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1. Full Text Pathogenic passengers: Edward C. Holmes welcomes a robust account of how viruses emerge and how pandemics can be prevented
by Holmes, Edward C
Nature, ISSN 0028-0836, 10/2011, Volume 478, Issue 7369, p. 319
Virus diseases | Prevention | Epidemics | Research | United States
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2. The evolution and emergence of RNA viruses
by Holmes, Edward C
2009, Oxford series in ecology and evolution, ISBN 0199211124, xii, 254
Virus diseases | RNA viruses | genetics | Viral genetics | RNA Virus Infections | Viruses | Evolution | Evolution, Molecular
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3. Molecular evolution
: a phylogenetic approach
by Page, Roderic D. M and Holmes, Edward C
1998, ISBN 9780865428898, v, 346
Molecular evolution | Evolutionary genetics
Book
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4. Full Text The Biological Object Notation (BON): A structured file format for biological data
by Buchmann, Jan P and Fourment, Mathieu and Holmes, Edward C
Scientific Reports, ISSN 2045-2322, 12/2018, Volume 8, Issue 1, pp. 9644 - 8
The large size and high complexity of biological data can represent a major methodological challenge for the analysis and exchange of data sets between... 
INFORMATION | MULTIDISCIPLINARY SCIENCES | SEQUENCE | Datasets | Computers | Metadata | Software reviews
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5. Full Text Can Sequence Phylogenies Safely Infer the Origin of the Global Virome?
by Holmes, EC and Duchene, S
MBIO, ISSN 2150-7511, 03/2019, Volume 10, Issue 2, p. e00289-19
phylogeny | MICROBIOLOGY | evolution | RNA polymerase | virus | Metagenomics | Phylogeny | RNA | Evolution, Molecular | Index Medicus
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6. Full Text What does virus evolution tell us about virus origins?
by Holmes, Edward C
Journal of Virology, ISSN 0022-538X, 09/2011, Volume 85, Issue 18, pp. 9655 - 9655
VIROLOGY | Author's
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7. Full Text The Evolutionary Genetics of Emerging Viruses
by Edward C. Holmes
Annual Review of Ecology, Evolution, and Systematics, ISSN 1543-592X, 1/2009, Volume 40, Issue 1, pp. 353 - 372
RNA viruses are the main agents of emerging disease. To understand how RNA viruses are able to jump species boundaries and spread in new hosts it is essential... 
RNA viruses | RNA | Ecological competition | Evolution | Viruses | Population size | Genomes | Epistasis | Genetic mutation | Natural selection | Recombination | RNA secondary structure | Emergence | Quasispecies | Complementation | Robustness | Mutation | Fitness | STRONG PURIFYING SELECTION | natural selection | recombination | epistasis | emergence | robustness | evolution | ANTAGONISTIC EPISTASIS | complementation | REPLICATION FIDELITY | quasispecies | mutation | EVOLUTIONARY BIOLOGY | POSITIVE SELECTION | fitness | IN-VIVO | DELETERIOUS MUTATION | VESICULAR STOMATITIS-VIRUS | RNA SECONDARY STRUCTURES | QUASI-SPECIES THEORY | HIGH MUTATION-RATES | Gene mutations | Analysis | Physiological aspects | Genetic aspects | Genetic epistasis | Evolutionary genetics | Research | Virus diseases | Genetic diversity | Ribonucleic acid--RNA
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8. Full Text Virome heterogeneity and connectivity in waterfowl and shorebird communities
by Wille, Michelle and Shi, Mang and Klaassen, Marcel and Hurt, Aeron C and Holmes, Edward C
The ISME journal, ISSN 1751-7362, 06/2019
Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations... 
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9. Full Text Exploring Host-Pathogen Interactions through Biological Control
: e1004865
by Francesca Di Giallonardo and Edward C Holmes
PLoS Pathogens, ISSN 1553-7366, 06/2015, Volume 11, Issue 6
  A new biocontrol intervention is planned in Australia with the release of koi herpesvirus (KHV, or cyprinid herpesvirus-3) against the common carp (Cyprinus... 
Endangered & extinct species | Rabbits | Carp | Viruses | Evolution | Islands | Biological diversity
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10. Full Text Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families
by Geoghegan, Jemma L and Duchêne, Sebastián and Holmes, Edward C
PLoS Pathogens, ISSN 1553-7366, 02/2017, Volume 13, Issue 2, pp. e1006215 - e1006215
The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear... 
