Virus Network Literature - serratus-bio/open-virome GitHub Wiki

• Eppley et al., 2022 Marine viral particles reveal an expansive repertoire of phage-parasitizing mobile elements: Use a bipartite network of virus satellite and VOGdb HMM (protein domain) to represent diversity and admixture of genomes.

"Larger was partitioned into modules 2 through 12 using the constant Potts model (57) as implemented by the leidenalg Python package."

• Carlson CJ et al., 2022 The Global Virome in One Network (VIRION): an Atlas of Vertebrate-Virus Associations: Harmonized database from reconciliation of existing static data sets and integration of dynamically updated databases.

"In total, the VIRION database is the largest open-source, open-access database of its kind, with roughly half a million unique records that include 9,521 resolved virus “species” (of which 1,661 are ICTV ratified), 3,692 resolved vertebrate host species, and 23,147 unique interactions between taxonomically valid organisms."

• Poisot et al., 2023 Network embedding unveils the hidden interactions in the mammalian virome: linear filtering and singular value decomposition (LF-SVD) model used for imputation to resolve sampling bias in data, then applying graph embeddings to predict virus-host associations.

• Ma et al., 2024 MetagenomicKG: a knowledge graph for metagenomic applications: MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information from widely used databases, and further links these with established biomedical knowledge graphs to expand biological connections.

"Through several use cases, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction."