{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,14]],"date-time":"2026-02-14T06:43:19Z","timestamp":1771051399458,"version":"3.50.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T00:00:00Z","timestamp":1567382400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T00:00:00Z","timestamp":1567382400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"crossref","award":["SFB-TR36"],"award-info":[{"award-number":["SFB-TR36"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005972","name":"Deutsche Krebshilfe","doi-asserted-by":"crossref","award":["111546"],"award-info":[{"award-number":["111546"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Berlin Institute of Health","award":["CRG-1"],"award-info":[{"award-number":["CRG-1"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2019,12]]},"DOI":"10.1186\/s12859-019-3043-7","type":"journal-article","created":{"date-parts":[[2019,9,2]],"date-time":"2019-09-02T18:07:41Z","timestamp":1567447661000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["SigsPack, a package for cancer mutational signatures"],"prefix":"10.1186","volume":"20","author":[{"given":"Franziska","family":"Schumann","sequence":"first","affiliation":[]},{"given":"Eric","family":"Blanc","sequence":"additional","affiliation":[]},{"given":"Clemens","family":"Messerschmidt","sequence":"additional","affiliation":[]},{"given":"Thomas","family":"Blankenstein","sequence":"additional","affiliation":[]},{"given":"Antonia","family":"Busse","sequence":"additional","affiliation":[]},{"given":"Dieter","family":"Beule","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2019,9,2]]},"reference":[{"key":"3043_CR1","doi-asserted-by":"publisher","unstructured":"Temko D, Tomlinson IPM, Severini S, Schuster-B\u00f6ckler B, Graham TA. The effects of mutational processes and selection on driver mutations across cancer types. Nat Commun. 2018; 9(1). \n                    https:\/\/doi.org\/10.1101\/149096\n                    \n                  .","DOI":"10.1101\/149096"},{"issue":"5","key":"3043_CR2","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1016\/j.cell.2012.04.023","volume":"149","author":"S Nik-Zainal","year":"2012","unstructured":"Nik-Zainal S, Van Loo P, Wedge DC, Alexandrov LB, Greenman CD, Lau KW, et al.The life history of 21 breast cancers. Cell. 2012; 149(5):994\u20131007.","journal-title":"Cell"},{"issue":"1","key":"3043_CR3","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1016\/j.celrep.2012.12.008","volume":"3","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov LB, Nik-Zainal S, Wedge DC, Campbell PJ, Stratton MR. Deciphering Signatures of Mutational Processes Operative in Human Cancer. Cell Rep. 2013; 3(1):246\u201359.","journal-title":"Cell Rep"},{"issue":"D1","key":"3043_CR4","doi-asserted-by":"publisher","first-page":"D941","DOI":"10.1093\/nar\/gky1015","volume":"47","author":"JG Tate","year":"2019","unstructured":"Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, et al.COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2019; 47(D1):D941\u2013D947.","journal-title":"Nucleic Acids Res"},{"key":"3043_CR5","unstructured":"Alexandrov LB, Kim J, Haradhvala NJ, Huang MN, Ng AWT, Boot A, et al.sigfit: flexible Bayesian inference of mutational signatures. bioRxiv. 2018."},{"issue":"8","key":"3043_CR6","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1186\/gm175","volume":"2","author":"GP Pfeifer","year":"2010","unstructured":"Pfeifer GP. Environmental exposures and mutational patterns of cancer genomes. Genome Med. 2010; 2(8):2\u20135.","journal-title":"Genome Med"},{"issue":"7463","key":"3043_CR7","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","volume":"500","author":"LB Alexandrov","year":"2013","unstructured":"Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SAJR, Behjati S, Biankin AV, et al.Signatures of mutational processes in human cancer. Nature. 2013; 500(7463):415\u201321.","journal-title":"Nature"},{"issue":"6360","key":"3043_CR8","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1126\/science.aao3130","volume":"358","author":"J Drost","year":"2017","unstructured":"Drost J, Van Boxtel R, Blokzijl F, Mizutani T, Sasaki N, Sasselli V, et al.Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer. Science. 2017; 358(6360):234\u20138.","journal-title":"Science"},{"issue":"3","key":"3043_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gm541","volume":"6","author":"SL Poon","year":"2014","unstructured":"Poon SL, McPherson JR, Tan P, Teh BT, Rozen SG. Mutation signatures of carcinogen exposure: Genome-wide detection and new opportunities for cancer prevention. Genome Med. 2014; 6(3):1\u201314.","journal-title":"Genome Med"},{"issue":"1","key":"3043_CR10","doi-asserted-by":"publisher","first-page":"3292","DOI":"10.1038\/s41467-018-05228-y","volume":"9","author":"J Ma","year":"2018","unstructured":"Ma J, Setton J, Lee NY, Riaz N, Powell SN. The therapeutic significance of mutational signatures from DNA repair deficiency in cancer. Nat Commun. 2018; 9(1):3292.","journal-title":"Nat Commun"},{"issue":"1","key":"3043_CR11","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s13073-018-0539-0","volume":"10","author":"F Blokzijl","year":"2018","unstructured":"Blokzijl F, Janssen R, van Boxtel R, Cuppen E. MutationalPatterns: comprehensive genome-wide analysis of mutational processes. Genome Med. 2018; 10(1):33.","journal-title":"Genome Med"},{"issue":"1","key":"3043_CR12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-016-0893-4","volume":"17","author":"R Rosenthal","year":"2016","unstructured":"Rosenthal R, McGranahan N, Herrero J, Taylor BS, Swanton C. deconstructSigs: Delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 2016; 17(1):1\u201311.","journal-title":"Genome Biol"},{"issue":"2","key":"3043_CR13","doi-asserted-by":"publisher","first-page":"330","DOI":"10.1093\/bioinformatics\/btx604","volume":"34","author":"X Huang","year":"2017","unstructured":"Huang X, Wojtowicz D, Przytycka TM. Detecting Presence Of Mutational Signatures In Cancer With Confidence. Bioinformatics. 