{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T00:34:42Z","timestamp":1771893282943,"version":"3.50.1"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average.<\/jats:p>\n               <jats:p>Results: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain.<\/jats:p>\n               <jats:p>Availability: Source code, precompiled binaries, test data and a web-based test installation are freely available at http:\/\/bioinformatics.fh-stralsund.de\/nucpos\/<\/jats:p>\n               <jats:p>Contact: \u00a0gero.wedemann@fh-stralsund.de<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt404","type":"journal-article","created":{"date-parts":[[2013,7,12]],"date-time":"2013-07-12T00:18:49Z","timestamp":1373588329000},"page":"2380-2386","source":"Crossref","is-referenced-by-count":43,"title":["Modeling nucleosome position distributions from experimental nucleosome positioning maps"],"prefix":"10.1093","volume":"29","author":[{"given":"Robert","family":"Sch\u00f6pflin","sequence":"first","affiliation":[{"name":"1 Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and 2Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany"}]},{"given":"Vladimir B.","family":"Teif","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and 2Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany"}]},{"given":"Oliver","family":"M\u00fcller","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and 2Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany"}]},{"given":"Christin","family":"Weinberg","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and 2Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany"}]},{"given":"Karsten","family":"Rippe","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and 2Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany"}]},{"given":"Gero","family":"Wedemann","sequence":"additional","affiliation":[{"name":"1 Institute for Applied Computer Science, University of Applied Sciences Stralsund, Zur Schwedenschanze 15, Stralsund 18435, Germany and 2Deutsches Krebsforschungszentrum (DKFZ) & BioQuant, Im Neuenheimer Feld 280, Heidelberg 69120, Germany"}]}],"member":"286","published-online":{"date-parts":[[2013,7,11]]},"reference":[{"key":"2023012810464025300_btt404-B1","doi-asserted-by":"crossref","first-page":"1305","DOI":"10.1093\/bioinformatics\/btn119","article-title":"GeneTrack\u2014a genomic data processing and visualization framework","volume":"24","author":"Albert","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012810464025300_btt404-B2","doi-asserted-by":"crossref","first-page":"152","DOI":"10.1016\/j.jmb.2012.01.043","article-title":"Micrococcal nuclease does not substantially bias nucleosome mapping","volume":"417","author":"Allan","year":"2012","journal-title":"J. Mol. Biol."},{"key":"2023012810464025300_btt404-B3","doi-asserted-by":"crossref","first-page":"711","DOI":"10.1093\/bioinformatics\/bts719","article-title":"NucleoFinder: a statistical approach for the detection of nucleosome positions","volume":"29","author":"Becker","year":"2013","journal-title":"Bioinformatics"},{"key":"2023012810464025300_btt404-B4","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-03163-2","volume-title":"Monte Carlo Simulation in Statistical Physics: An Introduction","author":"Binder","year":"2010","edition":"5th edn"},{"key":"2023012810464025300_btt404-B5","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/j.cell.2008.04.043","article-title":"Integration of external signaling pathways with the core transcriptional network in embryonic stem cells","volume":"133","author":"Chen","year":"2008","journal-title":"Cell"},{"key":"2023012810464025300_btt404-B6","doi-asserted-by":"crossref","first-page":"e15754","DOI":"10.1371\/journal.pone.0015754","article-title":"The effect of micrococcal nuclease digestion on nucleosome positioning data","volume":"5","author":"Chung","year":"2010","journal-title":"PLoS One"},{"key":"2023012810464025300_btt404-B7","doi-asserted-by":"crossref","first-page":"292","DOI":"10.1038\/35066075","article-title":"Chromosome territories, nuclear architecture and gene regulation in mammalian cells","volume":"2","author":"Cremer","year":"2001","journal-title":"Nat. Rev. Genet."},{"key":"2023012810464025300_btt404-B8","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1101\/gr.082800.108","article-title":"Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains","volume":"19","author":"Cuddapah","year":"2009","journal-title":"Genome Res."},{"key":"2023012810464025300_btt404-B9","doi-asserted-by":"crossref","first-page":"2149","DOI":"10.1093\/bioinformatics\/btr345","article-title":"nucleR: a package for non-parametric nucleosome positioning","volume":"27","author":"Flores","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012810464025300_btt404-B10","doi-asserted-by":"crossref","first-page":"e1000138","DOI":"10.1371\/journal.pgen.1000138","article-title":"The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome","volume":"4","author":"Fu","year":"2008","journal-title":"PLoS Genet."},{"key":"2023012810464025300_btt404-B30","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1101\/gr.229102","article-title":"The Human Genome Browser at UCSC","volume":"12","author":"Kent","year":"2002","journal-title":"Genome Res."},{"key":"2023012810464025300_btt404-B11","doi-asserted-by":"crossref","DOI":"10.1137\/1.9781611971217","volume-title":"Solving Least Squares Problems","author":"Lawson","year":"1995"},{"key":"2023012810464025300_btt404-B12","doi-asserted-by":"crossref","first-page":"1235","DOI":"10.1038\/ng2117","article-title":"A high-resolution atlas of nucleosome occupancy in yeast","volume":"39","author":"Lee","year":"2007","journal-title":"Nat. Genet."