{"id":"https://openalex.org/W4323319448","doi":"https://doi.org/10.1186/s12859-023-05184-5","title":"RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data","display_name":"RGT: a toolbox for the integrative analysis of high throughput regulatory genomics data","publication_year":2023,"publication_date":"2023-03-06","ids":{"openalex":"https://openalex.org/W4323319448","doi":"https://doi.org/10.1186/s12859-023-05184-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/36879236"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-023-05184-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05184-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05184-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05184-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100415193","display_name":"Zhijian Li","orcid":"https://orcid.org/0000-0002-1523-1333"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Zhijian Li","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany. zhijian.li@rwth-aachen.de","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany. zhijian.li@rwth-aachen.de","Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany. zhijian.li@rwth-aachen.de","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany. zhijian.li@rwth-aachen.de","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081112159","display_name":"Chao\u2010Chung Kuo","orcid":"https://orcid.org/0000-0001-8879-4754"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Chao-Chung Kuo","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071183779","display_name":"Fabio Ticconi","orcid":"https://orcid.org/0000-0001-8905-6657"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fabio Ticconi","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074789542","display_name":"Mina Shaigan","orcid":"https://orcid.org/0000-0003-1719-9944"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mina Shaigan","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049862200","display_name":"Julia Gehrmann","orcid":"https://orcid.org/0000-0002-4101-5458"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Julia Gehrmann","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030617406","display_name":"Eduardo Gade Gusmao","orcid":"https://orcid.org/0000-0001-7461-1443"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Eduardo Gade Gusmao","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067067865","display_name":"Manuel Allhoff","orcid":null},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Manuel Allhoff","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081005143","display_name":"Martin Manolov","orcid":null},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Manolov","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004290451","display_name":"Martin Zenke","orcid":"https://orcid.org/0000-0002-1107-3251"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Zenke","raw_affiliation_strings":["Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany","Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, 52074, Aachen, Germany","Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Institute of Biomedical Engineering, RWTH Aachen University Medical School, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057250270","display_name":"Ivan G. Costa","orcid":"https://orcid.org/0000-0003-2890-8697"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ivan G. Costa","raw_affiliation_strings":["Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany. ivan.costa@rwth-aachen.de","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany. ivan.costa@rwth-aachen.de","Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany. ivan.costa@rwth-aachen.de","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany. ivan.costa@rwth-aachen.de","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, 52074, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5100415193"],"corresponding_institution_ids":["https://openalex.org/I887968799"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":3.1981,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.92009848,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"24","issue":"1","first_page":"79","last_page":"79"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.98580002784729,"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":0.98580002784729,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.0013000000035390258,"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/T10604","display_name":"RNA Research and Splicing","score":0.0010999999940395355,"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/toolbox","display_name":"Toolbox","score":0.7623798847198486},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.6299413442611694},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.61025071144104},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5299521684646606},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5185883045196533},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4458615183830261},{"id":"https://openalex.org/keywords/functional-genomics","display_name":"Functional genomics","score":0.43298426270484924},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4197118282318115},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.416547954082489},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2918189764022827},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.22891128063201904},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2019818127155304},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11820381879806519},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.0785856544971466}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.7623798847198486},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6299413442611694},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.61025071144104},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5299521684646606},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5185883045196533},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4458615183830261},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.43298426270484924},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4197118282318115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.416547954082489},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2918189764022