TREE COMPARISON METRICS | PHYLOGENY | HIGH-THROUGHPUT | RECONSTRUCTION | MICROBIOLOGY | EMERGENCE | EVOLUTION | VIROLOGY | SELECTION | VIRUSES | PARASITOLOGY | HISTORY | TOOL | Genome, Viral | Zoonoses - genetics | Animals | Viruses - genetics | Humans | Host Specificity | Phylogeny | Evolution, Molecular | RNA | Comparative analysis | Health aspects | Trees | Extinction | Funding | Colleges & universities | Viruses | Genomes | Estimates | Endangered & extinct species | Infectious diseases | Environmental science | Phylogenetics | Evolution | Deoxyribonucleic acid--DNA | Index Medicus | Deoxyribonucleic acid | DNA
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11. Full Text New World Bats Harbor Diverse Influenza A Viruses
by Tong, Suxiang and Zhu, Xueyong and Li, Yan and Shi, Mang and Zhang, Jing and Bourgeois, Melissa and Yang, Hua and Chen, Xianfeng and Recuenco, Sergio and Gomez, Jorge and Chen, Li-Mei and Johnson, Adam and Tao, Ying and Dreyfus, Cyrille and Yu, Wenli and McBride, Ryan and Carney, Paul J and Gilbert, Amy T and Chang, Jessie and Guo, Zhu and Davis, Charles T and Paulson, James C and Stevens, James and Rupprecht, Charles E and Holmes, Edward C and Wilson, Ian A and Donis, Ruben O
PLoS Pathogens, ISSN 1553-7366, 10/2013, Volume 9, Issue 10, pp. e1003657 - e1003657
Aquatic birds harbor diverse influenza A viruses and are a major viral reservoir in nature. The recent discovery of influenza viruses of a new H17N10 subtype... 
HEMAGGLUTININ MEMBRANE GLYCOPROTEIN | MAXIMUM-LIKELIHOOD | PB2 PROTEIN | HOST | MICROBIOLOGY | CORONAVIRUSES | SARS-LIKE | NEURAMINIDASE | VIROLOGY | SEGMENT 3 | VIRAL POLYMERASE | BINDING | PARASITOLOGY | Orthomyxoviridae Infections - epidemiology | Chiroptera - virology | Animals | Orthomyxoviridae Infections - veterinary | Disease Reservoirs - virology | Influenza A virus - genetics | Peru - epidemiology | Phylogeny | Hemagglutinin Glycoproteins, Influenza Virus - genetics | Orthomyxoviridae Infections - genetics | Influenza viruses | Physiological aspects | Host-parasite relationships | Bats | Research | Health aspects | Index Medicus | Studies | Pandemics | Disease control | Influenza
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12. Full Text Phylogenetic Evidence for Rapid Rates of Molecular Evolution in the Single-Stranded DNA Begomovirus Tomato Yellow Leaf Curl Virus
by Siobain Duffy and Edward C. Holmes
Journal of Virology, ISSN 0022-538X, 01/2008, Volume 82, Issue 2, pp. 957 - 965
Article Usage Stats Services JVI Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley... 
MEDITERRANEAN BASIN | NATURAL RECOMBINATION | VIROLOGY | STREAK-MOSAIC-VIRUS | CHINA-VIRUS | INTERSPECIFIC-RECOMBINATION | RNA VIRUSES | COMPLETE NUCLEOTIDE-SEQUENCE | SPONTANEOUS MUTATION | INFECTIOUS CLONE | GENOME ORGANIZATION | Point Mutation | Begomovirus - genetics | Recombination, Genetic | Viral Proteins - genetics | Phylogeny | DNA, Intergenic - genetics | DNA, Viral - genetics | Cluster Analysis | Evolution, Molecular | Index Medicus | Genetic Diversity and Evolution
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13. Full Text Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive
by David A Duchêne and Sebastian Duchêne and Edward C Holmes and Simon YW Ho
Molecular Biology and Evolution, ISSN 0737-4038, 11/2015, Volume 32, Issue 11, p. 2986
  Molecular clock models are commonly used to estimate evolutionary rates and timescales from nucleotide sequences. The goal of these models is to account for... 
