{"id":"https://openalex.org/W4403677401","doi":"https://doi.org/10.1371/journal.pcbi.1011971","title":"On the identification of differentially-active transcription factors from ATAC-seq data","display_name":"On the identification of differentially-active transcription factors from ATAC-seq data","publication_year":2024,"publication_date":"2024-10-23","ids":{"openalex":"https://openalex.org/W4403677401","doi":"https://doi.org/10.1371/journal.pcbi.1011971","pmid":"https://pubmed.ncbi.nlm.nih.gov/39441876"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011971","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011971","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1011971","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5094111338","display_name":"Felix Ezequiel Gerbaldo","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Felix Ezequiel Gerbaldo","raw_affiliation_strings":["Computational Neurogenomics, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Neurogenomics, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020344098","display_name":"Emanuel Sonder","orcid":"https://orcid.org/0000-0003-4788-9508"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Emanuel Sonder","raw_affiliation_strings":["Computational Neurogenomics, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland","Systems Neuroscience, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-4788-9508","affiliations":[{"raw_affiliation_string":"Computational Neurogenomics, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423"]},{"raw_affiliation_string":"Systems Neuroscience, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102993506","display_name":"Vincent Fischer","orcid":"https://orcid.org/0009-0007-7332-6182"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vincent Fischer","raw_affiliation_strings":["Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113067123","display_name":"Selina Frei","orcid":"https://orcid.org/0009-0003-2948-1733"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Selina Frei","raw_affiliation_strings":["Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000786595","display_name":"Jiayi Wang","orcid":"https://orcid.org/0009-0004-6890-4732"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Jiayi Wang","raw_affiliation_strings":["Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland"],"raw_orcid":"https://orcid.org/0009-0004-6890-4732","affiliations":[{"raw_affiliation_string":"Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070879447","display_name":"Katharina Gapp","orcid":"https://orcid.org/0000-0002-9622-1478"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Katharina Gapp","raw_affiliation_strings":["Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Epigenetics and Neuroendocrinology, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029455059","display_name":"Mark D. Robinson","orcid":"https://orcid.org/0000-0002-3048-5518"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mark D. Robinson","raw_affiliation_strings":["Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087444401","display_name":"Pierre\u2010Luc Germain","orcid":"https://orcid.org/0000-0003-3418-4218"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Pierre-Luc Germain","raw_affiliation_strings":["Computational Neurogenomics, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-3418-4218","affiliations":[{"raw_affiliation_string":"Computational Neurogenomics, D-HEST Institute for Neurosciences, Z\u00fcrich, Switzerland","institution_ids":[]},{"raw_affiliation_string":"Department of Molecular Life Sciences, University of Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics, University of Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I202697423"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5094111338"],"corresponding_institution_ids":[],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2766,"currency":"EUR","value_usd":2983},"fwci":1.0924,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.77455559,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"10","first_page":"e1011971","last_page":"e1011971"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9991000294685364,"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":0.9986000061035156,"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/computational-biology","display_name":"Computational biology","score":0.6325723528862},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5384905338287354},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5214099884033203},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.5047179460525513},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.47922641038894653},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.454792320728302},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.42790746688842773},{"id":"https://openalex.org/keywords/epigenome","display_name":"Epigenome","score":0.42049872875213623},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4189381003379822},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21046647429466248},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.09234181046485901}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6325723528862},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5384905338287354},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5214099884033203},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.5047179460525513},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.47922641038894653},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.454792320728302},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.42790746688842773},{"id":"https://openalex.org/C117717151","wikidata":"https://www.wikidata.org/wiki/Q3589155","display_name":"Epigenome","level":5,"score":0.42049872875213623},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4189381003379822},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21046647429466248},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.09234181046485901},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081204","descriptor_name":"Chromatin