{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T20:44:12Z","timestamp":1783025052283,"version":"3.54.6"},"reference-count":36,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2019,4,2]],"date-time":"2019-04-02T00:00:00Z","timestamp":1554163200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100008730","name":"Kreftforeningen","doi-asserted-by":"publisher","award":["DNK 2192630-2014-33518"],"award-info":[{"award-number":["DNK 2192630-2014-33518"]}],"id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008730","name":"Kreftforeningen","doi-asserted-by":"publisher","award":["DNK 2192630-2013-33463"],"award-info":[{"award-number":["DNK 2192630-2013-33463"]}],"id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008730","name":"Kreftforeningen","doi-asserted-by":"publisher","award":["DNK 2192630-2012-33376"],"award-info":[{"award-number":["DNK 2192630-2012-33376"]}],"id":[{"id":"10.13039\/100008730","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006095","name":"Helse S\u00f8r-\u00d8st RHF","doi-asserted-by":"publisher","award":["HS\u00d8 2017061"],"award-info":[{"award-number":["HS\u00d8 2017061"]}],"id":[{"id":"10.13039\/501100006095","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006095","name":"Helse S\u00f8r-\u00d8st RHF","doi-asserted-by":"publisher","award":["HS\u00d8 2018107"],"award-info":[{"award-number":["HS\u00d8 2018107"]}],"id":[{"id":"10.13039\/501100006095","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Genet."],"DOI":"10.3389\/fgene.2019.00282","type":"journal-article","created":{"date-parts":[[2019,4,2]],"date-time":"2019-04-02T04:16:35Z","timestamp":1554178595000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["BayesPI-BAR2: A New Python Package for Predicting Functional Non-coding Mutations in Cancer Patient Cohorts"],"prefix":"10.3389","volume":"10","author":[{"given":"Kirill","family":"Batmanov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Delabie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junbai","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2019,4,2]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nature12477","article-title":"Signatures of mutational processes in human cancer.","volume":"500","author":"Alexandrov","year":"2013","journal-title":"Nature"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms10001","article-title":"A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.","volume":"6","author":"Alioto","year":"2015","journal-title":"Nat. Commun."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.3390\/genes8090233","article-title":"Predicting variation of DNA shape preferences in protein-DNA interaction in cancer cells with a new biophysical model.","volume":"8","author":"Batmanov","year":"2017","journal-title":"Genes"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-017-07226-4","article-title":"Integrative whole-genome sequence analysis reveals roles of regulatory mutations in BCL6 and BCL2 in follicular lymphoma.","volume":"7","author":"Batmanov","year":"2017","journal-title":"Sci. Rep."},{"key":"B5","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate - a practical and powerful approach to multiple testing.","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B Methodol."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1186\/1471-2105-9-114","article-title":"The control of the false discovery rate in multiple testing under dependency.","volume":"29","author":"Benjamini","year":"2001","journal-title":"Ann. Stat."},{"key":"B7","doi-asserted-by":"publisher","first-page":"2282","DOI":"10.1007\/s11999-008-0346-9","article-title":"Statistics in brief: the importance of sample size in the planning and interpretation of medical research.","volume":"466","author":"Biau","year":"2008","journal-title":"Clin. Orthopaedics Relat. Res."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments.","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"1428","DOI":"10.1038\/ng.3950","article-title":"Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.","volume":"49","author":"Cao","year":"2017","journal-title":"Nat. Genetics"},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-017-1266-3","article-title":"Identification of novel prostate cancer drivers using RegNetDriver: a framework for integration of genetic and epigenetic alterations with tissue-specific regulatory network.","volume":"18","author":"Dhingra","year":"2017","journal-title":"Genome Biol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"2381","DOI":"10.1101\/gr.1271603","article-title":"A biophysical approach to transcription factor binding site discovery.","volume":"13","author":"Djordjevic","year":"2003","journal-title":"Genome Res."},{"key":"B12","doi-asserted-by":"publisher","first-page":"2912","DOI":"10.18632\/oncotarget.2048","article-title":"A highly recurrent RPS27 5\u2032 UTR mutation in melanoma.","volume":"5","author":"Dutton-Regester","year":"2014","journal-title":"Oncotarget"},{"key":"B13","doi-asserted-by":"publisher","first-page":"e141","DOI":"10.1093\/bioinformatics\/btl223","article-title":"Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.","volume":"22","author":"Foat","year":"2006","journal-title":"Bioinformatics"},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1006773","article-title":"Recurrent promoter mutations in melanoma are defined by an extended context-specific mutational signature.","volume":"13","author":"Fredriksson","year":"2017","journal-title":"PLoS Genet."},{"key":"B15","doi-asserted-by":"publisher","first-page":"150","DOI":"10.1016\/j.tem.2007.03.002","article-title":"ETS transcription factors in endocrine systems.","volume":"18","author":"Gutierrez-Hartmann","year":"2007","journal-title":"Trends Endocrinol. Metab."