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List of works by Joseph Hughes

Absence of adaptive evolution is the main barrier against influenza emergence in horses in Asia despite frequent virus interspecies transmission from wild birds

article

Avian UCP: the killjoy in the evolution of the mitochondrial uncoupling proteins

scientific article published on 2 October 2007

Bioinformatics tools for analysing viral genomic data

scientific article

Characterization of a second open reading frame in genome segment 10 of bluetongue virus

scientific article published on 19 August 2015

Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

scientific article

Comparative tests of ectoparasite species richness in seabirds

scientific article

Complete Genome Sequence of Frog virus 3, Isolated from a Strawberry Poison Frog (Oophaga pumilio) Imported from Nicaragua into the Netherlands

scientific article published on 31 August 2017

Complete genome sequence of a common midwife toad virus-like ranavirus associated with mass mortalities in wild amphibians in the Netherlands

scientific article

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles).

scientific article published on 19 October 2005

Development of reverse genetics systems and investigation of host response antagonism and reassortment potential for Cache Valley and Kairi viruses, two emerging orthobunyaviruses of the Americas

scientific article published on 29 October 2018

DisCVR: Rapid viral diagnosis from high-throughput sequencing data

scientific article published on 01 July 2019

DisCVR: Rapid viral diagnosis from high-throughput sequencing data

scientific article published on 24 January 2019

Ecomorphological adaptation of acorn weevils to their oviposition site

scientific article published in September 2004

Emergence of a highly pathogenic avian influenza virus from a low-pathogenic progenitor

scientific article published on 05 February 2014

Evolution of an Eurasian avian-like influenza virus in naïve and vaccinated pigs

scientific article

Evolutionary history of the UCP gene family: gene duplication and selection

scientific article

Evolutionary trajectories of two distinct avian influenza epidemics: Parallelisms and divergences

scientific article published on 20 May 2015

Feline immunodeficiency virus (FIV) env recombinants are common in natural infections

scientific article

Full Genome Sequence and sfRNA Interferon Antagonist Activity of Zika Virus from Recife, Brazil

scientific article (publication date: October 2016)

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

scientific article published on 18 December 2017

GLUE: A flexible software system for virus sequence data

GLUE: a flexible software system for virus sequence data

2018 scholarly article published in BMC Bioinformatics

Gene expression in the gut of keratin-feeding clothes moths (Tineola) and keratin beetles (Trox) revealed by subtracted cDNA libraries

scientific article published on 4 May 2006

Genetic analysis of members of the species Oropouche virus and identification of a novel M segment sequence

scientific article

Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques

scientific article

Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

scholarly article

Host and viral determinants of Mx2 antiretroviral activity

scientific article

Human Cytomegalovirus Genomes Sequenced Directly From Clinical Material: Variation, Multiple-Strain Infection, Recombination, and Gene Loss

scientific article published on 01 July 2019

ICTV Virus Taxonomy Profile: Parvoviridae

scientific article published on 23 January 2019

In silico prediction of HIV-1-host molecular interactions and their directionality

scientific article published on 08 February 2022

Inferring epidemiological links from deep sequencing data: a statistical learning approach for human, animal and plant diseases.

scientific article published in June 2019

Interpreting Viral Deep Sequencing Data with GLUE

scientific article published on 03 April 2019

Investigation of Amphibian Mortality Events in Wildlife Reveals an On-Going Ranavirus Epidemic in the North of the Netherlands

scientific article

Late Ebola virus relapse causing meningoencephalitis: a case report

scientific article

M segment-based minigenomes and virus-like particle assays as an approach to assess the potential of tick-borne Phlebovirus genome reassortment ⬇️

scholarly article by Veronica V. Rezelj et al published 19 December 2018 in Journal of Virology

Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus

scientific article published on 17 September 2019

Multiple cophylogenetic analyses reveal frequent cospeciation between pelecaniform birds and Pectinopygus lice

scientific article

New highly diverse hepatitis C strains detected in sub-Saharan Africa have unknown susceptibility to direct-acting antiviral treatments

article

Next-generation sequencing sheds light on the natural history of hepatitis C infection in patients who fail treatment

scientific article published on 30 July 2014

On the origin of Halipeurus heraldicus on Round Island petrels: cophylogenetic relationships between petrels and their chewing lice

scientific article published on 15 January 2010

Origins and Evolutionary Dynamics of H3N2 Canine Influenza Virus.

scientific article

Phylodynamic analysis of porcine circovirus type 2 reveals global waves of emerging genotypes and the circulation of recombinant forms

scientific article published on 22 April 2016

Phylodynamic analysis of porcine circovirus type 2: Methodological approach and datasets

scientific article

Quantifying and Cataloguing Unknown Sequences within Human Microbiomes

scientific article published on 08 March 2022

Quasispecies Changes with Distinctive Point Mutations in the Hepatitis C Virus Internal Ribosome Entry Site (IRES) Derived from PBMCs and Plasma

scientific article published on 19 November 2018

Ranavirus genotypes in the Netherlands and their potential association with virulence in water frogs (Pelophylax spp.).

scientific article

Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus

scientific article

Response to DAA therapy in the NHS England Early Access Programme for rare HCV subtypes from low and middle income countries

scientific article

Synonymous Dinucleotide Usage: A Codon-Aware Metric for Quantifying Dinucleotide Representation in Viruses

scientific article published on 20 April 2020

TRIM69 Inhibits Vesicular Stomatitis Indiana Virus

scientific article published on 30 September 2019

The Envelope Gene of Transmitted HIV-1 Resists a Late Interferon Gamma-Induced Block.

scientific article published on 18 January 2017

The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: the problem of incomplete data

scientific article

The spatial scale of genetic differentiation in a model organism: the wild yeast Saccharomyces paradoxus

scientific article published in November 2006

Tracking TCRβ Sequence Clonotype Expansions during Antiviral Therapy Using High-Throughput Sequencing of the Hypervariable Region

scientific article published on 5 April 2016

Transmission of equine influenza virus during an outbreak is characterized by frequent mixed infections and loose transmission bottlenecks.

scientific article

TreeRipper web application: towards a fully automated optical tree recognition software ⬇️

scientific article published on May 20, 2011

Uneven genetic robustness of HIV-1 integrase

scientific article

Unexpected Interfarm Transmission Dynamics during a Highly Pathogenic Avian Influenza Epidemic

scientific article published on 04 May 2016

Vaccine immune pressure influences viral population complexity of avian influenza virus during infection

scientific article published on 27 February 2017

ViCTree: An automated framework for taxonomic classification from protein sequences

scientific article published on 20 February 2018

Widespread Reassortment Shapes the Evolution and Epidemiology of Bluetongue Virus following European Invasion ⬇️

scientific article published on 7 August 2015

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