{"id":"https://openalex.org/W2509628464","doi":"https://doi.org/10.1093/bioinformatics/btw448","title":"PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments","display_name":"PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments","publication_year":2016,"publication_date":"2016-08-29","ids":{"openalex":"https://openalex.org/W2509628464","doi":"https://doi.org/10.1093/bioinformatics/btw448","mag":"2509628464","pmid":"https://pubmed.ncbi.nlm.nih.gov/27587683"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw448","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/17/i629/49022232/bioinformatics_32_17_i629.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/17/i629/49022232/bioinformatics_32_17_i629.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005255184","display_name":"Tuomo Hartonen","orcid":"https://orcid.org/0000-0002-5535-1698"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Tuomo Hartonen","raw_affiliation_strings":["Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067387478","display_name":"Biswajyoti Sahu","orcid":"https://orcid.org/0000-0001-6576-5440"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Biswajyoti Sahu","raw_affiliation_strings":["Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026539556","display_name":"Kashyap Dave","orcid":"https://orcid.org/0000-0003-0332-8362"},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Kashyap Dave","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003007386","display_name":"Teemu Kivioja","orcid":"https://orcid.org/0000-0002-7732-2177"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Teemu Kivioja","raw_affiliation_strings":["Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031611528","display_name":"Jussi Taipale","orcid":"https://orcid.org/0000-0003-4204-0951"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["FI","SE"],"is_corresponding":true,"raw_author_name":"Jussi Taipale","raw_affiliation_strings":["Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden","Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Genome-Scale Biology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5005255184","https://openalex.org/A5031611528"],"corresponding_institution_ids":["https://openalex.org/I133731052","https://openalex.org/I28166907"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.9623,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.76947589,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"32","issue":"17","first_page":"i629","last_page":"i638"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8689000010490417,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8689000010490417,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.03999999910593033,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.027899999171495438,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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"}}],"keywords":[{"id":"https://openalex.org/keywords/nexus","display_name":"Nexus (standard)","score":0.9095234870910645},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6437974572181702},{"id":"https://openalex.org/keywords/chip","display_name":"Chip","score":0.6221701502799988},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5542944669723511},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.5303317308425903},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4966481328010559},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4242524206638336},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4182828664779663},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25223201513290405},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24080580472946167},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.221491277217865},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12904095649719238},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.12498992681503296},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12476220726966858},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.10615605115890503}],"concepts":[{"id":"https://openalex.org/C148609458","wikidata":"https://www.wikidata.org/wiki/Q7021281","display_name":"Nexus (standard)","level":2,"score":0.9095234870910645},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6437974572181702},{"id":"https://openalex.org/C165005293","wikidata":"https://www.wikidata.org/wiki/Q1074500","display_name":"Chip","level":2,"score":0.6221701502799988},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5542944669723511},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5303317308425903},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4966481328010559},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4242524206638336},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4182828664779663},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25223201513290405},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24080580472946167},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.221491277217865},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12904095649719238},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.12498992681503296},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12476220726966858},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.10615605115890503},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047369","descriptor_name":"Chromatin Immunoprecipitation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056426","descriptor_name":"Genetic Loci","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btw448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw448","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/17/i629/49022232/bioinformatics_32_17_i629.