{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:40Z","timestamp":1753875820195,"version":"3.41.2"},"reference-count":55,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2022,4,5]],"date-time":"2022-04-05T00:00:00Z","timestamp":1649116800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Multicriteria Data Structures and Algorithms: from compressed to learned indexes, and beyond","award":["2017WR7SHH"],"award-info":[{"award-number":["2017WR7SHH"]}]},{"name":"MISE-PON AMABILE","award":["B76G20000880005"],"award-info":[{"award-number":["B76G20000880005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Biological networks topology yields important insights into biological function, occurrence of diseases and drug design. In the last few years, different types of topological measures have been introduced and applied to infer the biological relevance of network components\/interactions, according to their position within the network structure. Although comparisons of such measures have been previously proposed, to what extent the topology per se may lead to the extraction of novel biological knowledge has never been critically examined nor formalized in the literature.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a comparative analysis of nine outstanding topological measures, based on compact views obtained from the rank they induce on a given input biological network. The goal is to understand their ability in correctly positioning nodes\/edges in the rank, according to the functional knowledge implicitly encoded in biological networks. To this aim, both internal and external (gold standard) validation criteria are taken into account, and six networks involving three different organisms (yeast, worm and human) are included in the comparison. The results show that a distinct handful of best-performing measures can be identified for each of the considered organisms, independently from the reference gold standard.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability<\/jats:title>\n                  <jats:p>Input files and code for the computation of the considered topological measures and K-haus distance are available at https:\/\/gitlab.com\/MaryBonomo\/ranking.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>simona.rombo@unipa.it<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Briefings in Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bib\/bbac101","type":"journal-article","created":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T12:09:13Z","timestamp":1646136553000},"source":"Crossref","is-referenced-by-count":6,"title":["Topological ranks reveal functional knowledge encoded in biological networks: a comparative analysis"],"prefix":"10.1093","volume":"23","author":[{"given":"Mariella","family":"Bonomo","sequence":"first","affiliation":[{"name":"Department of Engineering, University of Palermo, Palermo, 90121, Italy, Palermo"}]},{"given":"Raffaele","family":"Giancarlo","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Palermo, Palermo, 90121, Italy, Palermo"}]},{"given":"Daniele","family":"Greco","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Palermo, Palermo, 90121, Italy, Palermo"}]},{"given":"Simona E","family":"Rombo","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Computer Science, University of Palermo, Palermo, 90121, Italy, Palermo"}]}],"member":"286","published-online":{"date-parts":[[2022,4,5]]},"reference":[{"key":"2022051813463189700_ref1","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1186\/1471-2105-10-290","article-title":"Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information","volume":"10","author":"Acencio","year":"2009","journal-title":"BMC Bioinform"},{"issue":"5","key":"2022051813463189700_ref2","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1038\/nbt1203","article-title":"Gene prioritization through genomic data fusion","volume":"24","author":"Aerts","year":"2006","journal-title":"Nat Biotechnol"},{"key":"2022051813463189700_ref3","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":"2022051813463189700_ref4","first-page":"1:1","volume-title":"Proc. of the 4th Workshop on Soc. 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