{"entity": "publication", "iuid": "cb820107a9644d72934e001260a8f979", "timestamp": "2026-08-20T21:38:39.951Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/cb820107a9644d72934e001260a8f979.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/cb820107a9644d72934e001260a8f979"}}, "title": "PathBIX-a web server for network-based pathway annotation with adaptive null models.", "authors": [{"family": "Castresana-Aguirre", "given": "Miguel", "initials": "M"}, {"family": "Persson", "given": "Emma", "initials": "E", "orcid": "0000-0003-0532-8251", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c17b5ab61d4949d4818f653f43fa11f6.json"}}, {"family": "Sonnhammer", "given": "Erik L L", "initials": "ELL"}], "type": "journal article", "published": "2021-07-01", "journal": {"title": "Bioinform Adv", "issn": "2635-0041", "volume": "1", "issue": "1", "pages": "vbab010", "issn-l": null}, "abstract": "Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation.\n\nWe developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways.\n\nhttps://pathbix.sbc.su.se/.\n\nerik.sonnhammer@scilifelab.se.\n\nSupplementary data are available at Bioinformatics Advances online.", "doi": "10.1093/bioadv/vbab010", "pmid": "36700096", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9710673"}, {"db": "pii", "key": "vbab010"}], "notes": [], "created": "2026-08-20T09:39:06.725Z", "modified": "2026-08-20T09:39:06.811Z"}