{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:01Z","timestamp":1772138041621,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,10,16]],"date-time":"2020-10-16T00:00:00Z","timestamp":1602806400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["CCF-1617678"],"award-info":[{"award-number":["CCF-1617678"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["DBI-1759858"],"award-info":[{"award-number":["DBI-1759858"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"NSF","doi-asserted-by":"publisher","award":["MCB-1817736"],"award-info":[{"award-number":["MCB-1817736"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011038","name":"Office of the Director of National Intelligence","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011039","name":"Intelligence Advanced Research Projects Activity","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100011039","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000183","name":"Army Research Office","doi-asserted-by":"publisher","award":["W911NF-17-2-0105"],"award-info":[{"award-number":["W911NF-17-2-0105"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"publisher"}]},{"name":"US Government"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Nearly 40% of the genes in sequenced genomes have no experimentally or computationally derived functional annotations. To fill this gap, we seek to develop methods for network-based gene function prediction that can integrate heterogeneous data for multiple species with experimentally based functional annotations and systematically transfer them to newly sequenced organisms on a genome-wide scale. However, the large sizes of such networks pose a challenge for the scalability of current methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We develop a label propagation algorithm called FastSinkSource. By formally bounding its rate of progress, we decrease the running time by a factor of 100 without sacrificing accuracy. We systematically evaluate many approaches to construct multi-species bacterial networks and apply FastSinkSource and other state-of-the-art methods to these networks. We find that the most accurate and efficient approach is to pre-compute annotation scores for species with experimental annotations, and then to transfer them to other organisms. In this manner, FastSinkSource runs in under 3\u2009min for 200 bacterial species.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>An implementation of our framework and all data used in this research are available at https:\/\/github.com\/Murali-group\/multi-species-GOA-prediction.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa885","type":"journal-article","created":{"date-parts":[[2020,9,30]],"date-time":"2020-09-30T23:36:16Z","timestamp":1601508976000},"page":"800-806","source":"Crossref","is-referenced-by-count":1,"title":["Accurate and efficient gene function prediction using a multi-bacterial network"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2828-1273","authenticated-orcid":false,"given":"Jeffrey N","family":"Law","sequence":"first","affiliation":[{"name":"Genetics, Bioinformatics and Computational Biology Ph.D. Program , Blacksburg, VA 24061, USA"}]},{"given":"Shiv D","family":"Kale","sequence":"additional","affiliation":[{"name":"Fralin Life Sciences Institute , Blacksburg, VA 24061, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3688-4672","authenticated-orcid":false,"given":"T M","family":"Murali","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Virginia Tech , Blacksburg, VA 24061, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,10,16]]},"reference":[{"key":"2023051800332596700_btaa885-B1","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1016\/j.cels.2016.10.017","article-title":"Compact integration of multi-network topology for functional analysis of genes","volume":"3","author":"Cho","year":"2016","journal-title":"Cell Syst"},{"key":"2023051800332596700_btaa885-B2","doi-asserted-by":"crossref","first-page":"i53","DOI":"10.1093\/bioinformatics\/btt228","article-title":"Information-theoretic evaluation of predicted ontological annotations","volume":"29","author":"Clark","year":"2013","journal-title":"Bioinformatics"},{"key":"2023051800332596700_btaa885-B3","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1007\/978-1-4939-3743-1_5","volume-title":"The Gene Ontology Handbook. 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