{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,13]],"date-time":"2026-01-13T14:09:55Z","timestamp":1768313395738,"version":"3.49.0"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2020,9,29]],"date-time":"2020-09-29T00:00:00Z","timestamp":1601337600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Research Campus of Central Hessen"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The discovery of sequence motifs mediating DNA-protein binding usually implies the determination of binding sites using high-throughput sequencing and peak calling. The determination of peaks, however, depends strongly on data quality and is susceptible to noise.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present a novel approach to reliably identify transcription factor-binding motifs from ChIP-Seq data without peak detection. By evaluating the distributions of sequencing reads around the different k-mers in the genome, we are able to identify binding motifs in ChIP-Seq data that yield no results in traditional pipelines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>NoPeak is published under the GNU General Public License and available as a standalone console-based Java application at https:\/\/github.com\/menzel\/nopeak.<\/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\/btaa845","type":"journal-article","created":{"date-parts":[[2020,9,14]],"date-time":"2020-09-14T19:14:17Z","timestamp":1600110857000},"page":"596-602","source":"Crossref","is-referenced-by-count":8,"title":["NoPeak: k-mer-based motif discovery in ChIP-Seq data without peak calling"],"prefix":"10.1093","volume":"37","author":[{"given":"Michael","family":"Menzel","sequence":"first","affiliation":[{"name":"MNI, Technische Hochschule Mittelhessen, University of Applied Sciences , Giessen 35390, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2083-5198","authenticated-orcid":false,"given":"Sabine","family":"Hurka","sequence":"additional","affiliation":[{"name":"Institute for Insect Biotechnology, Justus Liebig University , Giessen 35392, Germany"}]},{"given":"Stefan","family":"Glasenhardt","sequence":"additional","affiliation":[{"name":"MNI, Technische Hochschule Mittelhessen, University of Applied Sciences , Giessen 35390, Germany"}]},{"given":"Andreas","family":"Gogol-D\u00f6ring","sequence":"additional","affiliation":[{"name":"MNI, Technische Hochschule Mittelhessen, University of Applied Sciences , Giessen 35390, Germany"}]}],"member":"286","published-online":{"date-parts":[[2020,9,29]]},"reference":[{"key":"2023051704101056600_btaa845-B1","doi-asserted-by":"crossref","first-page":"1723","DOI":"10.1101\/gr.127712.111","article-title":"Sequence and chromatin determinants of cell-type-specific transcription factor binding","volume":"22","author":"Arvey","year":"2012","journal-title":"Genome Res"},{"key":"2023051704101056600_btaa845-B2","doi-asserted-by":"crossref","first-page":"1720","DOI":"10.1126\/science.1162327","article-title":"Diversity and complexity in DNA recognition by transcription factors","volume":"324","author":"Badis","year":"2009","journal-title":"Science"},{"key":"2023051704101056600_btaa845-B3","doi-asserted-by":"crossref","first-page":"W202","DOI":"10.1093\/nar\/gkp335","article-title":"MEME SUITE: tools for motif discovery and searching","volume":"37","author":"Bailey","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023051704101056600_btaa845-B4","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1385\/1-59745-097-9:245","volume-title":"Gene Mapping, Discovery, and Expression","author":"Berger","year":"2006"},{"key":"2023051704101056600_btaa845-B5","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1093\/bioinformatics\/bts293","article-title":"MotifSuite: workflow for probabilistic motif detection and assessment","volume":"28","author":"Claeys","year":"2012","journal-title":"Bioinformatics"},{"key":"2023051704101056600_btaa845-B6","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1101\/gr.849004","article-title":"WebLogo: a sequence logo generator","volume":"14","author":"Crooks","year":"2004","journal-title":"Genome Res"},{"key":"2023051704101056600_btaa845-B7","doi-asserted-by":"crossref","DOI":"10.1186\/s12864-018-4630-0","article-title":"TrawlerWeb: an online de novo motif discovery tool for next-generation sequencing datasets","volume":"19","author":"Dang","year":"2018","journal-title":"BMC Genomics"},{"key":"2023051704101056600_btaa845-B8","doi-asserted-by":"crossref","first-page":"e1006921","DOI":"10.1371\/journal.pcbi.1006921","article-title":"ChIPulate: a comprehensive ChIP-seq simulation pipeline","volume":"15","author":"Datta","year":"2019","journal-title":"PLoS Comput. 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