},{"key":"2023012810464025300_btt404-B13","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1145\/272991.272995","article-title":"Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator","volume":"8","author":"Matsumoto","year":"1998","journal-title":"ACM Trans. Model. Comput. Simul."},{"key":"2023012810464025300_btt404-B14","volume-title":"nnls: The Lawson\u2013Hanson Algorithm for Non-negative Least Squares","author":"Mullen","year":"2012"},{"key":"2023012810464025300_btt404-B15","doi-asserted-by":"crossref","first-page":"9359","DOI":"10.1128\/MCB.24.21.9359-9370.2004","article-title":"Generic features of tertiary chromatin structure as detected in natural chromosomes","volume":"24","author":"M\u00fcller","year":"2004","journal-title":"Mol. Cell. Biol."},{"key":"2023012810464025300_btt404-B16","first-page":"320","article-title":"NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data","volume":"3","author":"Nellore","year":"2012","journal-title":"Front Genet."},{"key":"2023012810464025300_btt404-B17","doi-asserted-by":"crossref","first-page":"7799","DOI":"10.1073\/pnas.1015206108","article-title":"Nucleosome positioning in a model of active chromatin remodeling enzymes","volume":"108","author":"Padinhateeri","year":"2011","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012810464025300_btt404-B18","doi-asserted-by":"crossref","first-page":"i242","DOI":"10.1093\/bioinformatics\/bts206","article-title":"NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model","volume":"28","author":"Polishko","year":"2012","journal-title":"Bioinformatics"},{"key":"2023012810464025300_btt404-B19","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nsmb.2419","article-title":"Genome-wide nucleosome positioning during embryonic stem cell development","volume":"19","author":"Teif","year":"2012","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023012810464025300_btt404-B20","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1093\/bib\/bbr037","article-title":"Calculating transcription factor binding maps for chromatin","volume":"13","author":"Teif","year":"2012","journal-title":"Brief. Bioinform."},{"key":"2023012810464025300_btt404-B21","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1101\/gr.076463.108","article-title":"A high-resolution, nucleosome position map of C.elegans reveals a lack of universal sequence-dictated positioning","volume":"18","author":"Valouev","year":"2008","journal-title":"Genome Res."},{"key":"2023012810464025300_btt404-B22","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nature10002","article-title":"Determinants of nucleosome organization in primary human cells","volume":"474","author":"Valouev","year":"2011","journal-title":"Nature"},{"key":"2023012810464025300_btt404-B23","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1101\/gr.098509.109","article-title":"High-resolution nucleosome mapping reveals transcription-dependent promoter packaging","volume":"20","author":"Weiner","year":"2010","journal-title":"Genome Res."},{"key":"2023012810464025300_btt404-B24","doi-asserted-by":"crossref","first-page":"i139","DOI":"10.1093\/bioinformatics\/btn151","article-title":"Nucleosome positioning from tiling microarray data","volume":"24","author":"Yassour","year":"2008","journal-title":"Bioinformatics"},{"key":"2023012810464025300_btt404-B25","doi-asserted-by":"crossref","first-page":"e32095","DOI":"10.1371\/journal.pone.0032095","article-title":"Probabilistic inference for nucleosome positioning with MNase-Based or sonicated short-read data","volume":"7","author":"Zhang","year":"2012","journal-title":"PLoS One"},{"key":"2023012810464025300_btt404-B26","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1186\/1471-2164-9-537","article-title":"Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq","volume":"9","author":"Zhang","year":"2008","journal-title":"BMC Genomics"},{"key":"2023012810464025300_btt404-B27","doi-asserted-by":"crossref","first-page":"847","DOI":"10.1038\/nsmb.1636","article-title":"Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo","volume":"16","author":"Zhang","year":"2009","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2023012810464025300_btt404-B28","doi-asserted-by":"crossref","first-page":"977","DOI":"10.1126\/science.1200508","article-title":"A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome","volume":"332","author":"Zhang","year":"2011","journal-title":"Science"},{"key":"2023012810464025300_btt404-B29","doi-asserted-by":"crossref","first-page":"175","DOI":"10.1016\/j.cell.2011.01.003","article-title":"High-resolution genome-wide mapping of the primary structure of chromatin","volume":"144","author":"Zhang","year":"2011","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/19\/2380\/48893658\/bioinformatics_29_19_2380.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/19\/2380\/48893658\/bioinformatics_29_19_2380.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T12:36:03Z","timestamp":1674909363000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/19\/2380\/186820"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,7,11]]},"references-count":30,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2013,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt404","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,10,1]]},"published":{"date-parts":[[2013,7,11]]}}}