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Evolution, Virology, Open Science, Genomics

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United Kingdom, United States, Brazil, Chile, South Africa

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Works (50 of 78)

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Page 1 of 2

No evidence that mutations in SARS-CoV-2 variants of concern derive from homologous fragments in gut microbiota

Journal of Virology
2024-12-17 | Journal article
DOI: 10.1128/jvi.01468-24
Contributors: Rhys H. Parry; Spyros Lytras; Mary E. Petrone; Michelle Wille; Alexander Crits-Christoph; Robert J. Gifford; Akatsuki Saito; Teemu Smura; Thomas P. Peacock; Stacey Schultz-Cherry
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Crossref

A new lineage nomenclature to aid genomic surveillance of dengue virus.

PLoS biology
2024-09-16 | Journal article
DOI: 10.1371/journal.pbio.3002834
PMID: 39283942
PMC: PMC11426435
Contributors: Verity Hill; Cleemput S; Pereira JS; Gifford RJ; Fonseca V; Tegally H; Brito AF; Ribeiro G; de Souza VC; ISABELA BRCKO et al.
Source: Self-asserted source
Robert James Gifford

A novel approach to exploring the dark genome and its application to mapping of the vertebrate virus fossil record

Genome Biology
2024-05-13 | Journal article
DOI: 10.1186/s13059-024-03258-y
Contributors: Daniel Blanco-Melo; Matthew A. Campbell; Henan Zhu; Tristan P. W. Dennis; Sejal Modha; Spyros Lytras; Joseph Hughes; Anna Gatseva; Robert J. Gifford
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Crossref

A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK

Journal of General Virology
2023-12-07 | Journal article
DOI: 10.1099/jgv.0.001927
Contributors: Rhys H. Parry; Andrii Slonchak; Lewis J. Campbell; Natalee D. Newton; Humberto J. Debat; Robert J. Gifford; Alexander A. Khromykh
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Crossref

Development of evolutionarily conserved viral integration sites as safe harbors for human gene therapy

2023-09-10 | Preprint
DOI: 10.1101/2023.09.08.556857
Contributors: Marco A. Quezada-Ramírez; Shannon Loncar; Matthew A. Campbell; Krishna M. Parsi; Robert J. Gifford; Robert M. Kotin
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Crossref

Structures of the Hepaci-, Pegi-, and Pestiviruses envelope proteins suggest a novel membrane fusion mechanism

PLOS Biology
2023-07-11 | Journal article | Formal analysis
DOI: 10.1371/journal.pbio.3002174
Part of ISSN: 1545-7885
Contributors: Michael R. Oliver; Kamilla Toon; Charlotte B. Lewis; Stephen Devlin; Robert James Gifford; Joe Grove
Source: Self-asserted source
Robert James Gifford

Unraveling the origins of human adeno-associated virus 5

Cell and Gene Therapy Insights
2023-07-07 | Journal article
DOI: 10.18609/cgti.2023.085
Part of ISSN: 2059-7800
Part of ISSN: 2059-7800
Contributors: Robert James Gifford; Robert M Kotin
Source: Self-asserted source
Robert James Gifford

Antiviral Activity of an Endogenous Parvoviral Element

Viruses
2023-06-23 | Journal article
DOI: 10.3390/v15071420
Contributors: Angelica Bravo; Leandro Fernández-García; Rodrigo Ibarra-Karmy; Gonzalo A. Mardones; Luis Mercado; Fernando J. Bustos; Robert J. Gifford; Gloria Arriagada
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Crossref

Co-option of endogenous retroviruses through genetic escape from TRIM28 repression.

Cell reports
2023-06-07 | Journal article
DOI: 10.1016/j.celrep.2023.112625
PMID: 37294634
Contributors: Enriquez-Gasca R; Gould PA; Tunbak H; Conde L; Herrero J; Chittka A; Beck CR; Gifford R; Rowe HM
Source: Self-asserted source
Robert James Gifford

Emergence and pandemic spread of small ruminant lentiviruses

Virus Evolution
2023-02-13 | Journal article
DOI: 10.1093/ve/vead005
Contributors: Maria-Luisa Carrozza; Anna-Maria Niewiadomska; Maurizio Mazzei; Mounir R Abi-Said; Stéphane Hué; Joseph Hughes; Anna Gatseva; Robert J Gifford
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Crossref

An endogenous lentivirus in the germline of a rodent.