},{"key":"B16","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1016\/j.dib.2014.09.002","article-title":"Data set for the genome-wide transcriptome analysis of human epidermal melanocytes.","volume":"1","author":"Haltaufderhyde","year":"2014","journal-title":"Data Brief"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for The ENCODE Project.","volume":"22","author":"Harrow","year":"2012","journal-title":"Genome Res."},{"key":"B18","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.cell.2012.06.024","article-title":"A landscape of driver mutations in melanoma.","volume":"150","author":"Hodis","year":"2012","journal-title":"Cell"},{"key":"B19","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1126\/science.1229259","article-title":"Highly recurrent TERT promoter mutations in human melanoma.","volume":"339","author":"Huang","year":"2013","journal-title":"Science"},{"key":"B20","doi-asserted-by":"publisher","first-page":"2976","DOI":"10.1093\/nar\/gkt1249","article-title":"Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments.","volume":"42","author":"Kheradpour","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"B21","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nrg.2015.17","article-title":"Role of non-coding sequence variants in cancer.","volume":"17","author":"Khurana","year":"2016","journal-title":"Nat. Rev. Genet."},{"key":"B22","doi-asserted-by":"publisher","first-page":"D896","DOI":"10.1093\/nar\/gkw1133","article-title":"The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog).","volume":"45","author":"MacArthur","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"B23","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1016\/j.celrep.2013.12.027","article-title":"Genetics of follicular lymphoma transformation.","volume":"6","author":"Pasqualucci","year":"2014","journal-title":"Cell Rep."},{"key":"B24","doi-asserted-by":"publisher","first-page":"1218","DOI":"10.1158\/1541-7786.MCR-15-0146","article-title":"Systematic screening of promoter regions pinpoints functional cis-regulatory mutations in a cutaneous melanoma genome.","volume":"13","author":"Poulos","year":"2015","journal-title":"Mol. Cancer Res."},{"key":"B25","doi-asserted-by":"publisher","first-page":"786","DOI":"10.1038\/nrc3816","article-title":"Hypermutation in human cancer genomes: footprints and mechanisms.","volume":"14","author":"Roberts","year":"2014","journal-title":"Nat. Rev. Cancer"},{"key":"B26","doi-asserted-by":"publisher","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the catalogue of somatic mutations in cancer.","volume":"47","author":"Tate","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-15-289","article-title":"Quality versus accuracy: result of a reanalysis of protein-binding microarrays from the DREAM5 challenge by using BayesPI2 including dinucleotide interdependence.","volume":"15","author":"Wang","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"B28","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv733","article-title":"BayesPI-BAR: a new biophysical model for characterization of regulatory sequence variations.","volume":"43","author":"Wang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-16-S7-S12","article-title":"Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation.","volume":"16","author":"Wang","year":"2015","journal-title":"BMC Genomics"},{"key":"B30","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-10-345","article-title":"BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.","volume":"10","author":"Wang","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-14-70","article-title":"Genome-wide analysis uncovers high frequency, strong differential chromosomal interactions and their associated epigenetic patterns in E2-mediated gene regulation.","volume":"14","author":"Wang","year":"2013","journal-title":"BMC Genomics"},{"key":"B32","doi-asserted-by":"publisher","first-page":"1160","DOI":"10.1038\/ng.3101","article-title":"Genome-wide analysis of noncoding regulatory mutations in cancer.","volume":"46","author":"Weinhold","year":"2014","journal-title":"Nat. Genet."},{"key":"B33","article-title":"The Wilcoxon rank-sum test","author":"Wild","year":"2011","journal-title":"Chance Encounters: A First Course in Data Analysis and Inference"},{"key":"B34","doi-asserted-by":"publisher","first-page":"490","DOI":"10.1093\/bioinformatics\/btv565","article-title":"GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.","volume":"32","author":"Zeng","year":"2016","journal-title":"Bioinformatics"},{"key":"B35","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1038\/s41588-018-0295-5","article-title":"A primer on deep learning in genomics.","volume":"51","author":"Zou","year":"2018","journal-title":"Nat. Genet."},{"key":"B36","doi-asserted-by":"publisher","first-page":"3353","DOI":"10.1093\/bioinformatics\/btv328","article-title":"atSNP: transcription factor binding affinity testing for regulatory SNP detection.","volume":"31","author":"Zuo","year":"2015","journal-title":"Bioinformatics"}],"container-title":["Frontiers in Genetics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2019.00282\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,4,2]],"date-time":"2019-04-02T04:16:37Z","timestamp":1554178597000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fgene.2019.00282\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,2]]},"references-count":36,"alternative-id":["10.3389\/fgene.2019.00282"],"URL":"https:\/\/doi.org\/10.3389\/fgene.2019.00282","relation":{},"ISSN":["1664-8021"],"issn-type":[{"value":"1664-8021","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,2]]},"article-number":"282"}}