{"id":"https://openalex.org/W2953162397","doi":"https://doi.org/10.1371/journal.pcbi.1006731","title":"Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes","display_name":"Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes","publication_year":2019,"publication_date":"2019-02-19","ids":{"openalex":"https://openalex.org/W2953162397","doi":"https://doi.org/10.1371/journal.pcbi.1006731","mag":"2953162397","pmid":"https://pubmed.ncbi.nlm.nih.gov/30779737"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1006731","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006731","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006731&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006731&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055428069","display_name":"Ivar Grytten","orcid":"https://orcid.org/0000-0001-8941-942X"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ivar Grytten","raw_affiliation_strings":["Department of informatics, University of Oslo, Oslo, Norway"],"raw_orcid":"https://orcid.org/0000-0001-8941-942X","affiliations":[{"raw_affiliation_string":"Department of informatics, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035654730","display_name":"Knut Dagestad Rand","orcid":"https://orcid.org/0000-0003-3359-7619"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Knut D. Rand","raw_affiliation_strings":["Department of Mathematics, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065448492","display_name":"Alexander J. Nederbragt","orcid":"https://orcid.org/0000-0001-5539-0999"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Alexander J. Nederbragt","raw_affiliation_strings":["Department of Biosciences, University of Oslo, Oslo, Norway","Department of informatics, University of Oslo, Oslo, Norway"],"raw_orcid":"https://orcid.org/0000-0001-5539-0999","affiliations":[{"raw_affiliation_string":"Department of Biosciences, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]},{"raw_affiliation_string":"Department of informatics, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011128600","display_name":"Geir Storvik","orcid":"https://orcid.org/0000-0001-8198-1426"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Geir O. Storvik","raw_affiliation_strings":["Department of Mathematics, University of Oslo, Oslo, Norway"],"raw_orcid":"https://orcid.org/0000-0001-8198-1426","affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077821870","display_name":"Ingrid K. Glad","orcid":"https://orcid.org/0000-0002-5156-7109"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Ingrid K. Glad","raw_affiliation_strings":["Department of Mathematics, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054500587","display_name":"Geir Kjetil Sandve","orcid":"https://orcid.org/0000-0002-4959-1409"},"institutions":[{"id":"https://openalex.org/I184942183","display_name":"University of Oslo","ror":"https://ror.org/01xtthb56","country_code":"NO","type":"education","lineage":["https://openalex.org/I184942183"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Geir K. Sandve","raw_affiliation_strings":["Department of informatics, University of Oslo, Oslo, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of informatics, University of Oslo, Oslo, Norway","institution_ids":["https://openalex.org/I184942183"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5055428069"],"corresponding_institution_ids":["https://openalex.org/I184942183"],"apc_list":{"value":2350,"currency":"USD","value_usd":2350},"apc_paid":{"value":2350,"currency":"USD","value_usd":2350},"fwci":1.7151,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.84684961,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"15","issue":"2","first_page":"e1006731","last_page":"e1006731"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9961000084877014,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.6809059381484985},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6002110242843628},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5903844237327576},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.5322473049163818},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3656150698661804},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3650102913379669},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3083818256855011},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26472336053848267},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2173670530319214}],"concepts":[{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.6809059381484985},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6002110242843628},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5903844237327576},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.5322473049163818},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3656150698661804},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3650102913379669},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3083818256855011},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26472336053848267},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2173670530319214}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011485","descriptor_name":"Protein Binding","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1371/journal.pcbi.1006731","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006731","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006731&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:30779737","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30779737","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:5395126","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6396939","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6396939","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6396939","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:50eeba364f0a42efaa678aaba9fb19e4","is_oa":true,"landing_page_url":"https://doaj.org/article/50eeba364f0a42efaa678aaba9fb19e4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 15, Iss 2, p e1006731 (2019)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/7742330","is_oa":true,"landing_page_url":"https://figshare.com/articles/dataset/Graph_Peak_Caller_Calling_ChIP-seq_peaks_on_graph-based_reference_genomes/7742330","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Dataset"},{"id":"pmh:oai:www.duo.uio.no:10852/76717","is_oa":true,"landing_page_url":"http://hdl.handle.net/10852/76717","pdf_url":null,"source":{"id":"https://openalex.org/S7407064446","display_name":"NORA - Norwegian Open Research Archives","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"1553-734X","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1006731","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1006731","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1006731&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953162397.pdf","grobid_xml":"https://content.openalex.org/works/W2953162397.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1494075612","https://openalex.org/W1557976950","https://openalex.org/W2044164623","https://openalex.org/W2084620487","https://openalex.org/W2095680943","https://openalex.org/W2102904139","https://openalex.org/W2104549677","https://openalex.org/W2108234281","https://openalex.org/W2140952049","https://openalex.org/W2170551349","https://openalex.org/W2171808845","https://openalex.org/W2599090528","https://openalex.org/W2603734366","https://openalex.org/W2614266827","https://openalex.org/W2776539412","https://openalex.org/W4210922477","https://openalex.org/W4235690512","https://openalex.org/W6633205067"],"related_works":["https://openalex.org/W2279684808","https://openalex.org/W3137911940","https://openalex.org/W3217304749","https://openalex.org/W2894932706","https://openalex.org/W2066142713","https://openalex.org/W2767606877","https://openalex.org/W3140471545","https://openalex.org/W2582968398","https://openalex.org/W4223446368","https://openalex.org/W4232517363"],"abstract_inverted_index":{"Graph-based":[0],"representations":[1],"are":[2,129,143],"considered":[3],"to":[4,40,68,101],"be":[5],"the":[6,17,41,80,97,133],"future":[7],"for":[8,60],"reference":[9,33,71,121,135],"genomes,":[10,34],"as":[11,44,46],"they":[12],"allow":[13,27],"integrated":[14],"representation":[15,43],"of":[16,31,36,79,105,132],"steadily":[18],"increasing":[19],"data":[20,66],"on":[21,64],"individual":[22],"variation.":[23],"Currently":[24],"available":[25],"tools":[26],"de":[28],"novo":[29],"assembly":[30],"graph-based":[32,70],"alignment":[35],"new":[37],"read":[38,65],"sets":[39],"graph":[42,77,122],"well":[45],"certain":[47],"analyses":[48],"like":[49],"variant":[50],"calling":[51,61],"and":[52,84,137],"haplotyping.":[53],"We":[54],"here":[55],"present":[56],"a":[57,69,76,103,119],"first":[58],"method":[59,74],"ChIP-Seq":[62],"peaks":[63,127,139],"aligned":[67],"genome.":[72],"The":[73],"is":[75,85],"generalization":[78],"peak":[81],"caller":[82],"MACS2,":[83],"implemented":[86],"in":[87,141],"an":[88],"open":[89],"source":[90],"tool,":[91],"Graph":[92,115],"Peak":[93,116],"Caller.":[94],"By":[95],"using":[96],"existing":[98],"tool":[99],"vg":[100],"build":[102],"pan-genome":[104,120],"Arabidopsis":[106],"thaliana,":[107],"we":[108],"validate":[109],"our":[110],"approach":[111],"by":[112,149],"showing":[113],"that":[114,128,140],"Caller":[117],"with":[118],"can":[123],"trace":[124],"variants":[125],"within":[126],"not":[130],"part":[131],"linear":[134],"genome,":[136],"find":[138],"general":[142],"more":[144],"motif-enriched":[145],"than":[146],"those":[147],"found":[148],"MACS2.":[150]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":12},{"year":2020,"cited_by_count":5}],"updated_date":"2026-09-11T09:22:31.653822","created_date":"2025-10-10T00:00:00"}
