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Author: Edward C Holmes

  • ORCiD: http://orcid.org/0000-0001-9596-3552
  • Most recently observed institution: Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney

Rankings

  • All-time downloads: 77,667 (rank: 1,516 out of 513,923)
  • Categories:
    • bioinformatics: 1,736 (rank: 7,368 (tie) out of 37,095)
    • ecology: 1,918 (rank: 1,293 (tie) out of 19,433)
    • epidemiology: 2,577 (rank: 3,266 out of 23,860)
    • evolutionary biology: 5,190 (rank: 455 (tie) out of 22,356)
    • genetic and genomic medicine: 231 (rank: 4,314 (tie) out of 6,816)
    • immunology: 408 (rank: 15,383 (tie) out of 27,980)
    • infectious diseases: 6,150 (rank: 4,907 (tie) out of 32,280)
    • microbiology: 43,439 (rank: 206 out of 52,513)
    • molecular biology: 1,950 (rank: 1,813 out of 24,319)
    • pathology: 13,208 (rank: 39 out of 5,914)
    • public and global health: 860 (rank: 2,693 (tie) out of 8,079)

Downloads per author, site-wide

Preprints

Meta-transcriptomic identification of divergent Amnoonviridae in fish

microbiology more details view paper

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Identification of 2019-nCoV related coronaviruses in Malayan pangolins in southern China

microbiology more details view paper
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    • In microbiology: 25 out of 9,409
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    • Site-wide: 219 out of 119,198
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    • Site-wide: 1,781 out of 119,198

Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

pathology more details view paper
  • Downloaded 12,875 times
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    • In pathology: 4 out of 700
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A novel bat coronavirus reveals natural insertions at the S1/S2 cleavage site of the Spike protein and a possible recombinant origin of HCoV-19

microbiology more details view paper
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    • In microbiology: 99 out of 9,409
  • Year to date:
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    • Site-wide: 3,273 out of 119,198

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

microbiology more details view paper
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    • In microbiology: 117 out of 9,409
  • Year to date:
    • Site-wide: 871 out of 119,198
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    • Site-wide: 1,988 out of 119,198

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

infectious diseases more details view paper
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    • In infectious diseases: 497 out of 3,634
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Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

epidemiology more details view paper
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    • In epidemiology: 382 out of 4,690
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REVEALING COVID-19 TRANSMISSION BY SARS-CoV-2 GENOME SEQUENCING AND AGENT BASED MODELLING

microbiology more details view paper
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    • In microbiology: 300 out of 9,409
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CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

bioinformatics more details view paper
  • Downloaded 1,736 times
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    • In bioinformatics: 974 out of 9,634
  • Year to date:
    • Site-wide: 7,561 out of 119,198
  • Since beginning of last month:
    • Site-wide: 16,871 out of 119,198

Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom

infectious diseases more details view paper
  • Downloaded 1,579 times
  • Download rankings, all-time:
    • Site-wide: 8,646 out of 119,198
    • In infectious diseases: 945 out of 3,634
  • Year to date:
    • Site-wide: 3,550 out of 119,198
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    • Site-wide: 8,054 out of 119,198

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

microbiology more details view paper
  • Downloaded 1,414 times
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    • In microbiology: 552 out of 9,409
  • Year to date:
    • Site-wide: 4,038 out of 119,198
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    • Site-wide: 16,366 out of 119,198

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

ecology more details view paper
  • Downloaded 1,414 times
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    • Site-wide: 10,188 out of 119,198
    • In ecology: 147 out of 4,617
  • Year to date:
    • Site-wide: 21,666 out of 119,198
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    • Site-wide: 50,405 out of 119,198

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

evolutionary biology more details view paper
  • Downloaded 1,079 times
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    • Site-wide: 15,313 out of 119,198
    • In evolutionary biology: 655 out of 6,216
  • Year to date:
    • Site-wide: 37,149 out of 119,198
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    • Site-wide: 70,765 out of 119,198

Genome-scale rates of evolutionary change in bacteria

evolutionary biology more details view paper
  • Downloaded 1,010 times
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    • Site-wide: 16,921 out of 119,198
    • In evolutionary biology: 762 out of 6,216
  • Year to date:
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    • Site-wide: 86,405 out of 119,198

The ongoing COVID-19 epidemic in Minas Gerais, Brazil: insights from epidemiological data and SARS-CoV-2 whole genome sequencing.

