{"id":"https://openalex.org/W4200536374","doi":"https://doi.org/10.1093/bib/bbab469","title":"DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data","display_name":"DeNOPA: decoding nucleosome positions sensitively with sparse ATAC-seq data","publication_year":2021,"publication_date":"2021-10-16","ids":{"openalex":"https://openalex.org/W4200536374","doi":"https://doi.org/10.1093/bib/bbab469","pmid":"https://pubmed.ncbi.nlm.nih.gov/34875002"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab469","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab469","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101597985","display_name":"Bingxiang Xu","orcid":"https://orcid.org/0000-0001-9406-6569"},"institutions":[{"id":"https://openalex.org/I18925743","display_name":"Shanghai University of Sport","ror":"https://ror.org/0056pyw12","country_code":"CN","type":"education","lineage":["https://openalex.org/I18925743"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bingxiang Xu","raw_affiliation_strings":["CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","School of Kinesiology, Shanghai University of Sport, Shanghai, China","School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"School of Kinesiology, Shanghai University of Sport, Shanghai, China","institution_ids":["https://openalex.org/I18925743"]},{"raw_affiliation_string":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077867509","display_name":"Xiaoli Li","orcid":"https://orcid.org/0000-0001-8280-0877"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoli Li","raw_affiliation_strings":["CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087739419","display_name":"Xiaomeng Gao","orcid":"https://orcid.org/0000-0003-1717-6494"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaomeng Gao","raw_affiliation_strings":["CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010966796","display_name":"Yan Jia","orcid":"https://orcid.org/0000-0002-0769-4389"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Jia","raw_affiliation_strings":["CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056287526","display_name":"Jing Liu","orcid":"https://orcid.org/0000-0001-9050-8067"},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Liu","raw_affiliation_strings":["School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100450471","display_name":"Feifei Li","orcid":"https://orcid.org/0009-0007-0254-0368"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feifei Li","raw_affiliation_strings":["CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100393610","display_name":"Zhihua Zhang","orcid":"https://orcid.org/0000-0002-7706-9247"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I2801577699","display_name":"Beijing Institute of Genomics","ror":"https://ror.org/049gn7z52","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhihua Zhang","raw_affiliation_strings":["CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China","School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China"],"raw_orcid":"https://orcid.org/0000-0002-7706-9247","affiliations":[{"raw_affiliation_string":"CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing 100101, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I2801577699"]},{"raw_affiliation_string":"School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, P.R. China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"School of Life Science, University of Chinese Academy of Sciences, Beijing, P.R. China","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100393610","https://openalex.org/A5101597985"],"corresponding_institution_ids":["https://openalex.org/I18925743","https://openalex.org/I19820366","https://openalex.org/I2801577699","https://openalex.org/I4210165038"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.8142,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.70935002,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"23","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9987000226974487,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/nucleosome","display_name":"Nucleosome","score":0.8576911687850952},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.7615920305252075},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6006708741188049},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5127359628677368},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3269476890563965},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.25021904706954956},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.20391398668289185}],"concepts":[{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.8576911687850952},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.7615920305252075},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6006708741188049},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5127359628677368},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3269476890563965},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.25021904706954956},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.20391398668289185}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009707","descriptor_name":"Nucleosomes","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab469","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab469","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34875002","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34875002","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/11","score":0.6700000166893005,"display_name":"Sustainable cities and communities"}],"awards":[{"id":"https://openalex.org/G2130279530","display_name":null,"funder_award_id":"31671342","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2620486851","display_name":null,"funder_award_id":"91940304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3080630271","display_name":null,"funder_award_id":"2018YFC2000400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G4257951738","display_name":null,"funder_award_id":"XDA24020307","funder_id":"https://openalex.org/F4320321133","funder_display_name":"Chinese Academy of