Robert James Gifford

The paper introduces Flu Mutation Explorer, a web tool that integrates IAV genomic data with mutation annotations to help interpret host adaptation mutations.

The paper identifies genome safe harbor loci for gene therapy using evolutionary biology and comparative genomics, finding nine loci with sustained transgene expression in human hematopoietic stem cells.

The paper reveals that AAV capsid genes have undergone extensive horizontal transfer across host species and rep lineages, with some variants originating from historical adenovirus stocks.

The paper identifies gaps in genomic surveillance of West Nile Virus in Africa and proposes strategies to improve public health response.

The paper introduces a database-integrated genome screening approach to explore the dark genome, identifying over 1.1 million endogenous viral elements across 874 vertebrate species.

The paper tracks the epigenetic fate of endogenous retroviruses during neural differentiation, identifying genetic escapees that evade TRIM28 repression and contribute to gene expression differences.

This paper introduces a lineage classification system for rabies virus based on SARS-CoV-2 nomenclature, enabling high-resolution tracking of viral spread and improving disease control.

This study shows segmented negative-strand RNA viruses use upstream translation initiation to expand their coding capacity through non-AUG initiation and host mRNA leader sequence appropriation.

The paper analyzes whole genome sequences of canids to trace the origin and recent expansion of an active gammaretroviral lineage, identifying new insertions and polymorphisms across multiple species.

GLUE is a flexible software system for organizing and processing virus sequence data, demonstrated with a hepatitis C virus case study.

This study investigates the origins and spread of small ruminant lentiviruses using genomic data, finding no clear evidence that the Fertile Crescent was the pandemic origin but suggesting historical breed exports may have contributed to disease emergence.

The paper identifies the first endogenous ophiovirus sequence in eelgrass, expanding the known host range of ophioviruses and providing evolutionary timing insights.

The paper introduces a computational framework called DIGS for systematically screening genomes using sequence similarity search tools and a relational database, demonstrating its application in identifying novel endogenous viral elements in mammalian genomes.

The paper uses whole-genome sequencing to analyze parvoviruses from wild and domestic animals in Brazil, identifying new species and expanding known host and geographic ranges.