2017; 34(2):330\u20137.","journal-title":"Bioinformatics"},{"key":"3043_CR14","unstructured":"Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv. 2013. \n                    https:\/\/arxiv.org\/abs\/1303.3997\n                    \n                  ."},{"issue":"17","key":"3043_CR15","doi-asserted-by":"publisher","first-page":"2503","DOI":"10.1093\/bioinformatics\/btu314","volume":"30","author":"GG Faust","year":"2014","unstructured":"Faust GG, Hall IM. SAMBLASTER: Fast duplicate marking and structural variant read extraction. Bioinformatics. 2014; 30(17):2503\u20135.","journal-title":"Bioinformatics"},{"issue":"3","key":"3043_CR16","doi-asserted-by":"publisher","first-page":"213","DOI":"10.1038\/nbt.2514","volume":"31","author":"K Cibulskis","year":"2013","unstructured":"Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al.Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples Kristian. Nat Biotechnol. 2013; 31(3):213\u20139.","journal-title":"Nat Biotechnol"},{"issue":"4","key":"3043_CR17","doi-asserted-by":"publisher","first-page":"858","DOI":"10.1016\/j.cell.2013.10.015","volume":"155","author":"TM Kim","year":"2013","unstructured":"Kim TM, Laird PW, Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 2013; 155(4):858\u201368.","journal-title":"Cell"},{"issue":"12","key":"3043_CR18","doi-asserted-by":"publisher","first-page":"1402","DOI":"10.1038\/ng.3441","volume":"47","author":"LB Alexandrov","year":"2015","unstructured":"Alexandrov LB, Jones PH, Wedge DC, Sale JE, Peter J. Clock-like mutational processes in human somatic cells. Nat Genet. 2015; 47(12):1402\u20137.","journal-title":"Nat Genet"},{"issue":"1","key":"3043_CR19","doi-asserted-by":"publisher","first-page":"1315","DOI":"10.1038\/s41467-017-01358-x","volume":"8","author":"J Shinde","year":"2017","unstructured":"Letouz\u00e9 E, Shinde J, Renault V, Couchy G, Blanc JF, Tubacher E, et al. Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis. Nat Commun. 2017; 8(1):1315.","journal-title":"Nat Commun"},{"issue":"1","key":"3043_CR20","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1093\/bib\/bbx082","volume":"20","author":"A Baez-Ortega","year":"2019","unstructured":"Baez-Ortega A, Gori K. Computational approaches for discovery of mutational signatures in cancer. Brief Bioinforma. 2019; 20(1):77\u201388.","journal-title":"Brief Bioinforma"},{"issue":"12","key":"3043_CR21","doi-asserted-by":"publisher","first-page":"e1005657","DOI":"10.1371\/journal.pgen.1005657","volume":"11","author":"Y Shiraishi","year":"2015","unstructured":"Shiraishi Y, Tremmel G, Miyano S, Stephens M. A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures. PLoS Genet. 2015; 11(12):e1005657.","journal-title":"PLoS Genet"},{"issue":"4","key":"3043_CR22","doi-asserted-by":"publisher","first-page":"R39","DOI":"10.1186\/gb-2013-14-4-r39","volume":"14","author":"A Fischer","year":"2013","unstructured":"Fischer A, Illingworth CJ, Campbell PJ, Mustonen V. EMu: probabilistic inference of mutational processes and their localization in the cancer genome. Genome Biol. 2013; 14(4):R39.","journal-title":"Genome Biol"},{"key":"3043_CR23","doi-asserted-by":"publisher","unstructured":"Gori K, Baez-Ortega A. sigfit: flexible Bayesian inference of mutational signatures. bioRxiv. 2018. \n                    https:\/\/doi.org\/10.1101\/372896\n                    \n                  .","DOI":"10.1101\/372896"},{"key":"3043_CR24","unstructured":"R Core Team. R: A Language and Environment for Statistical Computing. Vienna; 2018. \n                    https:\/\/www.R-project.org\n                    \n                  ."},{"issue":"2","key":"3043_CR25","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/nmeth.3252","volume":"12","author":"Wolfgang Huber","year":"2015","unstructured":"Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al.Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2):115\u201321. \n                    http:\/\/www.nature.com\/nmeth\/journal\/v12\/n2\/full\/nmeth.3252.html\n                    \n                  .","journal-title":"Nature Methods"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3043-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-019-3043-7\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-019-3043-7.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T23:09:35Z","timestamp":1598915375000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-019-3043-7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,2]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2019,12]]}},"alternative-id":["3043"],"URL":"https:\/\/doi.org\/10.1186\/s12859-019-3043-7","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,9,2]]},"assertion":[{"value":"21 May 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"21 August 2019","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 September 2019","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Ethic approval was obtained by the local ethic committe of the Charit\u00e9 - Universit\u00e4tsmedizin Berlin (E A1\/265\/14). All patients gave written informed consent for sample acquisition and analyses of patient data.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"All patients gave written informed consent for publication of patient data.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"450"}}