VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

Guirimand, Thibaut; Delmotte, Stéphane; Navratil, Vincent

doi:10.1093/nar/gku1121

Cited by 208 publications

(193 citation statements)

References 26 publications

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“…Nevertheless, much less is known about the transpososphere than about the virosphere and their impacts on cellular organisms. Over the last years, there has been a growing appreciation of the importance of host–virus interactions, and there are now hundreds of host proteins known to be involved in antiviral response . A recent study conservatively estimated that about a third of all adaptive mutations in human proteins occurred as a response to viruses .…”

Section: The Genomic Microcosm Of Transposons and Repressorsmentioning

confidence: 99%

Evolution of bird genomes—a transposon's‐eye view

Kapusta

Suh

2016

Annals of the New York Academy of Sciences

148

158

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Birds, the most species-rich monophyletic group of land vertebrates, have been subject to some of the most intense sequencing efforts to date, making them an ideal case study for recent developments in genomics research. Here, we review how our understanding of bird genomes has changed with the recent sequencing of more than 75 species from all major avian taxa. We illuminate avian genome evolution from a previously neglected perspective: their repetitive genomic parasites, transposable elements (TEs) and endogenous viral elements (EVEs). We show that (1) birds are unique among vertebrates in terms of their genome organization; (2) information about the diversity of avian TEs and EVEs is changing rapidly; (3) flying birds have smaller genomes yet more TEs than flightless birds; (4) current second-generation genome assemblies fail to capture the variation in avian chromosome number and genome size determined with cytogenetics; (5) the genomic microcosm of bird-TE "arms races" has yet to be explored; and (6) upcoming third-generation genome assemblies suggest that birds exhibit stability in gene-rich regions and instability in TE-rich regions. We emphasize that integration of cytogenetics and single-molecule technologies with repeat-resolved genome assemblies is essential for understanding the evolution of (bird) genomes.

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Section: The Genomic Microcosm Of Transposons and Repressorsmentioning

confidence: 99%

Evolution of bird genomes—a transposon's‐eye view

Kapusta

Suh

2016

Annals of the New York Academy of Sciences

148

158

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“…Some PHI databases specialize on only one specific pathogen species such as HCVpro [24]. A wider range of human specific viruses are covered by VirHostNet [25] and others ( Table 3).…”

Section: Virus-human Host Protein-protein Interaction Databasesmentioning

confidence: 99%

Protein-protein interactions of human viruses

Goodacre

Devkota

Bae

et al. 2020

Seminars in Cell & Developmental Biology

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Viruses infect their human hosts by a series of interactions between viral and host proteins, indicating that detailed knowledge of such virus-host interaction interfaces are critical for our understanding of viral infection mechanisms, disease etiology and the development of new drugs. In this review, we primarily survey human host-virus interaction data that are available from public databases following the standardized PSI-MS format. Notably, available host-virus protein interaction information is strongly biased toward a small number of virus families including herpesviridae, papillomaviridae, orthomyxoviridae and retroviridae. While we explore the reliability and relevance of these protein interactions we also survey the current knowledge about viruses functional and topological targets. Furthermore, we assess emerging frontiers of host-virus protein interaction research, focusing on protein interaction interfaces of hosts that are infected by different viruses and viruses that infect multiple hosts. Finally, we cover the current status of research that investigates the relationships of virus-targeted host proteins to other comorbidities as well as the influence of host-virus protein interactions on human metabolism.

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“…Recent data suggest that viral oncoproteins E6 and E7 bind and modify the activity of numerous proteins and molecular pathways [51]. E6 has been reported to interact with 83 cellular proteins and E7 with 254 [52]. …”

Section: Canonical Mechanisms Of Hpv-driven Carcinogenesismentioning

confidence: 99%

Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer

Faraji

Zaidi

Fakhry

et al. 2017

Microbes and Infection

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This review examines the general cellular and molecular underpinnings of human papillomavirus (HPV)-related carcinogenesis in the context of head and neck squamous cell carcinoma (HNSCC) and focuses on HPV-positive oropharyngeal squamous cell carcinoma in areas for which specific data is available. It covers the major pathways dysregulated in HPV-positive HNSCC and the genome-wide changes associated with this disease.

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VirHostNet 2.0: surfing on the web of virus/host molecular interactions data

Cited by 208 publications

References 26 publications

Evolution of bird genomes—a transposon's‐eye view

Evolution of bird genomes—a transposon's‐eye view

Protein-protein interactions of human viruses

Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer

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