{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:44:39Z","timestamp":1740185079796,"version":"3.37.3"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2017,1,23]],"date-time":"2017-01-23T00:00:00Z","timestamp":1485129600000},"content-version":"vor","delay-in-days":55,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002341","name":"Academy of Finland","doi-asserted-by":"crossref","award":["276864"],"award-info":[{"award-number":["276864"]}],"id":[{"id":"10.13039\/501100002341","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["GR 4587\/1-1"],"award-info":[{"award-number":["GR 4587\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of binding motifs. Here, we present the Java application InMoDe, a collection of tools for learning, leveraging and visualizing such dependencies of putative higher order. The distinguishing feature of InMoDe is a robust model selection from a class of parsimonious models, taking into account dependencies only if justified by the data while choosing for simplicity otherwise.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>InMoDe is implemented in Java and is available as command line application, as application with a graphical user-interface, and as an integration into Galaxy on the project website at http:\/\/www.jstacs.de\/index.php\/InMoDe.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btw689","type":"journal-article","created":{"date-parts":[[2016,10,27]],"date-time":"2016-10-27T19:06:40Z","timestamp":1477595200000},"page":"580-582","source":"Crossref","is-referenced-by-count":17,"title":["InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites"],"prefix":"10.1093","volume":"33","author":[{"given":"Ralf","family":"Eggeling","sequence":"first","affiliation":[{"name":"Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Helsinki, Finland"}]},{"given":"Ivo","family":"Grosse","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Martin Luther University Halle\u2013Wittenberg, Halle (Saale), Germany"},{"name":"German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany"}]},{"given":"Jan","family":"Grau","sequence":"additional","affiliation":[{"name":"Institute of Computer Science, Martin Luther University Halle\u2013Wittenberg, Halle (Saale), Germany"}]}],"member":"286","published-online":{"date-parts":[[2016,11,29]]},"reference":[{"year":"2004","author":"Bourguignon","key":"2023020204422162400_btw689-B1"},{"year":"2016","author":"Eggeling","key":"2023020204422162400_btw689-B2"},{"key":"2023020204422162400_btw689-B3","doi-asserted-by":"crossref","first-page":"e85629.","DOI":"10.1371\/journal.pone.0085629","article-title":"On the value of intra-motif dependencies of human insulator protein CTCF","volume":"9","author":"Eggeling","year":"2014","journal-title":"PLoS One"},{"year":"2014","author":"Eggeling","key":"2023020204422162400_btw689-B4"},{"key":"2023020204422162400_btw689-B5","doi-asserted-by":"crossref","first-page":"375.","DOI":"10.1186\/s12859-015-0797-4","article-title":"Inferring intra-motif dependencies of DNA binding sites from ChIP-seq data","volume":"16","author":"Eggeling","year":"2015","journal-title":"BMC Bioinform"},{"key":"2023020204422162400_btw689-B6","first-page":"1967","article-title":"Jstacs: a Java framework for statistical analysis and classification of biological sequences","volume":"13","author":"Grau","year":"2012","journal-title":"J. Mach. Learn. 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