{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T10:52:31Z","timestamp":1740135151819,"version":"3.37.3"},"reference-count":17,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1569-0","type":"journal-article","created":{"date-parts":[[2017,3,7]],"date-time":"2017-03-07T07:16:41Z","timestamp":1488871001000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":15,"title":["Benchmarking and refining probability-based models for nucleosome-DNA interaction"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4275-2262","authenticated-orcid":false,"given":"Marco","family":"Tompitak","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerard T.","family":"Barkema","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Helmut","family":"Schiessel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,3,7]]},"reference":[{"key":"1569_CR1","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.cis.2016.01.007","volume":"232","author":"B Eslami-Mossallam","year":"2016","unstructured":"Eslami-Mossallam B, Schiessel H, van Noort J. Nucleosome dynamics: Sequence matters. Adv Colloid Interface Sci. 2016; 232:101\u201313.","journal-title":"Adv Colloid Interface Sci"},{"issue":"19","key":"1569_CR2","doi-asserted-by":"crossref","first-page":"11163","DOI":"10.1073\/pnas.95.19.11163","volume":"95","author":"WK Olson","year":"1998","unstructured":"Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc Natl Acad Sci USA. 1998; 95(19):11163\u201311168.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"1569_CR3","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.str.2009.01.013","volume":"17","author":"NB Becker","year":"2009","unstructured":"Becker NB, Everaers R. DNA Nanomechanics in the Nucleosome. Structure. 2009; 17(4):579\u201389.","journal-title":"Structure"},{"issue":"26","key":"1569_CR4","doi-asserted-by":"crossref","first-page":"5855","DOI":"10.1021\/acs.jpcb.6b00391","volume":"120","author":"L De Bruin","year":"2016","unstructured":"De Bruin L, Tompitak M, Eslami-Mossallam B, Schiessel H. Why Do Nucleosomes Unwrap Asymmetrically?J Phys Chem B. 2016; 120(26):5855\u2013863.","journal-title":"J Phys Chem B"},{"issue":"6","key":"1569_CR5","doi-asserted-by":"crossref","first-page":"0156905","DOI":"10.1371\/journal.pone.0156905","volume":"11","author":"B Eslami-Mossallam","year":"2016","unstructured":"Eslami-Mossallam B, Schram RD, Tompitak M, van Noort J, Schiessel H. Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach. PLoS One. 2016; 11(6):0156905.","journal-title":"PLoS One"},{"issue":"3","key":"1569_CR6","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1140\/epje\/i2013-13021-4","volume":"36","author":"A Fathizadeh","year":"2013","unstructured":"Fathizadeh A, Besya AB, Ejtehadi MR, Schiessel H. Rigid-body molecular dynamics of DNA inside a nucleosome. Eur Phys J E. 2013; 36(3):21.","journal-title":"Eur Phys J E"},{"issue":"14","key":"1569_CR7","doi-asserted-by":"crossref","first-page":"4707","DOI":"10.1093\/nar\/gkp475","volume":"37","author":"AV Morozov","year":"2009","unstructured":"Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED. Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res. 2009; 37(14):4707\u2013722.","journal-title":"Nucleic Acids Res"},{"key":"1569_CR8","doi-asserted-by":"crossref","unstructured":"Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. J Mol Biol. 2007; 371(3):725\u201338.","DOI":"10.1016\/j.jmb.2007.05.048"},{"issue":"21","key":"1569_CR9","doi-asserted-by":"crossref","first-page":"218103","DOI":"10.1103\/PhysRevLett.99.218103","volume":"99","author":"C Vaillant","year":"2007","unstructured":"Vaillant C, Audit B, Arneodo A. Experiments confirm the influence of genome long-range correlations on nucleosome positioning. Phys Rev Lett. 2007; 99(21):218103.","journal-title":"Phys Rev Lett"},{"key":"1569_CR10","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1038\/nature04979","volume":"442","author":"E Segal","year":"2006","unstructured":"Segal E, Fondufe-Mittendorf Y, Chen L, Th\u00e5str\u00f6m A, Field Y, Moore IK, Wang J-PZ, Widom J. A genomic code for nucleosome positioning. Nature. 2006; 442:772\u20138.","journal-title":"Nature"},{"issue":"3","key":"1569_CR11","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1016\/j.bpj.2016.12.041","volume":"112","author":"M Tompitak","year":"2017","unstructured":"Tompitak M, Vaillant C, Schiessel H. Genomes of Multicellular Organisms Have Evolved to Attract Nucleosomes to Promoter Regions. Biophys J. 2017; 112(3):505\u201311.","journal-title":"Biophys J"},{"issue":"6","key":"1569_CR12","doi-asserted-by":"crossref","first-page":"1014","DOI":"10.1093\/bib\/bbt062","volume":"15","author":"H Liu","year":"2013","unstructured":"Liu H, Zhang R, Xiong W, Guan J, Zhuang Z, Zhou S. A comparative evaluation on prediction methods of nucleosome positioning. Brief Bioinform. 2013; 15(6):1014\u20131027.","journal-title":"Brief Bioinform"},{"issue":"11","key":"1569_CR13","doi-asserted-by":"crossref","first-page":"e1000216","DOI":"10.1371\/journal.pcbi.1000216","volume":"4","author":"Y Field","year":"2008","unstructured":"Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol. 2008; 4(11):e1000216.","journal-title":"PLoS Comput Biol"},{"key":"1569_CR14","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1038\/nature07667","volume":"458","author":"N Kaplan","year":"2009","unstructured":"Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Leproust EM, Hughes TR, Lieb JD, Widom J, Segal E. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature. 2009; 458:362\u20136.","journal-title":"Nature"},{"issue":"5","key":"1569_CR15","doi-asserted-by":"crossref","first-page":"844","DOI":"10.1016\/j.molcel.2014.04.006","volume":"54","author":"I Barozzi","year":"2014","unstructured":"Barozzi I, Simonatto M, Bonifacio S, Yang L, Rohs R, Ghisletti S, Natoli G. Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers. Mol Cell. 2014; 54(5):844\u201357.","journal-title":"Mol Cell"},{"issue":"7352","key":"1569_CR16","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1038\/nature10002","volume":"474","author":"A Valouev","year":"2011","unstructured":"Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells. Nature. 2011; 474(7352):516\u201320.","journal-title":"Nature"},{"issue":"6","key":"1569_CR17","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1002\/bip.22608","volume":"103","author":"G Rosanio","year":"2015","unstructured":"Rosanio G, Widom J, Uhlenbeck OC. In vitro selection of DNAs with an increased propensity to form small circles. Biopolymers. 2015; 103(6):303\u201320.","journal-title":"Biopolymers"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1569-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,6,25]],"date-time":"2017-06-25T08:04:50Z","timestamp":1498377890000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1569-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,3,7]]},"references-count":17,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1569"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1569-0","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2017,3,7]]},"article-number":"157"}}