta-transcriptomic analysis and finds potential viral causes of neurological and muscular diseases.

Journal of Virology · Aug 31, 2020Peer-reviewedMicrobiology

Meta-transcriptomic discovery of a divergent circovirus and a chaphamaparvovirus in captive reptiles with proliferative respiratory syndrome

W.-S. Chang, C.-X. Li, J. Hall, J.-S. Eden, T. H. Hyndman, E. C. Holmes, K. Rose

The paper identifies two novel viruses in captive bearded dragons with respiratory disease using meta-transcriptomic sequencing.

bioRxiv · Aug 24, 2020Microbiology

A divergent Articulavirus in an Australian gecko identified using meta-transcriptomics and protein structure comparisons

S. Ortiz, J.-S. Eden, C. Moritz, E. C. Holmes

The paper identifies a divergent Articulavirus in an Australian gecko using meta-transcriptomics and protein structure comparisons, revealing a new genus in the Amnoonviridae family.

bioRxiv · May 21, 2020Microbiology

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

A. F. Porter, J. H.- O. Pettersson, W.-S. Chang, E. Harvey, K. Rose, M. Shi, J.-S. Eden, J. Buchmann, C. Moritz, E. C. Holmes

The paper identifies novel hepaciviruses and pegiviruses in Australian wildlife and supports virus-host co-divergence through phylogenetic analysis.

bioRxiv · May 16, 2020 · PreprintMicrobiology

REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING

R. J. Rockett, A. Arnott, C. Lam, R. Sadsad, V. Timms, K.-A. Gray, J.-S. Eden, S. L. Chang, M. Gall, J. Draper, E. Sim, N. L. Bachmann, I. Carter, K. Basile, R. Byun, , V. Sintchenko

The paper uses SARS-CoV-2 genome sequencing and agent-based modeling to estimate local transmission rates during the early stages of the COVID-19 outbreak in New South Wales.

bioRxiv · Apr 19, 2020 · PreprintMicrobiology

An emergent clade of SARS-CoV-2 linked to returned travellers from Iran

J.-S. Eden, R. Rockett, I. Carter, H. Rahman, J. de Ligt, J. Hadfield, M. Storey, X. Ren, R. Tulloch, K. Basile, J. Wells, R. Byun, N. Gliroy, M. V. O'Sullivan, V. Sintchenko, , J. Kok

The paper identifies a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand through whole genome sequencing and phylogenetic analysis.

bioRxiv · Mar 15, 2020Microbiology

Metagenomic discovery and co-infection of diverse wobbly possum disease viruses and novel hepaciviruses in Australian brushtail possums

W.-S. Chang, J.-S. Eden, K. Rose, M. Shi, E. C. Holmes

The paper identifies a new lineage of arteriviruses and a novel hepacivirus in Australian brushtail possums, showing co-infection and genetic divergence from New Zealand strains.

bioRxiv · Oct 7, 2019Pathology

Meta-transcriptomic comparison of the RNA viromes of the mosquito vectors Culex pipiens and Culex torrentium in northern Europe

J. H.- O. Pettersson, M. Shi, J.-S. Eden, E. C. Holmes, J. C. Hesson

The paper compares the RNA viromes of two northern European Culex mosquito species, identifying 40 viruses including 28 novel ones, and shows geographical factors influence virome diversity.

bioRxiv · Aug 5, 2019Evolutionary Biology

Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria

J. Charon, M. J. Grigg, J.-S. Eden, K. A. Piera, T. William, K. Rose, M. P. Davenport, N. M. Anstey, E. C. Holmes

The paper identifies a novel RNA virus, MaRNAV-1, associated with Plasmodium vivax in humans and mosquitoes, and a related virus in birds infected with Leucocytozoon parasites.

bioRxiv · May 1, 2019 · PreprintEvolutionary Biology

High levels of antibiotic resistance gene expression among birds living in a wastewater treatment plant

V. Rossetto Marcelino, M. Wille, A. C. Hurt, D. Gonzalez-Acuna, M. Klaassen, J.-S. Eden, M. Shi, J. R. Iredell, T. C. Sorrell, E. C. Holmes

The paper assesses antibiotic resistance gene expression in birds across different habitats, finding higher levels in wastewater treatment plant birds.

BMC Biology · Apr 8, 2019Peer-reviewedEcology

Novel hepatitis D-like agents in vertebrates and invertebrates

W.-S. Chang, J. H.- O. Pettersson, C. Le Lay, M. Shi, N. Lo, M. Wille, J.-S. Eden, E. Holmes

The paper identifies HDV-like viruses in non-human vertebrates and invertebrates, showing they share genomic features with HDV but are not associated with hepadnavirus infection.

bioRxiv · Feb 4, 2019Evolutionary Biology

Punctuated evolution of myxoma virus: rapid and disjunct evolution of a recent viral lineage in Australia

P. J. Kerr, J.-S. Eden, F. Di Giallonardo, D. Peacock, J. Liu, T. Strive, A. F. Read, E. C. Holmes

This paper shows that Myxoma virus in Australia experienced a sudden evolutionary change with a faster mutation rate and disrupted clock-like evolution between 1996 and 2012, likely due to environmental changes affecting rabbit populations.

bioRxiv · Nov 8, 2018Evolutionary Biology

Extensive Diversity of RNA Viruses in Australian Ticks

E. Harvey, K. Rose, J.-S. Eden, N. Lo, T. Abeyasuriya, M. Shi, S. L. Doggett, E. C. Holmes

This study identifies 19 novel RNA viruses in Australian ticks, including some potentially capable of infecting mammals, and finds no evidence of Borrelia burgdorferi s.l., the causative agent of Lyme disease.

bioRxiv · Aug 7, 2018Microbiology