public and global health more details view paper
  • Downloaded 860 times
  • Download rankings, all-time:
    • Site-wide: 21,401 out of 119,198
    • In public and global health: 303 out of 1,247
  • Year to date:
    • Site-wide: 7,247 out of 119,198
  • Since beginning of last month:
    • Site-wide: 26,425 out of 119,198

Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities

molecular biology more details view paper
  • Downloaded 779 times
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    • In molecular biology: 694 out of 3,637
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    • Site-wide: 83,392 out of 119,198

Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

microbiology more details view paper
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    • In microbiology: 1,508 out of 9,409
  • Year to date:
    • Site-wide: 111,879 out of 119,198
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COVID-19 severity is associated with immunopathology and multi-organ damage

infectious diseases more details view paper
  • Downloaded 736 times
  • Download rankings, all-time:
    • Site-wide: 26,629 out of 119,198
    • In infectious diseases: 1,600 out of 3,634
  • Year to date:
    • Site-wide: 8,787 out of 119,198
  • Since beginning of last month:
    • Site-wide: 18,481 out of 119,198

Characterisation of the faecal virome of captive and wild Tasmanian devils using virus-like particles metagenomics and meta-transcriptomics

molecular biology more details view paper
  • Downloaded 729 times
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    • In molecular biology: 769 out of 3,637
  • Year to date:
    • Site-wide: 32,972 out of 119,198
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    • Site-wide: 73,388 out of 119,198

Infectious disease phylodynamics with occurrence data

evolutionary biology more details view paper
  • Downloaded 643 times
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    • In evolutionary biology: 1,720 out of 6,216
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    • Site-wide: 28,801 out of 119,198
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    • Site-wide: 21,901 out of 119,198

The Impact of Migratory Flyways on the Spread of Avian Influenza Virus in North America

evolutionary biology more details view paper
  • Downloaded 556 times
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    • Site-wide: 38,524 out of 119,198
    • In evolutionary biology: 2,151 out of 6,216
  • Year to date:
    • Site-wide: 94,389 out of 119,198
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    • Site-wide: 105,835 out of 119,198

How accurately can we assess zoonotic risk?

microbiology more details view paper
  • Downloaded 541 times
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    • Site-wide: 39,855 out of 119,198
    • In microbiology: 2,427 out of 9,409
  • Year to date:
    • Site-wide: 12,832 out of 119,198
  • Since beginning of last month:
    • Site-wide: 12,212 out of 119,198

Virome heterogeneity and connectivity in waterfowl and shorebird communities

ecology more details view paper
  • Downloaded 504 times
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    • In ecology: 1,138 out of 4,617
  • Year to date:
    • Site-wide: 49,948 out of 119,198
  • Since beginning of last month:
    • Site-wide: 60,338 out of 119,198

Pathogenicity, tissue tropism and potential vertical transmission of SARSr-CoV-2 in Malayan pangolins

microbiology more details view paper
  • Downloaded 495 times
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    • Site-wide: 44,310 out of 119,198
    • In microbiology: 2,763 out of 9,409
  • Year to date:
    • Site-wide: 14,428 out of 119,198
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    • Site-wide: 16,167 out of 119,198

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

evolutionary biology more details view paper
  • Downloaded 477 times
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    • Site-wide: 46,193 out of 119,198
    • In evolutionary biology: 2,677 out of 6,216
  • Year to date:
    • Site-wide: 32,016 out of 119,198
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    • Site-wide: 32,727 out of 119,198

Extensive Diversity of RNA Viruses in Australian Ticks

microbiology more details view paper
  • Downloaded 457 times
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    • In microbiology: 3,079 out of 9,409
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    • Site-wide: 107,651 out of 119,198
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    • Site-wide: 107,616 out of 119,198

A divergent hepatitis D-like agent in birds

molecular biology more details view paper
  • Downloaded 442 times
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    • In molecular biology: 1,438 out of 3,637
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Novel hepatitis D-like agents in vertebrates and invertebrates

evolutionary biology more details view paper
  • Downloaded 423 times
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    • In evolutionary biology: 3,063 out of 6,216
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    • Site-wide: 61,263 out of 119,198

Limited intra-host diversity and background evolution accompany 40 years of canine parvovirus host adaptation and spread

evolutionary biology more details view paper
  • Downloaded 415 times
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    • In evolutionary biology: 3,144 out of 6,216
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    • Site-wide: 27,715 out of 119,198

Host evolutionary history and ecology shape virome composition in fishes

microbiology more details view paper
  • Downloaded 409 times
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    • In microbiology: 3,573 out of 9,409
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    • Site-wide: 18,303 out of 119,198
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    • Site-wide: 30,103 out of 119,198

