{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:29Z","timestamp":1740185129003,"version":"3.37.3"},"reference-count":4,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2019,5,22]],"date-time":"2019-05-22T00:00:00Z","timestamp":1558483200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100021373","name":"Swiss Institute of Bioinformatics","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100021373","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Swiss Federal Institute of Technology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>We present SPar-K (Signal Partitioning with K-means), a method to search for archetypical chromatin architectures by partitioning a set of genomic regions characterized by chromatin signal profiles around ChIP-seq peaks and other kinds of functional sites. This method efficiently deals with problems of data heterogeneity, limited misalignment of anchor points and unknown orientation of asymmetric patterns.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SPar-K is a C++ program available on GitHub https:\/\/github.com\/romaingroux\/SPar-K and Docker Hub https:\/\/hub.docker.com\/r\/rgroux\/spar-k.<\/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\/btz416","type":"journal-article","created":{"date-parts":[[2019,5,17]],"date-time":"2019-05-17T19:15:04Z","timestamp":1558120504000},"page":"4440-4441","source":"Crossref","is-referenced-by-count":1,"title":["SPar-K: a method to partition NGS signal data"],"prefix":"10.1093","volume":"35","author":[{"given":"Romain","family":"Groux","sequence":"first","affiliation":[{"name":"The Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland"}]},{"given":"Philipp","family":"Bucher","sequence":"additional","affiliation":[{"name":"The Swiss Institute for Experimental Cancer Research (ISREC), Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne 1015, Switzerland"},{"name":"Swiss Institute of Bioinformatics (SIB), Lausanne 1015, Switzerland"}]}],"member":"286","published-online":{"date-parts":[[2019,5,22]]},"reference":[{"key":"2023062712491363900_btz416-B1","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":"2023062712491363900_btz416-B2","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","year":"2012","journal-title":"Nature"},{"key":"2023062712491363900_btz416-B3","doi-asserted-by":"crossref","first-page":"1735","DOI":"10.1101\/gr.136366.111","article-title":"Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements","volume":"22","author":"Kundaje","year":"2012","journal-title":"Genome Res"},{"key":"2023062712491363900_btz416-B4","doi-asserted-by":"crossref","first-page":"2406","DOI":"10.1093\/bioinformatics\/btu318","article-title":"Probabilistic partitioning methods to find significant patterns in ChIP-Seq data","volume":"30","author":"Nair","year":"2014","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btz416\/28833201\/btz416.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4440\/50721716\/bioinformatics_35_21_4440.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/21\/4440\/50721716\/bioinformatics_35_21_4440.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T12:49:33Z","timestamp":1687870173000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/21\/4440\/5497248"}},"subtitle":[],"editor":[{"given":"Bonnie","family":"Berger","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,5,22]]},"references-count":4,"journal-issue":{"issue":"21","published-print":{"date-parts":[[2019,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz416","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,11,1]]},"published":{"date-parts":[[2019,5,22]]}}}