{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T16:13:39Z","timestamp":1775664819741,"version":"3.50.1"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2022,2,14]],"date-time":"2022-02-14T00:00:00Z","timestamp":1644796800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Manna Center Program for Food Safety and Security at Tel Aviv University"},{"name":"Edmond J. Safra Center for Bioinformatics at Tel Aviv University"},{"name":"Dalia and Eli Hurvits foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Type-III secretion systems are utilized by many Gram-negative bacteria to inject type-3 effectors (T3Es) to eukaryotic cells. These effectors manipulate host processes for the benefit of the bacteria and thus promote disease. They can also function as host-specificity determinants through their recognition as avirulence proteins that elicit immune response. Identifying the full effector repertoire within a set of bacterial genomes is of great importance to develop appropriate treatments against the associated pathogens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present Effectidor, a user-friendly web server that harnesses several machine-learning techniques to predict T3Es within bacterial genomes. We compared the performance of Effectidor to other available tools for the same task on three pathogenic bacteria. Effectidor outperformed these tools in terms of classification accuracy (area under the precision\u2013recall curve above 0.98 in all cases).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Effectidor is available at: https:\/\/effectidor.tau.ac.il, and the source code is available at: https:\/\/github.com\/naamawagner\/Effectidor.<\/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\/btac087","type":"journal-article","created":{"date-parts":[[2022,2,8]],"date-time":"2022-02-08T20:13:27Z","timestamp":1644351207000},"page":"2341-2343","source":"Crossref","is-referenced-by-count":30,"title":["Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors"],"prefix":"10.1093","volume":"38","author":[{"given":"Naama","family":"Wagner","sequence":"first","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1984-2139","authenticated-orcid":false,"given":"Oren","family":"Avram","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"}]},{"given":"Dafna","family":"Gold-Binshtok","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"}]},{"given":"Ben","family":"Zerah","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"}]},{"given":"Doron","family":"Teper","sequence":"additional","affiliation":[{"name":"Department of Plant Pathology and Weed Research, Institute of Plant Protection Agricultural Research Organization (ARO), Volcani Center , Rishon LeZion 7505101, Israel"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9463-2575","authenticated-orcid":false,"given":"Tal","family":"Pupko","sequence":"additional","affiliation":[{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"}]}],"member":"286","published-online":{"date-parts":[[2022,2,14]]},"reference":[{"key":"2023020109030345700_btac087-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. 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