Comparative analysis reveals adaptive evolution of bat IFITMs and a novel antiviral determinant

immunology more details view paper
  • Downloaded 408 times
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    • Site-wide: 54,682 out of 119,198
    • In immunology: 1,425 out of 3,345
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    • Site-wide: 34,242 out of 119,198
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    • Site-wide: 93,841 out of 119,198

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

microbiology more details view paper
  • Downloaded 353 times
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    • In microbiology: 4,245 out of 9,409
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    • Site-wide: 98,441 out of 119,198

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

evolutionary biology more details view paper
  • Downloaded 337 times
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    • Site-wide: 97,986 out of 119,198

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

pathology more details view paper
  • Downloaded 333 times
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    • In pathology: 315 out of 700
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    • Site-wide: 110,984 out of 119,198

Divergent influenza-like viruses of amphibians and fish support an ancient evolutionary association

microbiology more details view paper
  • Downloaded 319 times
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    • In microbiology: 4,696 out of 9,409
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    • Site-wide: 68,623 out of 119,198

Metagenomic identification of diverse animal hepaciviruses and pegiviruses

microbiology more details view paper
  • Downloaded 311 times
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    • In microbiology: 4,841 out of 9,409
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    • Site-wide: 51,391 out of 119,198

Sustained virome diversity in Antarctic penguins and their ticks: geographical connectedness and no evidence for low pathogen pressure

microbiology more details view paper
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    • In microbiology: 4,856 out of 9,409
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Influenza Viruses in Mice: Deep Sequencing Analysis of Serial Passage and Effects of Sialic Acid Structural Variation

microbiology more details view paper
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    • In microbiology: 4,943 out of 9,409
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    • Site-wide: 60,687 out of 119,198

Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae

microbiology more details view paper
  • Downloaded 263 times
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    • Site-wide: 78,768 out of 119,198
    • In microbiology: 5,581 out of 9,409
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    • Site-wide: 44,518 out of 119,198

Influenza A viruses serially passaged in different MDCK cell lines exhibit limited sequence variation across their genomes, with the exception of the hemagglutinin gene

microbiology more details view paper
  • Downloaded 256 times
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    • In microbiology: 5,686 out of 9,409
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    • Site-wide: 75,178 out of 119,198

Limited overlap in RNA virome composition among rabbits and their ectoparasites reveals barriers to virus transmission

microbiology more details view paper
  • Downloaded 252 times
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    • Site-wide: 100,591 out of 119,198

A Reptilian Endogenous Foamy Virus Sheds Light on the Early Evolution of Retroviruses

evolutionary biology more details view paper
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The power and limitations of genomics to track COVID-19 outbreaks: a case study from New Zealand

infectious diseases more details view paper
  • Downloaded 246 times
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    • Site-wide: 82,301 out of 119,198
    • In infectious diseases: 2,726 out of 3,634
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    • Site-wide: 1,299 out of 119,198

Portable sequencing in the field and the classroom: a retrospective examination of the circulation of DENV1 and DENV2 in Brazil

genetic and genomic medicine more details view paper
  • Downloaded 231 times
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    • In genetic and genomic medicine: 242 out of 497
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    • Site-wide: 5,071 out of 119,198

The discovery of three new hare lagoviruses reveals unexplored viral diversity in this genus

microbiology more details view paper
  • Downloaded 217 times
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    • In microbiology: 6,420 out of 9,409
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    • Site-wide: 87,298 out of 119,198

Circumpolar diversification of the Ixodes uriae tick virome

microbiology more details view paper
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    • Site-wide: 51,363 out of 119,198

Red fox viromes across an urban-rural gradient

microbiology more details view paper
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    • In microbiology: 6,619 out of 9,409
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    • Site-wide: 35,354 out of 119,198

The impact of early public health interventions on SARS-CoV-2 transmission and evolution

epidemiology more details view paper
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    • In epidemiology: 3,701 out of 4,690
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    • Site-wide: 1,803 out of 119,198

A household case evidences shorter shedding of SARS-CoV-2 in naturally infected cats compared to their human owners.

infectious diseases more details view paper
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    • Site-wide: 1,825 out of 119,198

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

microbiology more details view paper
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    • Site-wide: 78,568 out of 119,198

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

microbiology more details view paper
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Retrospective meta-transcriptomic identification of severe dengue in a traveller returning from Africa to Sweden, 1990

infectious diseases more details view paper
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    • In infectious diseases: 3,429 out of 3,634
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