{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,17]],"date-time":"2025-10-17T00:20:08Z","timestamp":1760660408436,"version":"build-2065373602"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2025,9,17]],"date-time":"2025-09-17T00:00:00Z","timestamp":1758067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013060","name":"EMBL","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100013060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["KR 5247\/1-2","KR 5247\/1-3"],"award-info":[{"award-number":["KR 5247\/1-2","KR 5247\/1-3"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Single molecule footprinting profiles the heterogeneity of TF occupancy at cis-regulatory elements across cell populations at unprecedented resolution. The single molecule nature of the data in principle allows for observing the footprint of individual transcription factors and nucleosomes. However, we currently lack algorithms to quantify these occupancy patterns of chromatin binding factors in an automated way and without prior assumptions on their genomic location. Here we present FootprintCharter, an unsupervised tool to detect and quantify footprints for transcription factors (TFs) and nucleosomes from single molecule footprinting data. After detection, TF footprints can be labeled with orthogonal motif annotations provided by the user. FootprintCharter allows for the quantification of complex molecular states such as positioning of unphased nucleosomes and combinatorial co-binding of multiple TFs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FootprintCharter is freely available on Bioconductor with version 2.2.0 of https:\/\/bioconductor.org\/packages\/SingleMoleculeFootprinting through the functions FootprintCharter, PlotFootprints, and Plot_FootprintCharter_SM.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf502","type":"journal-article","created":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T23:17:16Z","timestamp":1758323836000},"source":"Crossref","is-referenced-by-count":0,"title":["FootprintCharter: unsupervised detection and quantification of footprints in single molecule footprinting data"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6066-3920","authenticated-orcid":false,"given":"Guido","family":"Barzaghi","sequence":"first","affiliation":[{"name":"Genome Biology Unit, EMBL Heidelberg , Meyerhofstra\u00dfe 1 , Heidelberg, 69117,","place":["Germany"]},{"name":"Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University , Im Neuenheimer Feld 234 , Heidelberg, 69120,","place":["Germany"]}]},{"given":"Arnaud R","family":"Krebs","sequence":"additional","affiliation":[{"name":"Genome Biology Unit, EMBL Heidelberg , Meyerhofstra\u00dfe 1 , Heidelberg, 69117,","place":["Germany"]}]},{"given":"Judith B","family":"Zaugg","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit, EMBL Heidelberg , Meyerhofstra\u00dfe 1 , Heidelberg, 69117,","place":["Germany"]},{"name":"Department of Biomedicine, University of Basel , Hebelstrasse 20 , Basel, 4031,","place":["Switzerland"]}]}],"member":"286","published-online":{"date-parts":[[2025,9,17]]},"reference":[{"year":"2025","author":"Baderna","key":"2025101607421374400_btaf502-B1","doi-asserted-by":"publisher","DOI":"10.1101\/2025.03.26.645413"},{"year":"2000","author":"Bates","key":"2025101607421374400_btaf502-B2","doi-asserted-by":"publisher","DOI":"10.32614\/CRAN.package.Matrix"},{"key":"2025101607421374400_btaf502-B3","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/s44320-025-00094-5","author":"Chatsirisupachai","year":"2025"},{"author":"Doughty","key":"2025101607421374400_btaf502-B4","first-page":"745"},{"key":"2025101607421374400_btaf502-B5","doi-asserted-by":"publisher","first-page":"1130","DOI":"10.1093\/bioinformatics\/btu781","article-title":"QuasR: quantification and annotation of short reads in R","volume":"31","author":"Gaidatzis","year":"2015","journal-title":"Bioinformatics"},{"key":"2025101607421374400_btaf502-B6","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","article-title":"Bioconductor: open software development for computational biology and bioinformatics","volume":"5","author":"Gentleman","year":"2004","journal-title":"Genome Biol"},{"key":"2025101607421374400_btaf502-B7","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with Bioconductor","volume":"12","author":"Huber","year":"2015","journal-title":"Nat Methods"},{"key":"2025101607421374400_btaf502-B8","doi-asserted-by":"publisher","first-page":"5673","DOI":"10.1038\/s41596-021-00630-1","article-title":"Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting","volume":"16","author":"Kleinendorst","year":"2021","journal-title":"Nat Protoc"},{"key":"2025101607421374400_btaf502-B9","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1016\/j.molcel.2017.06.027","article-title":"Genome-wide single-molecule footprinting reveals high RNA polymerase II turnover at paused promoters","volume":"67","author":"Krebs","year":"2017","journal-title":"Mol Cell"},{"key":"2025101607421374400_btaf502-B10","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.molcel.2023.01.017","article-title":"Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation","volume":"83","author":"Kreibich","year":"2023","journal-title":"Mol Cell"},{"key":"2025101607421374400_btaf502-B11","doi-asserted-by":"publisher","first-page":"e1003118","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Genomic ranges\u2019, (A. 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