{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T17:18:07Z","timestamp":1790183887433,"version":"4.1.0"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2017,11,3]],"date-time":"2017-11-03T00:00:00Z","timestamp":1509667200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/G037280\/1, EP\/K032402\/1"],"award-info":[{"award-number":["EP\/G037280\/1, EP\/K032402\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules\/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favor communities of well-studied proteins.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker\u2019s ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities and identifies functional modules that may correspond to more novel biology.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The CommWalker algorithm is freely available at opig.stats.ox.ac.uk\/resources or as a docker image on the Docker Hub at hub.docker.com\/r\/lueckenmd\/commwalker\/.<\/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\/btx706","type":"journal-article","created":{"date-parts":[[2017,11,2]],"date-time":"2017-11-02T12:14:22Z","timestamp":1509624862000},"page":"994-1000","source":"Crossref","is-referenced-by-count":6,"title":["CommWalker: correctly evaluating modules in molecular networks in light of annotation bias"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7464-7921","authenticated-orcid":false,"given":"M D","family":"Luecken","sequence":"first","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"},{"name":"Doctoral Training Centre, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"M J T","family":"Page","sequence":"additional","affiliation":[{"name":"Department of Informatics, UCB Pharma, Slough, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A J","family":"Crosby","sequence":"additional","affiliation":[{"name":"Immunology Therapeutic Area, UCB Pharma, Slough, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S","family":"Mason","sequence":"additional","affiliation":[{"name":"Immunology Therapeutic Area, UCB Pharma, Slough, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"G","family":"Reinert","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C M","family":"Deane","sequence":"additional","affiliation":[{"name":"Department of Statistics, University of Oxford, Oxford, UK"},{"name":"Doctoral Training Centre, University of Oxford, Oxford, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,11,3]]},"reference":[{"key":"2023012712575596400_btx706-B1","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1038\/nature09182","article-title":"Link communities reveal multiscale complexity in networks","volume":"466","author":"Ahn","year":"2010","journal-title":"Nature"},{"key":"2023012712575596400_btx706-B2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nature Genetics"},{"key":"2023012712575596400_btx706-B3","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1038\/nmeth0605-477a","article-title":"Standardizing global gene expression analysis between laboratories and across platforms","volume":"2","author":"Bammler","year":"2005","journal-title":"Nature Methods"},{"key":"2023012712575596400_btx706-B4","doi-asserted-by":"crossref","first-page":"P10008","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"Blondel","year":"2008","journal-title":"J. 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