{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T19:22:26Z","timestamp":1761765746607},"reference-count":13,"publisher":"Springer Science and Business Media LLC","issue":"S1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2014,1]]},"DOI":"10.1186\/1471-2105-15-s1-s8","type":"journal-article","created":{"date-parts":[[2014,1,10]],"date-time":"2014-01-10T13:58:23Z","timestamp":1389362303000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["AnnotateGenomicRegions: a web application"],"prefix":"10.1186","volume":"15","author":[{"given":"Luca","family":"Zammataro","sequence":"first","affiliation":[]},{"given":"Rita","family":"DeMolfetta","sequence":"additional","affiliation":[]},{"given":"Gabriele","family":"Bucci","sequence":"additional","affiliation":[]},{"given":"Arnaud","family":"Ceol","sequence":"additional","affiliation":[]},{"given":"Heiko","family":"Muller","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2014,1,10]]},"reference":[{"issue":"3","key":"6251_CR1","doi-asserted-by":"publisher","first-page":"e13","DOI":"10.1093\/nar\/gkp1012","volume":"38","author":"KR Blahnik","year":"2010","unstructured":"Blahnik KR, Dou L, O'Geen H, McPhillips T, Xu X, Cao AR, Iyengar S, Nicolet CM, Ludascher B, Korf I, Farnham PJ: Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data. Nucleic Acids Res. 2010, 38 (3): e13-10.1093\/nar\/gkp1012.","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"6251_CR2","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1093\/bioinformatics\/btq669","volume":"27","author":"X Lan","year":"2011","unstructured":"Lan X, Bonneville R, Apostolos J, Wu W, Jin VX: W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics. 2011, 27 (3): 428-430. 10.1093\/bioinformatics\/btq669.","journal-title":"Bioinformatics"},{"issue":"11","key":"6251_CR3","doi-asserted-by":"publisher","first-page":"1293","DOI":"10.1038\/nbt.1505","volume":"26","author":"H Ji","year":"2008","unstructured":"Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 2008, 26 (11): 1293-1300. 10.1038\/nbt.1505.","journal-title":"Nat Biotechnol"},{"issue":"2","key":"6251_CR4","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1515\/jib-2011-155","volume":"8","author":"M Alawi","year":"2011","unstructured":"Alawi M, Kurtz S, Beckstette M: CASSys: an integrated software-system for the interactive analysis of ChIP-seq data. J Integr Bioinform. 2011, 8 (2): 155-","journal-title":"J Integr Bioinform"},{"issue":"6","key":"6251_CR5","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","volume":"26","author":"AR Quinlan","year":"2010","unstructured":"Quinlan AR, Hall IM: BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010, 26 (6): 841-842. 10.1093\/bioinformatics\/btq033.","journal-title":"Bioinformatics"},{"key":"6251_CR6","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1186\/1471-2105-11-237","volume":"11","author":"LJ Zhu","year":"2010","unstructured":"Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, Green MR: ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics. 2010, 11: 237-10.1186\/1471-2105-11-237.","journal-title":"BMC Bioinformatics"},{"issue":"7","key":"6251_CR7","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.1093\/bioinformatics\/btr050","volume":"27","author":"F Strozzi","year":"2011","unstructured":"Strozzi F, Aerts J: A Ruby API to query the Ensembl database for genomic features. Bioinformatics. 2011, 27 (7): 1013-1014. 10.1093\/bioinformatics\/btr050.","journal-title":"Bioinformatics"},{"issue":"10","key":"6251_CR8","doi-asserted-by":"publisher","first-page":"1451","DOI":"10.1101\/gr.4086505","volume":"15","author":"B Giardine","year":"2005","unstructured":"Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y, Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A: Galaxy: a platform for interactive large-scale genome analysis. Genome Res. 2005, 15 (10): 1451-1455. 10.1101\/gr.4086505.","journal-title":"Genome Res"},{"issue":"Database","key":"6251_CR9","doi-asserted-by":"publisher","first-page":"D493","DOI":"10.1093\/nar\/gkh103","volume":"32","author":"D Karolchik","year":"2004","unstructured":"Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ: The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004, 32 (Database): D493-496.","journal-title":"Nucleic Acids Res"},{"issue":"Supplement B","key":"6251_CR10","first-page":"135","volume":"18","author":"H Muller","year":"2012","unstructured":"Muller H, Zammataro L, Bucci G: AnnotateGenomicRegions: a web application. EMBnetjournal. 2012, 18 (Supplement B): 135-137.","journal-title":"EMBnetjournal"},{"issue":"Database","key":"6251_CR11","first-page":"D501","volume":"33","author":"KD Pruitt","year":"2005","unstructured":"Pruitt KD, Tatusova T, Maglott DR: NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005, 33 (Database): D501-504.","journal-title":"Nucleic Acids Res"},{"issue":"Database","key":"6251_CR12","doi-asserted-by":"publisher","first-page":"D800","DOI":"10.1093\/nar\/gkq1064","volume":"39","author":"P Flicek","year":"2011","unstructured":"Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M: Ensembl 2011. Nucleic Acids Res. 2011, 39 (Database): D800-806. 10.1093\/nar\/gkq1064.","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"6251_CR13","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1101\/gr.229102. Article published online before print in May 2002","volume":"12","author":"WJ Kent","year":"2002","unstructured":"Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. Genome Res. 2002, 12 (6): 996-1006. 10.1101\/gr.229102. Article published online before print in May 2002.","journal-title":"Genome Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-15-S1-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,2]],"date-time":"2021-09-02T02:43:48Z","timestamp":1630550628000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-15-S1-S8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,1]]},"references-count":13,"journal-issue":{"issue":"S1","published-print":{"date-parts":[[2014,1]]}},"alternative-id":["6251"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-15-s1-s8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,1]]},"assertion":[{"value":"10 January 2014","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S8"}}