Retrovirology
2022-12-20 | Journal article
DOI: 10.1186/s12977-022-00615-2
PMID: 36539757
PMC: PMC9768972
Contributors: Kambol R; Gatseva A; Gifford RJ
Source: Self-asserted source
Robert James Gifford

Comparative analysis reveals the long-term coevolutionary history of parvoviruses and vertebrates

PLOS Biology
2022-11-29 | Journal article
DOI: 10.1371/journal.pbio.3001867
Contributors: Matthew A. Campbell; Tiago Bosisio Quental; Shannon Loncar; Robert M. Kotin; Robert J. Gifford
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Crossref

A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819

Science Advances
2022-10-28 | Journal article
DOI: 10.1126/sciadv.abp8085
Contributors: Liane P. Fernandes; Rocio Enriquez-Gasca; Poppy A. Gould; James H. Holt; Lucia Conde; Gabriela Ecco; Javier Herrero; Robert Gifford; Didier Trono; George Kassiotis et al.
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Crossref

Emergence of Compensatory Mutations Reveals the Importance of Electrostatic Interactions between HIV-1 Integrase and Genomic RNA

mBio
2022-10-26 | Journal article
DOI: 10.1128/mbio.00431-22
Contributors: Christian Shema Mugisha; Tung Dinh; Abhishek Kumar; Kasyap Tenneti; Jenna E. Eschbach; Keanu Davis; Robert Gifford; Mamuka Kvaratskhelia; Sebla B. Kutluay; Kellie Jurado
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Crossref

Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae).

Virus Evolution
2022-09-06 | Journal article
DOI: 10.1093/ve/veac085
Contributors: Connor G G Bamford; William M de Souza; Rhys Parry; Robert J Gifford
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Making genomic surveillance deliver: A lineage classification and nomenclature system to inform rabies elimination

PLOS Pathogens
2022-05-02 | Journal article
DOI: 10.1371/journal.ppat.1010023
Contributors: Kathryn Campbell; Adam S. Lauring; Robert J. Gifford; Joshua Singer; Verity Hill; Aine O’Toole; Andrew Rambaut; Katie Hampson; Kirstyn Brunker
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Crossref

Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures

Science Advances
2021-11-26 | Journal article
DOI: 10.1126/sciadv.abl6096
Contributors: Martina Zafferani; Christina Haddad; Le Luo; Jesse Davila-Calderon; Liang-Yuan Chiu; Christian Shema Mugisha; Adeline G. Monaghan; Andrew A. Kennedy; Joseph D. Yesselman; Robert J. Gifford et al.
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No evidence of SARS-CoV-2 reverse transcription and integration as the origin of chimeric transcripts in patient tissues

Proceedings of the National Academy of Sciences
2021-08-17 | Journal article
DOI: 10.1073/pnas.2109066118
Contributors: Rhys Parry; Robert J. Gifford; Spyros Lytras; Stuart C. Ray; Lachlan J. M. Coin
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Mapping the evolution of bornaviruses across geological timescales

Proceedings of the National Academy of Sciences
2021-06-29 | Journal article
DOI: 10.1073/pnas.2108123118
Contributors: Robert J. Gifford
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Crossref

Ancient evolution of hepadnaviral paleoviruses and their impact on host genomes

Virus Evolution
2021-01-20 | Journal article
DOI: 10.1093/ve/veab012
Contributors: Spyros Lytras; Gloria Arriagada; Robert J Gifford
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Crossref

SARS-CoV-2 ORF3b Is a Potent Interferon Antagonist Whose Activity Is Increased by a Naturally Occurring Elongation Variant.

Cell reports
2020-09-04 | Journal article
DOI: 10.1016/j.celrep.2020.108185
PMID: 32941788
PMC: PMC7473339
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Evolution of dependoparvoviruses across geological timescales—implications for design of AAV-based gene therapy vectors

Virus Evolution
2020-07-01 | Journal article
DOI: 10.1093/ve/veaa043
Contributors: Evin Hildebrandt; Judit J Penzes; Robert J Gifford; Mavis Agbandje-Mckenna; Robert M Kotin
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Crossref

CoV-GLUE: A Web Application for Tracking SARS-CoV-2 Genomic Variation

2020-06-18 | Other
DOI: 10.20944/preprints202006.0225.v1
Contributors: Joshua Singer; Robert Gifford; Matthew Cotten; David Robertson
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Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes.

