{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T17:31:57Z","timestamp":1767893517151,"version":"3.49.0"},"reference-count":10,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,10,27]],"date-time":"2021-10-27T00:00:00Z","timestamp":1635292800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,10,27]],"date-time":"2021-10-27T00:00:00Z","timestamp":1635292800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>ANAT is a Cytoscape plugin for the inference of functional protein\u2013protein interaction networks in yeast and human. It is a flexible graphical tool for scientists to explore and elucidate the protein\u2013protein interaction pathways of a process under study.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here we present ANAT3.0, which comes with updated PPI network databases of 544,455 (human) and 155,504 (yeast) interactions, and a new machine-learning layer for refined network elucidation. Together they improve network reconstruction to more than twofold increase in the quality of reconstructing known signaling pathways from KEGG.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>ANAT3.0 includes improved network reconstruction algorithms and more comprehensive protein\u2013protein interaction networks than previous versions. ANAT is available for download on the Cytoscape Appstore and at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/www.cs.tau.ac.il\/~bnet\/ANAT\/\">https:\/\/www.cs.tau.ac.il\/~bnet\/ANAT\/<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04449-1","type":"journal-article","created":{"date-parts":[[2021,10,27]],"date-time":"2021-10-27T16:03:03Z","timestamp":1635350583000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches"],"prefix":"10.1186","volume":"22","author":[{"given":"L. F.","family":"Signorini","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"T.","family":"Almozlino","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"R.","family":"Sharan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,10,27]]},"reference":[{"key":"4449_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-017-1932-1","volume":"18","author":"Y Almozlino","year":"2017","unstructured":"Almozlino Y, Atias N, Silverbush D, Sharan R. ANAT 2.0: reconstructing functional protein subnetworks. 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Nucleic Acids Res. 2014;42:D358\u201363.","journal-title":"Nucleic Acids Res"},{"key":"4449_CR8","doi-asserted-by":"publisher","first-page":"D529","DOI":"10.1093\/nar\/gky1079","volume":"47","author":"R Oughtred","year":"2019","unstructured":"Oughtred R, Stark C, Breitkreutz BJ, Rust J, Boucher L, Chang C, Kolas N, et al. The BioGRID interaction database: 2019 update. Nucleic Acids Res. 2019;47:D529\u201341.","journal-title":"Nucleic Acids Res"},{"key":"4449_CR9","doi-asserted-by":"publisher","first-page":"551","DOI":"10.1038\/nrg.2017.38","volume":"18","author":"L Cowen","year":"2017","unstructured":"Cowen L, Ideker T, Raphael BJ, Sharan R. Network propagation: a universal amplifier of genetic associations. 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