{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T03:51:31Z","timestamp":1791258691649,"version":"4.1.0"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006731","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000}}],"reference-count":17,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2019,2,19]],"date-time":"2019-02-19T00:00:00Z","timestamp":1550534400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Centre for Computational Inference in Evolutionary Life Science, Faculty of Mathematics and Natural Sciences (CELS), University of Oslo, Oslo, Norway"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1006731","type":"journal-article","created":{"date-parts":[[2019,2,19]],"date-time":"2019-02-19T14:07:38Z","timestamp":1550585258000},"page":"e1006731","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":35,"title":["Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8941-942X","authenticated-orcid":true,"given":"Ivar","family":"Grytten","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Knut D.","family":"Rand","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5539-0999","authenticated-orcid":true,"given":"Alexander J.","family":"Nederbragt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8198-1426","authenticated-orcid":true,"given":"Geir O.","family":"Storvik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ingrid K.","family":"Glad","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geir K.","family":"Sandve","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,2,19]]},"reference":[{"issue":"9","key":"ref1","doi-asserted-by":"crossref","first-page":"R137","DOI":"10.1186\/gb-2008-9-9-r137","article-title":"Model-based Analysis of ChIP-Seq (MACS)","volume":"9","author":"Y Zhang","year":"2008","journal-title":"Genome Biology"},{"issue":"12","key":"ref2","doi-asserted-by":"crossref","first-page":"1351","DOI":"10.1038\/nbt.1508","article-title":"Design and Analysis of ChIP-seq Experiments for DNA-binding Proteins","volume":"26","author":"PV Kharchenko","year":"2008","journal-title":"Nature Biotechnology"},{"issue":"7","key":"ref3","doi-asserted-by":"crossref","first-page":"e11471","DOI":"10.1371\/journal.pone.0011471","article-title":"Evaluation of Algorithm Performance in ChIP-seq Peak Detection","volume":"5","author":"EG Wilbanks","year":"2010","journal-title":"PloS One"},{"issue":"5","key":"ref4","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1101\/gr.214155.116","article-title":"Genome Graphs and the Evolution of Genome Inference","volume":"27","author":"B Paten","year":"2017","journal-title":"Genome Research"},{"key":"ref5","doi-asserted-by":"crossref","unstructured":"Novak AM, Hickey G, Garrison E, Blum S, Connelly A, Dilthey A, Eizenga J, Elmohamed MS, Guthrie S, Kahles A, Keenan S. Genome Graphs. bioRxiv. 2017 Jan 1:101378.","DOI":"10.1101\/101378"},{"key":"ref6","doi-asserted-by":"crossref","unstructured":"Garrison E, Sir\u00e9n J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Lin MF, Paten B, Durbin R. Sequence Variation aware Genome References and Read Mapping with the Variation Graph Toolkit. bioRxiv. 2017 Jan 1:234856.","DOI":"10.1101\/234856"},{"key":"ref7","unstructured":"Li H. Aligning Sequence Reads, clone Sequences and Assembly Contigs with BWA-MEM. arXiv preprint arXiv:1303.3997. 2013 Mar 16."},{"issue":"4","key":"ref8","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast Gapped-read Alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nature Methods"},{"issue":"1","key":"ref9","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1186\/s12859-017-1678-9","article-title":"Coordinates and Intervals in Graph-based Reference Genomes","volume":"18","author":"KD Rand","year":"2017","journal-title":"BMC Bioinformatics"},{"issue":"6814","key":"ref10","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/35048692","article-title":"Analysis of the Genome Sequence of the flowering Plant Arabidopsis thaliana","volume":"408","year":"2000","journal-title":"Nature"},{"key":"ref11","first-page":"519","article-title":"Modern Mathematical Statistics with Applications","author":"JL Devore","year":"2012"},{"issue":"7","key":"ref12","doi-asserted-by":"crossref","first-page":"1017","DOI":"10.1093\/bioinformatics\/btr064","article-title":"FIMO: Scanning for Occurrences of a given Motif","volume":"27","author":"CE Grant","year":"2011","journal-title":"Bioinformatics"},{"issue":"7571","key":"ref13","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global Reference for Human genetic Variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"ref14","doi-asserted-by":"crossref","DOI":"10.12688\/f1000research.10041.1","article-title":"Expresso: A Database and Web Server for exploring the Interaction of Transcription Factors and their Target Genes in Arabidopsis thaliana using ChIP-Seq peak Data","volume":"6","author":"D Aghamirzaie","year":"2017","journal-title":"F1000Research"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"D91","DOI":"10.1093\/nar\/gkh012","article-title":"JASPAR: an open-access database for eukaryotic transcription factor binding profiles","volume":"32","author":"A Sandelin","year":"2004","journal-title":"Nucleic acids research"},{"key":"ref16","unstructured":"Krueger F. Trim galore. A Wrapper Tool around Cutadapt and FastQC to consistently apply Quality and Adapter trimming to FastQ files. 2015."},{"issue":"16","key":"ref17","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map Format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006731","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2019,3,1]],"date-time":"2019-03-01T00:00:00Z","timestamp":1551398400000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006731","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T16:44:55Z","timestamp":1588956295000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006731"}},"subtitle":[],"editor":[{"given":"Alice Carolyn","family":"McHardy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,2,19]]},"references-count":17,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2019,2,19]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006731","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/286823","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,2,19]]}}}