Simulation | Phylogenetics | Evolution | Viruses | Molecular biology | Biological clocks
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14. Full Text Redefining the invertebrate RNA virosphere
by Shi, Mang and Lin, Xian-Dan and Tian, Jun-Hua and Chen, Liang-Jun and Chen, Xiao and Li, Ci-Xiu and Qin, Xin-Cheng and Li, Jun and Cao, Jian-Ping and Eden, John-Sebastian and Buchmann, Jan and Wang, Wen and Xu, Jianguo and Holmes, Edward C and Zhang, Yong-Zhen
Nature, ISSN 0028-0836, 12/2016, Volume 540, Issue 7634, pp. 539 - 543
Current knowledge of RNA virus biodiversity is both biased and fragmentary, reflecting a focus on culturable or disease-causing agents. Here we profile the... 
EVOLUTION | ALIGNMENT | GENOMES | PERFORMANCE | MULTIDISCIPLINARY SCIENCES | VIRUSES | DISCOVERY | INSIGHTS | RNA viruses | Microbiological research | Distribution | Genetic aspects | Research | Invertebrates | Biological diversity | Phylogenetics | Viruses | Evolution | Genomes | Genetic diversity | Ribonucleic acid--RNA
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15. Full Text Pandemics: spend on surveillance, not prediction
by Holmes, EC and Rambaut, A and Andersen, KG
NATURE, ISSN 0028-0836, 06/2018, Volume 558, Issue 7709, pp. 180 - 182
Trust is undermined when scientists make overblown promises about disease prevention, warn Edward C. Holmes, Andrew Rambaut and Kristian G. Andersen. 
TRANSMISSION | MULTIDISCIPLINARY SCIENCES | Viruses - genetics | Hemorrhagic Fever, Ebola - prevention & control | Humans | Pandemics - economics | Pandemics - prevention & control | Zoonoses - virology | Communicable Diseases, Emerging - prevention & control | Time Factors | Hemorrhagic Fever, Ebola - virology | Zoonoses - epidemiology | Congo - epidemiology | Hemorrhagic Fever, Ebola - economics | Population Surveillance - methods | Forecasting - methods | Viruses - isolation & purification | World Health Organization | Environmental Monitoring - economics | Animals, Wild - virology | Pandemics - statistics & numerical data | Communicable Diseases, Emerging - epidemiology | Hemorrhagic Fever, Ebola - epidemiology | Trust | Zoonoses - transmission | Animals | Communicable Diseases, Emerging - transmission | Communicable Diseases, Emerging - virology | Zoonoses - prevention & control | Prevention | Epidemics | Cell culture | Pandemics | Viruses | Genomes | Epidemiology | Biological diversity | Human populations | Ebola virus | Disease prevention | Infectious diseases | Researchers | Surveillance | Influenza | Index Medicus
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16. Full Text The genomic and epidemiological dynamics of human influenza A virus
by Nelson, Martha I and Viboud, Cecile and Rambaut, Andrew and Taubenberger, Jeffery K and Holmes, Edward C and Pybus, Oliver G
Nature, ISSN 0028-0836, 05/2008, Volume 453, Issue 7195, pp. 615 - 619
The evolutionary interaction between influenza A virus and the human immune system, manifest as 'antigenic drift' of the viral haemagglutinin, is one of the... 
GENETIC EVOLUTION | H3N2 VIRUSES | HEMAGGLUTININ | PHYLOGENETIC ANALYSIS | MULTIDISCIPLINARY SCIENCES | MATRIX PROTEIN | GLYCOPROTEINS | M PROTEIN | H1N1 | MEMBRANE ASSOCIATION | REASSORTMENT | Influenza A Virus, H1N1 Subtype - immunology | Genetic Drift | Genome, Viral - genetics | Humans | Neuraminidase - genetics | Reassortant Viruses - genetics | Influenza, Human - epidemiology | Influenza A Virus, H3N2 Subtype - genetics | Phylogeny | Influenza A Virus, H3N2 Subtype - immunology | Hemagglutinin Glycoproteins, Influenza Virus - genetics | Genetic Variation | Reassortant Viruses - immunology | Models, Biological | Influenza, Human - virology | New York - epidemiology | Influenza A Virus, H1N1 Subtype - genetics | Evolution, Molecular | New Zealand - epidemiology | Avian influenza viruses | Genetic aspects | Research | Viral genetics | Natural history | Proteins | Epidemics | Winter | Mortality | Influenza | Genomics | Comparative studies | Amino acids | Genetic diversity | Index Medicus
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