Wellcome open research
2020-05-19 | Journal article
DOI: 10.12688/wellcomeopenres.15518.2
PMID: 32090172
PMC: PMC7001756
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Retroviruses drive the rapid evolution of mammalian APOBEC3 genes

Proceedings of the National Academy of Sciences
2020-01-07 | Journal article
DOI: 10.1073/pnas.1914183116
Contributors: Jumpei Ito; Robert J. Gifford; Kei Sato
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Deltaretroviruses have circulated since at least the Paleogene and infected a broad range of mammalian species

Retrovirology
2019-12 | Journal article
DOI: 10.1186/s12977-019-0495-9
Contributors: Tomáš Hron; Daniel Elleder; Robert J. Gifford
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Crossref

Upstream translation initiation expands the coding capacity of segmented negative-strand RNA viruses

2019-10-08 | Other
DOI: 10.1101/795815
Contributors: Elizabeth Sloan; Marta Alenquer; Liliane Chung; Sara Clohisey; Adam M. Dinan; Robert Gifford; Quan Gu; Nerea Irigoyen; Joshua D. Jones; Ingeborg van Knippenberg et al.
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Molecular Properties and Evolutionary Origins of a Parvovirus-Derived Myosin Fusion Gene in Guinea Pigs

Journal of Virology
2019-09 | Journal article
DOI: 10.1128/JVI.00404-19
Contributors: Ignacio Valencia-Herrera; Fernando Faunes; Eduardo Cena-Ahumada; Rodrigo Ibarra-Karmy; Robert J. Gifford; Gloria Arriagada; Julie K. Pfeiffer
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Crossref

An Ancient Lineage of Highly Divergent Parvoviruses Infects both Vertebrate and Invertebrate Hosts

Viruses
2019-06-06 | Journal article
DOI: 10.3390/v11060525
Contributors: Judit J. Pénzes; William Marciel de Souza; Mavis Agbandje-McKenna; Robert J. Gifford
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Derivation of simian tropic HIV-1 infectious clone reveals virus adaptation to a new host

Proceedings of the National Academy of Sciences
2019-05-21 | Journal article
DOI: 10.1073/pnas.1818059116
Contributors: Fabian Schmidt; Brandon F. Keele; Gregory Q. Del Prete; Dennis Voronin; Christine M. Fennessey; Steven Soll; Melissa Kane; Alice Raymond; Robert J. Gifford; Vineet KewalRamani et al.
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Interpreting Viral Deep Sequencing Data with GLUE

Viruses
2019-04 | Journal article | Author
DOI: 10.3390/v11040323
Contributors: Joshua Singer; Emma Thomson; Joseph Hughes; Elihu Aranday-Cortes; John McLauchlan; Ana da Silva Filipe; Lily Tong; Carmen Manso; Robert James Gifford; David Robertson et al.
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Multidisciplinary Digital Publishing Institute

Examination and Reconstruction of Three Ancient Endogenous Parvovirus Capsid Protein Gene Remnants Found in Rodent Genomes

Journal of Virology
2019-03-15 | Journal article
DOI: 10.1128/JVI.01542-18
Contributors: Heather M. Callaway; Suriyasri Subramanian; Christian A. Urbina; Karen N. Barnard; Robert A. Dick; Carol M. Bator; Susan L. Hafenstein; Robert J. Gifford; Colin R. Parrish; Wesley I. Sundquist
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Origin and recent expansion of an endogenous gammaretroviral lineage in domestic and wild canids.

Retrovirology
2019-03-07 | Journal article
DOI: 10.1186/s12977-019-0468-z
PMID: 30845962
PMC: PMC6407205
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes

Journal of Virology
2018-12 | Journal article
DOI: 10.1128/JVI.00927-18
Contributors: Henan Zhu; Robert James Gifford; Pablo Ramiro Murcia; Viviana Simon
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Nomenclature for endogenous retrovirus (ERV) loci

Retrovirology
2018-12 | Journal article
DOI: 10.1186/s12977-018-0442-1
Contributors: Robert J. Gifford; Jonas Blomberg; John M. Coffin; Hung Fan; Thierry Heidmann; Jens Mayer; Jonathan Stoye; Michael Tristem; Welkin E. Johnson
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GLUE: a flexible software system for virus sequence data.

