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For such proteins, the genome context can give further information about their functional context.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We describe a Bayesian method, based on a probabilistic topic model, which directly identifies functional modules of protein families. The method explores the co-occurrence patterns of protein families across a collection of sequence samples to infer a probabilistic model of arbitrarily-sized functional modules.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We show that our method identifies protein modules - some of which correspond to well-known biological processes - that are tightly interconnected with known functional interactions and are different from the interactions identified by pairwise co-occurrence. The modules are not specific to any given organism and may combine different realizations of a protein complex or pathway within different taxa.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-141","type":"journal-article","created":{"date-parts":[[2011,5,11]],"date-time":"2011-05-11T06:17:47Z","timestamp":1305094667000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":8,"title":["Inferring functional modules of protein families with probabilistic topic models"],"prefix":"10.1186","volume":"12","author":[{"given":"Sebastian GA","family":"Konietzny","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laura","family":"Dietz","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alice C","family":"McHardy","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2011,5,9]]},"reference":[{"key":"4484_CR1","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1038\/nature07190","volume":"454","author":"EM Rubin","year":"2008","unstructured":"Rubin EM: Genomics of cellulosic biofuels. 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