{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T16:11:28Z","timestamp":1774627888245,"version":"3.50.1"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2022,2,24]],"date-time":"2022-02-24T00:00:00Z","timestamp":1645660800000},"content-version":"vor","delay-in-days":1,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008273","name":"Novartis Research Foundation","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100008273","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["31003A_149573"],"award-info":[{"award-number":["31003A_149573"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["31003A_175776"],"award-info":[{"award-number":["31003A_175776"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Research Council under the European Union\u2019s Horizon 2020 research and innovation programme","award":["810111-EpiCrest2Reg"],"award-info":[{"award-number":["810111-EpiCrest2Reg"]}]},{"DOI":"10.13039\/501100001711","name":"Swiss National Science Foundation","doi-asserted-by":"publisher","award":["310030B_176394"],"award-info":[{"award-number":["310030B_176394"]}],"id":[{"id":"10.13039\/501100001711","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Research Council under the European Union\u2019s","award":["ReadMe-667951"],"award-info":[{"award-number":["ReadMe-667951"]}]},{"name":"European Research Council under the European Union\u2019s","award":["DNAaccess-884664"],"award-info":[{"award-number":["DNAaccess-884664"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Proteins binding to specific nucleotide sequences, such as transcription factors, play key roles in the regulation of gene expression. Their binding can be indirectly observed via associated changes in transcription, chromatin accessibility, DNA methylation and histone modifications. Identifying candidate factors that are responsible for these observed experimental changes is critical to understand the underlying biological processes. Here, we present monaLisa, an R\/Bioconductor package that implements approaches to identify relevant transcription factors from experimental data. The package can be easily integrated with other Bioconductor packages and enables seamless motif analyses without any software dependencies outside of R.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>monaLisa is implemented in R and available on Bioconductor at https:\/\/bioconductor.org\/packages\/monaLisa with the development version hosted on GitHub at https:\/\/github.com\/fmicompbio\/monaLisa.<\/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\/btac102","type":"journal-article","created":{"date-parts":[[2022,2,22]],"date-time":"2022-02-22T07:32:45Z","timestamp":1645515165000},"page":"2624-2625","source":"Crossref","is-referenced-by-count":102,"title":["monaLisa: an R\/Bioconductor package for identifying regulatory motifs"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2578-6930","authenticated-orcid":false,"given":"Dania","family":"Machlab","sequence":"first","affiliation":[{"name":"Friedrich Miescher Institute for Biomedical Research , Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel, Switzerland"},{"name":"Faculty of Science, University of Basel, Basel, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5596-7567","authenticated-orcid":false,"given":"Lukas","family":"Burger","sequence":"additional","affiliation":[{"name":"Friedrich Miescher Institute for Biomedical Research , Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3833-2169","authenticated-orcid":false,"given":"Charlotte","family":"Soneson","sequence":"additional","affiliation":[{"name":"Friedrich Miescher Institute for Biomedical Research , Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0515-0182","authenticated-orcid":false,"given":"Filippo M","family":"Rijli","sequence":"additional","affiliation":[{"name":"Friedrich Miescher Institute for Biomedical Research , Basel, Switzerland"},{"name":"Faculty of Science, University of Basel, Basel, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9229-2228","authenticated-orcid":false,"given":"Dirk","family":"Sch\u00fcbeler","sequence":"additional","affiliation":[{"name":"Friedrich Miescher Institute for Biomedical Research , Basel, Switzerland"},{"name":"Faculty of Science, University of Basel, Basel, Switzerland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2269-4934","authenticated-orcid":false,"given":"Michael B","family":"Stadler","sequence":"additional","affiliation":[{"name":"Friedrich Miescher Institute for Biomedical Research , Basel, Switzerland"},{"name":"SIB Swiss Institute of Bioinformatics , Basel, Switzerland"},{"name":"Faculty of Science, University of Basel, Basel, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2022,2,23]]},"reference":[{"key":"2023041402551541900_","doi-asserted-by":"crossref","first-page":"W39","DOI":"10.1093\/nar\/gkv416","article-title":"The MEME Suite","volume":"43","author":"Bailey","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2023041402551541900_","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1101\/gr.169508.113","article-title":"ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs","volume":"24","author":"Balwierz","year":"2014","journal-title":"Genome Res"},{"key":"2023041402551541900_","doi-asserted-by":"crossref","first-page":"e155","DOI":"10.1093\/nar\/gkt599","article-title":"Identification of active regulatory regions from DNA methylation data","volume":"41","author":"Burger","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2023041402551541900_","first-page":"D87","article-title":"JASPAR 2020: update of the open-access database of transcription factor binding profiles","volume":"48","author":"Fornes","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2023041402551541900_","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. 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