{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T16:33:14Z","timestamp":1771259594043,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2019,6,22]],"date-time":"2019-06-22T00:00:00Z","timestamp":1561161600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009417","name":"Care-for-Rare Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009417","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","award":["01GM1517A"],"award-info":[{"award-number":["01GM1517A"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"DZD"},{"name":"German Center for Diabetes Research"},{"name":"Helmholtz Alliance AMPro"}],"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>Summary<\/jats:title>\n                  <jats:p>Despite their fundamental role in various biological processes, the analysis of small RNA sequencing data remains a challenging task. Major obstacles arise when short RNA sequences map to multiple locations in the genome, align to regions that are not annotated or underwent post-transcriptional changes which hamper accurate mapping. In order to tackle these issues, we present a novel profiling strategy that circumvents the need for read mapping to a reference genome by utilizing the actual read sequences to determine expression intensities. After differential expression analysis of individual sequence counts, significant sequences are annotated against user defined feature databases and clustered by sequence similarity. This strategy enables a more comprehensive and concise representation of small RNA populations without any data loss or data distortion.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Code and documentation of our R package at http:\/\/ibis.helmholtz-muenchen.de\/deus\/.<\/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\/btz495","type":"journal-article","created":{"date-parts":[[2019,6,18]],"date-time":"2019-06-18T11:10:36Z","timestamp":1560856236000},"page":"4834-4836","source":"Crossref","is-referenced-by-count":14,"title":["DEUS: an R package for accurate small RNA profiling based on differential expression of unique sequences"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2511-4699","authenticated-orcid":false,"given":"Tim","family":"Jeske","sequence":"first","affiliation":[{"name":"Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum M\u00fcnchen , Neuherberg 85764, Germany"},{"name":"Department of Pediatrics, Dr. von Hauner Children\u2019s Hospital, University Hospital, LMU Munich , M\u00fcnchen 80337, Germany"}]},{"given":"Peter","family":"Huypens","sequence":"additional","affiliation":[{"name":"Institute of Experimental Genetics, Helmholtz Zentrum M\u00fcnchen GmbH , Neuherberg 85764, Germany"},{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"}]},{"given":"Laura","family":"Stirm","sequence":"additional","affiliation":[{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"},{"name":"Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum M\u00fcnchen at the University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}]},{"given":"Selina","family":"H\u00f6ckele","sequence":"additional","affiliation":[{"name":"Institute of Experimental Genetics, Helmholtz Zentrum M\u00fcnchen GmbH , Neuherberg 85764, Germany"},{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"}]},{"given":"Christine M","family":"Wurmser","sequence":"additional","affiliation":[{"name":"Chair of Animal Breeding, Technische Universit\u00e4t M\u00fcnchen, Wissenschaftszentrum Weihenstephan , Freising 85354, Germany"}]},{"given":"Anja","family":"B\u00f6hm","sequence":"additional","affiliation":[{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"},{"name":"Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum M\u00fcnchen at the University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}]},{"given":"Cora","family":"Weigert","sequence":"additional","affiliation":[{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"},{"name":"Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum M\u00fcnchen at the University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}]},{"given":"Harald","family":"Staiger","sequence":"additional","affiliation":[{"name":"Institute of Experimental Genetics, Helmholtz Zentrum M\u00fcnchen GmbH , Neuherberg 85764, Germany"},{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"},{"name":"Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Zentrum M\u00fcnchen at the University of T\u00fcbingen , T\u00fcbingen 72076, Germany"}]},{"given":"Christoph","family":"Klein","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Dr. von Hauner Children\u2019s Hospital, University Hospital, LMU Munich , M\u00fcnchen 80337, Germany"}]},{"given":"Johannes","family":"Beckers","sequence":"additional","affiliation":[{"name":"Institute of Experimental Genetics, Helmholtz Zentrum M\u00fcnchen GmbH , Neuherberg 85764, Germany"},{"name":"German Center for Diabetes Research (DZD) , Neuherberg 85764, Germany"},{"name":"Chair of Experimental Genetics, Technische Universit\u00e4t M\u00fcnchen, Wissenschaftszentrum Weihenstephan , Freising 85354, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3288-4229","authenticated-orcid":false,"given":"Maximilian","family":"Hastreiter","sequence":"additional","affiliation":[{"name":"Institute of Computational Biology, Helmholtz Zentrum M\u00fcnchen GmbH , Neuherberg 85764, Germany"},{"name":"Chair of Genome-oriented Bioinformatics, Technische Universit\u00e4t M\u00fcnchen, Wissenschaftszentrum Weihenstephan , Freising 85354, Germany"}]}],"member":"286","published-online":{"date-parts":[[2019,6,22]]},"reference":[{"key":"2023013108365925000_btz495-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search 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