{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:41Z","timestamp":1740185141313,"version":"3.37.3"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,4,16]],"date-time":"2019-04-16T00:00:00Z","timestamp":1555372800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"German Federal Ministry for Education and Research"},{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","award":["031A538A"],"award-info":[{"award-number":["031A538A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Council for Scientific Research of Lebanon"},{"DOI":"10.13039\/501100001655","name":"German Academic Exchange Service","doi-asserted-by":"publisher","award":["57390771"],"award-info":[{"award-number":["57390771"]}],"id":[{"id":"10.13039\/501100001655","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>MicroRNAs form an important class of RNA regulators that has been studied extensively. The miRBase and Rfam database provide rich, frequently updated information on both pre-miRNAs and their mature forms. These data sources, however, rely on individual data submission and thus are neither complete nor consistent in their coverage across different miRNA families. Quantitative studies of miRNA evolution therefore are difficult or impossible on this basis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present here a workflow and a corresponding implementation, MIRfix, that automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MIRfix can be downloaded from https:\/\/github.com\/Bierinformatik\/MIRfix.<\/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\/btz271","type":"journal-article","created":{"date-parts":[[2019,4,10]],"date-time":"2019-04-10T11:14:22Z","timestamp":1554894862000},"page":"4553-4559","source":"Crossref","is-referenced-by-count":4,"title":["Automatic curation of large comparative animal MicroRNA datasets"],"prefix":"10.1093","volume":"35","author":[{"given":"Ali M","family":"Yazbeck","sequence":"first","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics , D-04107 Leipzig, Germany"},{"name":"Doctoral School of Science and Technology, Center for Biotechnology Research, Lebanese University , Hadath Campus, Beirut, Lebanon"},{"name":"Helmholtz Centre for Environmental Research - UFZ, Young Investigators Group Bioinformatics and Transcriptomics , D-04318 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter F","family":"Stadler","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics , D-04107 Leipzig, Germany"},{"name":"German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig , D-04107 Leipzig, Germany"},{"name":"Max Planck Institute for Mathematics in the Sciences , D-04103 Leipzig, Germany"},{"name":"Institute for Theoretical Chemistry, University of Vienna , A-1090 Wien, Austria"},{"name":"Facultad de Ciencias, Universidad National de Colombia , Sede Bogot\u00e1, Colombia"},{"name":"Santa Fe Institute , Santa Fe, NM 87501, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kifah","family":"Tout","sequence":"additional","affiliation":[{"name":"Doctoral School of Science and Technology, Center for Biotechnology Research, Lebanese University , Hadath Campus, Beirut, Lebanon"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4573-9939","authenticated-orcid":false,"given":"J\u00f6rg","family":"Fallmann","sequence":"additional","affiliation":[{"name":"Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics , D-04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,4,16]]},"reference":[{"key":"2023013108314991200_btz271-B1","doi-asserted-by":"crossref","first-page":"4421","DOI":"10.1007\/s00018-014-1698-9","article-title":"DLK1-DIO3 imprinted cluster in induced pluripotency: landscape in the mist","volume":"71","author":"Benetatos","year":"2014","journal-title":"Cell Mol. 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