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27587683","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27587683","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/17/i629","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/17/i629","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw448","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw448","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/17/i629/49022232/bioinformatics_32_17_i629.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2509628464.pdf","grobid_xml":"https://content.openalex.org/works/W2509628464.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1565385417","https://openalex.org/W1596515083","https://openalex.org/W1783785476","https://openalex.org/W1964733653","https://openalex.org/W1975036436","https://openalex.org/W1989419347","https://openalex.org/W1994122295","https://openalex.org/W2009570821","https://openalex.org/W2015416439","https://openalex.org/W2026690931","https://openalex.org/W2030209169","https://openalex.org/W2030498876","https://openalex.org/W2033781392","https://openalex.org/W2041677964","https://openalex.org/W2068379897","https://openalex.org/W2078236750","https://openalex.org/W2082414039","https://openalex.org/W2091303550","https://openalex.org/W2096482937","https://openalex.org/W2097220641","https://openalex.org/W2102619694","https://openalex.org/W2103441770","https://openalex.org/W2104865962","https://openalex.org/W2108234281","https://openalex.org/W2113312463","https://openalex.org/W2132215769","https://openalex.org/W2134199796","https://openalex.org/W2136347228","https://openalex.org/W2142808828","https://openalex.org/W2144813417","https://openalex.org/W2145091349","https://openalex.org/W2146516445","https://openalex.org/W2155718935","https://openalex.org/W2156626022","https://openalex.org/W2160444236","https://openalex.org/W2171777347","https://openalex.org/W2171808845","https://openalex.org/W2259938310","https://openalex.org/W2339240569","https://openalex.org/W2885727518","https://openalex.org/W4245668478","https://openalex.org/W6635617995"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W2367493320","https://openalex.org/W2090848290","https://openalex.org/W2131580913"],"abstract_inverted_index":{"MOTIVATION:":[0],"Transcription":[1],"factor":[2],"(TF)":[3],"binding":[4,20,30,40,67,127,192,198],"can":[5,53,173],"be":[6,174],"studied":[7],"accurately":[8],"in":[9,139,143,196],"vivo":[10,197],"with":[11,109,157,176,189],"ChIP-exo":[12,135],"and":[13,26,32,107,134,142],"ChIP-Nexus":[14,133],"experiments.":[15],"Only":[16],"fraction":[17],"of":[18,29,34,60,71,80,105,112,117,125,185,199,207],"TF":[19,66,191],"mechanisms":[21],"are":[22],"yet":[23],"fully":[24],"understood":[25],"accurate":[27],"knowledge":[28],"locations":[31],"patterns":[33],"TFs":[35],"is":[36,42,76,97,209],"key":[37],"to":[38,100,122,132,181],"understanding":[39],"that":[41,96,150],"not":[43],"explained":[44],"by":[45],"simple":[46],"positional":[47],"weight":[48],"matrix":[49],"models.":[50],"ChIP-exo/Nexus":[51,106],"experiments":[52,136],"also":[54],"offer":[55],"insight":[56],"on":[57,69,194],"the":[58,72,102,110,118,183,195,200],"effect":[59,184],"single":[61],"nucleotide":[62],"polymorphism":[63],"(SNP)":[64],"at":[65,85,211],"sites":[68],"expression":[70],"target":[73],"genes.":[74],"This":[75],"an":[77,166],"important":[78],"mechanism":[79],"action":[81],"for":[82],"disease-causing":[83],"SNPs":[84],"non-coding":[86],"genomic":[87],"regions.":[88],"RESULTS:":[89],"We":[90,129,148],"describe":[91],"a":[92,158,186,190],"peak":[93],"caller":[94],"PeakXus":[95,131,151,172,208],"specifically":[98],"designed":[99],"leverage":[101],"increased":[103],"resolution":[104],"developed":[108],"aim":[111],"making":[113],"as":[114,120],"few":[115],"assumptions":[116],"data":[119],"possible":[121],"allow":[123],"discoveries":[124],"novel":[126],"patterns.":[128],"apply":[130],"performed":[137],"both":[138],"Homo":[140],"sapiens":[141],"Drosophila":[144],"melanogaster":[145],"cell":[146],"lines.":[147],"show":[149],"consistently":[152],"finds":[153],"more":[154],"peaks":[155],"overlapping":[156,188],"TF-specific":[159],"recognition":[160],"sequence":[161],"than":[162],"published":[163],"methods.":[164],"As":[165],"application":[167],"example":[168],"we":[169],"demonstrate":[170],"how":[171],"coupled":[175],"unique":[177],"molecular":[178],"identifiers":[179],"(UMIs)":[180],"measure":[182],"SNP":[187],"site":[193],"TF.":[201],"AVAILABILITY":[202],"AND":[203],"IMPLEMENTATION:":[204],"Source":[205],"code":[206],"available":[210],"https://github.com/hartonen/PeakXus":[212],"CONTACT:":[213],"tuomo.hartonen@helsinki.fi":[214],"or":[215],"jussi.taipale@ki.se.":[216]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":4},{"year":2017,"cited_by_count":1}],"updated_date":"2026-08-10T07:06:39.071514","created_date":"2025-10-10T00:00:00"}