Sciences"},{"id":"https://openalex.org/G540281570","display_name":null,"funder_award_id":"31871331","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6705445272","display_name":null,"funder_award_id":"Z200021","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"},{"id":"https://openalex.org/G777936316","display_name":null,"funder_award_id":"2019FY100102","funder_id":"https://openalex.org/F4320322919","funder_display_name":"Natural Science Foundation of Beijing Municipality"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320322919","display_name":"Natural Science Foundation of Beijing Municipality","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":83,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W1602702667","https://openalex.org/W1937291806","https://openalex.org/W1971615450","https://openalex.org/W1992005588","https://openalex.org/W1995360258","https://openalex.org/W1996270170","https://openalex.org/W1997519837","https://openalex.org/W2008226163","https://openalex.org/W2014002637","https://openalex.org/W2014119967","https://openalex.org/W2014677321","https://openalex.org/W2016597274","https://openalex.org/W2018363492","https://openalex.org/W2023350320","https://openalex.org/W2037777253","https://openalex.org/W2042450235","https://openalex.org/W2042930277","https://openalex.org/W2049361027","https://openalex.org/W2064537118","https://openalex.org/W2069545688","https://openalex.org/W2072152932","https://openalex.org/W2080569293","https://openalex.org/W2080641060","https://openalex.org/W2086038224","https://openalex.org/W2090098862","https://openalex.org/W2092394310","https://openalex.org/W2093146349","https://openalex.org/W2093304538","https://openalex.org/W2095881412","https://openalex.org/W2099397128","https://openalex.org/W2106448802","https://openalex.org/W2110065044","https://openalex.org/W2111353388","https://openalex.org/W2111607063","https://openalex.org/W2117757143","https://openalex.org/W2118661197","https://openalex.org/W2122780133","https://openalex.org/W2126888219","https://openalex.org/W2129633222","https://openalex.org/W2131192238","https://openalex.org/W2136144150","https://openalex.org/W2140783715","https://openalex.org/W2154077612","https://openalex.org/W2154109129","https://openalex.org/W2168333121","https://openalex.org/W2171432823","https://openalex.org/W2232899585","https://openalex.org/W2259938310","https://openalex.org/W2264592275","https://openalex.org/W2269478656","https://openalex.org/W2293206103","https://openalex.org/W2514448720","https://openalex.org/W2553449527","https://openalex.org/W2582450548","https://openalex.org/W2583735774","https://openalex.org/W2587862433","https://openalex.org/W2598674694","https://openalex.org/W2621109613","https://openalex.org/W2736547131","https://openalex.org/W2743018412","https://openalex.org/W2745967441","https://openalex.org/W2750416916","https://openalex.org/W2765843788","https://openalex.org/W2790768464","https://openalex.org/W2893467866","https://openalex.org/W2949460676","https://openalex.org/W2950842418","https://openalex.org/W2951054376","https://openalex.org/W2951644416","https://openalex.org/W2952339916","https://openalex.org/W2953311893","https://openalex.org/W2965805195","https://openalex.org/W2965985232","https://openalex.org/W2979464975","https://openalex.org/W2989837622","https://openalex.org/W2995813779","https://openalex.org/W3007825745","https://openalex.org/W3087671657","https://openalex.org/W3187014282","https://openalex.org/W4247545505","https://openalex.org/W6770304583","https://openalex.org/W6782961268"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W4225831698","https://openalex.org/W3198436517"],"abstract_inverted_index":{"As":[0],"the":[1,4,11,60,72,124,136,152,163,185,198,219],"basal":[2],"bricks,":[3],"dynamics":[5,186,220],"and":[6,54,139,161,173],"arrangement":[7,61],"of":[8,14,62,119,132,187,221],"nucleosomes":[9,63],"orchestrate":[10],"higher":[12],"architecture":[13],"chromatin":[15,36,195,222],"in":[16,135,197],"a":[17,45,67,77,212],"fundamental":[18],"way,":[19],"thereby":[20],"affecting":[21],"almost":[22],"all":[23],"nuclear":[24],"biology":[25],"processes.":[26],"Thanks":[27],"to":[28,58,92,205,217],"its":[29],"rather":[30],"simple":[31],"protocol,":[32],"assay":[33],"for":[34,48],"transposase-accessible":[35],"using":[37,176,180],"sequencing":[38],"(ATAC)-seq":[39],"has":[40],"been":[41],"rapidly":[42],"adopted":[43],"as":[44],"major":[46],"tool":[47,214],"chromatin-accessible":[49],"profiling":[50],"at":[51,223],"both":[52,171],"bulk":[53],"single-cell":[55],"levels;":[56],"however,":[57],"picture":[59],"per":[64,113],"se":[65],"remains":[66],"challenge":[68],"with":[69,103,194,215,227],"ATAC-seq.":[70],"In":[71],"present":[73],"work,":[74],"we":[75,149,182],"introduce":[76],"novel":[78],"ATAC-seq":[79,89,105,137,229],"analysis":[80],"toolkit,":[81],"named":[82],"decoding":[83],"nucleosome":[84,94,145,159,188,224],"organization":[85,189],"profile":[86],"based":[87],"on":[88,158],"data":[90],"(deNOPA),":[91],"predict":[93],"positions.":[95],"Assessments":[96],"showed":[97,183],"that":[98,151,162,184],"deNOPA":[99,120,210],"outperformed":[100],"state-of-the-art":[101,144],"tools":[102],"ultra-sparse":[104,228],"data,":[106],"e.g.":[107],"no":[108],"more":[109],"than":[110],"0.5":[111],"fragment":[112,126,154],"base":[114],"pair.":[115],"The":[116],"remarkable":[117],"performance":[118],"was":[121],"fueled":[122],"by":[123,143,168],"short":[125,153,172],"reads,":[127],"which":[128,216],"compose":[129],"nearly":[130],"half":[131],"sequenced":[133],"reads":[134,155,169],"libraries":[138],"are":[140],"commonly":[141],"discarded":[142],"positioning":[146],"tools.":[147],"However,":[148],"found":[150],"enrich":[156],"information":[157],"positions":[160],"linker":[164],"regions":[165,200],"were":[166],"predicted":[167],"from":[170],"long":[174],"fragments":[175],"Gaussian":[177],"smoothing.":[178],"Last,":[179],"deNOPA,":[181],"may":[190],"not":[191],"directly":[192],"couple":[193],"accessibility":[196],"cis-regulatory":[199],"when":[201],"human":[202],"cells":[203],"respond":[204],"heat":[206],"shock":[207],"stimulation.":[208],"Our":[209],"provides":[211],"powerful":[213],"analyze":[218],"position":[225],"level":[226],"data.":[230]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}