BMC bioinformatics
2018-12-18 | Journal article
DOI: 10.1186/s12859-018-2459-9
PMID: 30563445
PMC: PMC6299651
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Insights into Circovirus Host Range from the Genomic Fossil Record

Journal of Virology
2018-08-15 | Journal article
DOI: 10.1128/JVI.00145-18
Contributors: Tristan P. W. Dennis; Peter J. Flynn; William Marciel de Souza; Joshua B. Singer; Corrie S. Moreau; Sam J. Wilson; Robert J. Gifford; Frank Kirchhoff
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Endogenous amdoparvovirus-related elements reveal insights into the biology and evolution of vertebrate parvoviruses

Virus Evolution
2018-07-01 | Journal article
DOI: 10.1093/ve/vey026
Contributors: Judit J Pénzes; Soledad Marsile-Medun; Mavis Agbandje-McKenna; Robert James Gifford
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Predicting the Effectiveness of Hepatitis C Virus Neutralizing Antibodies by Bioinformatic Analysis of Conserved Epitope Residues Using Public Sequence Data.

Frontiers in immunology
2018-06-27 | Journal article
DOI: 10.3389/fimmu.2018.01470
PMID: 30013555
PMC: PMC6036255
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford
grade
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Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L.

Retrovirology
2018-05-02 | Journal article
DOI: 10.1186/s12977-018-0416-3
PMID: 29716624
PMC: PMC5930517
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Remnants of an Ancient Deltaretrovirus in the Genomes of Horseshoe Bats (Rhinolophidae).

Viruses
2018-04-10 | Journal article
DOI: 10.3390/v10040185
PMID: 29642581
PMC: PMC5923479
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford
grade
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Novel Parvoviruses from Wild and Domestic Animals in Brazil Provide New Insights into Parvovirus Distribution and Diversity

Viruses
2018-03 | Journal article
DOI: 10.3390/v10040143
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Multidisciplinary Digital Publishing Institute
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The evolution, distribution and diversity of endogenous circoviral elements in vertebrate genomes.

Virus research
2018-03-27 | Journal article
DOI: 10.1016/j.virusres.2018.03.014
PMID: 29601845
PMC: PMC6372831
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Fundamental properties of the mammalian innate immune system revealed by multispecies comparison of type I interferon responses.

PLoS biology
2017-12-18 | Journal article
DOI: 10.1371/journal.pbio.2004086
PMID: 29253856
PMC: PMC5747502
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Hepatitis C and the absence of genomic data in low-income countries: a barrier on the road to elimination?

The lancet. Gastroenterology & hepatology
2017-10-01 | Journal article
DOI: 10.1016/s2468-1253(17)30257-1
PMID: 28895545
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors

eLife
2017-04-11 | Journal article
DOI: 10.7554/eLife.22519
Contributors: Daniel Blanco-Melo; Robert J Gifford; Paul D Bieniasz
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Crossref

Discovery of an endogenous Deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae)

Proceedings of the National Academy of Sciences
2017-03-21 | Journal article
DOI: 10.1073/pnas.1621224114
Contributors: Helena Farkašová; Tomáš Hron; Jan Pačes; Pavel Hulva; Petr Benda; Robert James Gifford; Daniel Elleder
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Crossref

An Intact Retroviral Gene Conserved in Spiny-Rayed Fishes for over 100 My.

Molecular biology and evolution
2017-03-01 | Journal article
DOI: 10.1093/molbev/msw262
PMID: 28039384
PMC: PMC5939848
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Chapparvoviruses occur in at least three vertebrate classes and have a broad biogeographic distribution.

The Journal of general virology
2017-02-01 | Journal article
DOI: 10.1099/jgv.0.000671
PMID: 28284244
PMC: PMC5646239
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford

Late Ebola virus relapse causing meningoencephalitis: a case report.

Lancet (London, England)
2016-05-18 | Journal article
DOI: 10.1016/s0140-6736(16)30386-5
PMID: 27209148
PMC: PMC4967715
Contributors: Robert James Gifford
Source: Self-asserted source
Robert James Gifford
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Peer review (8 reviews for 8 publications/grants)

Review activity for Journal of general virology. (1)
Review activity for PLoS biology. (1)
Review activity for PLOS genetics. (1)
Review activity for PloS one. (1)
Review activity for PLOS pathogens : (1)
Review activity for Retrovirology. (1)
Review activity for Trends in genetics. (1)
Review activity for Virus genes. (1)
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