827},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.22891128063201904},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2019818127155304},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11820381879806519},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.0785856544971466},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-023-05184-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05184-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05184-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36879236","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36879236","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9990262","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9990262","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9990262/pdf/12859_2023_Article_5184.pdf","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":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ebd553fe4f374c11b81204a9c95da07a","is_oa":true,"landing_page_url":"https://doaj.org/article/ebd553fe4f374c11b81204a9c95da07a","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":"BMC Bioinformatics, Vol 24, Iss 1, Pp 1-12 (2023)","raw_type":"article"},{"id":"doi:10.18154/rwth-2023-03052","is_oa":true,"landing_page_url":"https://doi.org/10.18154/rwth-2023-03052","pdf_url":null,"source":{"id":"https://openalex.org/S4306401033","display_name":"RWTH Publications (RWTH Aachen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887968799","host_organization_name":"RWTH Aachen University","host_organization_lineage":["https://openalex.org/I887968799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s12859-023-05184-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-023-05184-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-023-05184-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324232","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4323319448.pdf"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1545656771","https://openalex.org/W1964951991","https://openalex.org/W1966278477","https://openalex.org/W2033781392","https://openalex.org/W2035769168","https://openalex.org/W2059604791","https://openalex.org/W2071206791","https://openalex.org/W2092988184","https://openalex.org/W2099698839","https://openalex.org/W2100061607","https://openalex.org/W2103441770","https://openalex.org/W2115789198","https://openalex.org/W2117757143","https://openalex.org/W2124163981","https://openalex.org/W2131478115","https://openalex.org/W2140952049","https://openalex.org/W2140966642","https://openalex.org/W2161849959","https://openalex.org/W2167967077","https://openalex.org/W2169353679","https://openalex.org/W2171111703","https://openalex.org/W2207263671","https://openalex.org/W2280567170","https://openalex.org/W2341539131","https://openalex.org/W2486498812","https://openalex.org/W2767749844","https://openalex.org/W2898215009","https://openalex.org/W2907027444","https://openalex.org/W2912031480","https://openalex.org/W2925775506","https://openalex.org/W3025098045","https://openalex.org/W3080775827","https://openalex.org/W3104377313","https://openalex.org/W3113079251","https://openalex.org/W3119774682","https://openalex.org/W3131055609","https://openalex.org/W3131443014","https://openalex.org/W3199543973","https://openalex.org/W3207946156","https://openalex.org/W3208967609","https://openalex.org/W3212537999","https://openalex.org/W3215596355","https://openalex.org/W4247053599","https://openalex.org/W4290989128","https://openalex.org/W4291710954","https://openalex.org/W4311362568","https://openalex.org/W4324129565"],"related_works":["https://openalex.org/W2360935227","https://openalex.org/W2364993072","https://openalex.org/W2115576822","https://openalex.org/W2356429006","https://openalex.org/W2380568150","https://openalex.org/W2385787406","https://openalex.org/W2155595079","https://openalex.org/W4362472570","https://openalex.org/W2263355832","https://openalex.org/W284518807"],"abstract_inverted_index":{"BACKGROUND:":[0],"Massive":[1],"amounts":[2],"of":[3,28,75,104,113,121,149],"data":[4,31,54,155,175],"are":[5,40],"produced":[6],"by":[7],"combining":[8],"next-generation":[9],"sequencing":[10],"with":[11],"complex":[12],"biochemistry":[13],"techniques":[14],"to":[15,51,83,96,145,152],"characterize":[16],"regulatory":[17,76,136,158,173],"genomics":[18,77,159,174],"profiles,":[19],"such":[20,29],"as":[21],"protein-DNA":[22],"interaction":[23],"and":[24,87,119,126,130,165,176],"chromatin":[25],"accessibility.":[26],"Interpretation":[27],"high-throughput":[30],"typically":[32],"requires":[33],"different":[34,81],"computation":[35],"methods.":[36],"However,":[37],"existing":[38],"tools":[39,95],"usually":[41],"developed":[42,93],"for":[43,71,156,169],"a":[44,68,143,163],"specific":[45,157],"task,":[46],"which":[47],"makes":[48],"it":[49],"challenging":[50],"analyze":[52,153],"the":[53,63,72,102,147],"in":[55],"an":[56,132],"integrative":[57,73],"manner.":[58],"RESULTS:":[59],"We":[60,139],"here":[61,141],"describe":[62],"Regulatory":[64],"Genomics":[65],"Toolbox":[66],"(RGT),":[67],"computational":[69,150],"library":[70],"analysis":[74],"data.":[78],"RGT":[79,161],"provides":[80],"functionalities":[82],"handle":[84],"genomic":[85,154],"signals":[86],"regions.":[88],"Based":[89],"on":[90],"that,":[91],"we":[92],"several":[94],"perform":[97],"distinct":[98,135],"downstream":[99],"analyses,":[100],"including":[101],"prediction":[103],"transcription":[105],"factor":[106],"binding":[107],"sites":[108],"using":[109],"ATAC-seq":[110],"data,":[111,118],"identification":[112],"differential":[114],"peaks":[115],"from":[116],"ChIP-seq":[117],"detection":[120],"triple":[122],"helix":[123],"mediated":[124],"RNA":[125],"DNA":[127],"interactions,":[128],"visualization,":[129],"finding":[131],"association":[133],"between":[134],"factors.":[137],"CONCLUSION:":[138],"present":[140],"RGT;":[142],"framework":[144],"facilitate":[146],"customization":[148],"methods":[151],"problems.":[160],"is":[162,177,184],"comprehensive":[164],"flexible":[166],"Python":[167],"package":[168],"analyzing":[170],"high":[171],"throughput":[172],"available":[178,185],"at:":[179,186],"https://github.com/CostaLab/reg-gen":[180],".":[181],"The":[182],"documentation":[183],"https://reg-gen.readthedocs.io.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2023-03-07T00:00:00"}