Immunoprecipitation Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011971","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011971","pdf_url":null,"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:39441876","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39441876","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11534267","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11534267","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11534267/pdf/pcbi.1011971.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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:e8e2afb34f544ea5840b33a014b843db","is_oa":false,"landing_page_url":"https://doaj.org/article/e8e2afb34f544ea5840b33a014b843db","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 20, Iss 10, p e1011971 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011971","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011971","pdf_url":null,"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":[{"id":"https://openalex.org/G1181015141","display_name":null,"funder_award_id":"23-2 ETH-015","funder_id":"https://openalex.org/F4320321652","funder_display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich"},{"id":"https://openalex.org/G4821378362","display_name":null,"funder_award_id":"ETH-25 02-2","funder_id":"https://openalex.org/F4320321652","funder_display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320321652","display_name":"Eidgen\u00f6ssische Technische Hochschule Z\u00fcrich","ror":"https://ror.org/05a28rw58"},{"id":"https://openalex.org/F4320335238","display_name":"Staatssekretariat f\u00fcr Bildung, Forschung und Innovation","ror":"https://ror.org/01kw63t33"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":46,"referenced_works":["https://openalex.org/W1602702667","https://openalex.org/W1971617105","https://openalex.org/W1980438612","https://openalex.org/W2014677321","https://openalex.org/W2016053674","https://openalex.org/W2052474826","https://openalex.org/W2102619694","https://openalex.org/W2107018762","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2117757143","https://openalex.org/W2120160926","https://openalex.org/W2131271579","https://openalex.org/W2135782451","https://openalex.org/W2140952049","https://openalex.org/W2146512944","https://openalex.org/W2149175672","https://openalex.org/W2170551349","https://openalex.org/W2259938310","https://openalex.org/W2472255748","https://openalex.org/W2617068500","https://openalex.org/W2620797288","https://openalex.org/W2750049634","https://openalex.org/W2750416916","https://openalex.org/W2767749844","https://openalex.org/W2772692099","https://openalex.org/W2887625843","https://openalex.org/W2945883683","https://openalex.org/W2951393041","https://openalex.org/W2953622121","https://openalex.org/W2964142306","https://openalex.org/W2993816863","https://openalex.org/W3046196569","https://openalex.org/W3049656208","https://openalex.org/W3084464257","https://openalex.org/W3099862724","https://openalex.org/W3144996175","https://openalex.org/W3161116336","https://openalex.org/W3177586536","https://openalex.org/W3182781403","https://openalex.org/W4213271427","https://openalex.org/W4214876469","https://openalex.org/W4308041337","https://openalex.org/W4395694463","https://openalex.org/W4396835129","https://openalex.org/W6785161123"],"related_works":["https://openalex.org/W3004038459","https://openalex.org/W2172945310","https://openalex.org/W4388200994","https://openalex.org/W2379997263","https://openalex.org/W1557222478","https://openalex.org/W2367493320","https://openalex.org/W2131580913","https://openalex.org/W2125854412","https://openalex.org/W3083097828","https://openalex.org/W2796029694"],"abstract_inverted_index":{"ATAC-seq":[0],"has":[1],"emerged":[2],"as":[3,71,73,86,88],"a":[4,57,117,157],"rich":[5],"epigenome":[6],"profiling":[7],"technique,":[8],"and":[9,103,116,124,141],"is":[10,41],"commonly":[11],"used":[12,27],"to":[13,28,100,160],"identify":[14,29,104],"Transcription":[15],"Factors":[16],"(TFs)":[17],"underlying":[18],"given":[19],"phenomena.":[20],"A":[21],"number":[22],"of":[23,35,59,65,84,119,133,138,144,152,167],"methods":[24,55,78,155],"can":[25,91,174],"be":[26,92],"differentially-active":[30],"TFs":[31],"through":[32],"the":[33,44,130,136,142,150,153,162,180],"accessibility":[34,166],"their":[36],"DNA-binding":[37],"motif,":[38],"however":[39],"little":[40],"known":[42,69],"on":[43,68,156,164],"best":[45],"approaches":[46,108],"for":[47,81,94],"doing":[48],"so.":[49],"Here":[50],"we":[51,148],"benchmark":[52],"several":[53],"such":[54],"using":[56],"combination":[58,118,137],"curated":[60],"datasets":[61],"with":[62,112],"various":[63],"forms":[64],"short-term":[66],"perturbations":[67],"TFs,":[70],"well":[72,87],"semi-simulations.":[74],"We":[75,96,127],"include":[76],"both":[77],"specifically":[79],"designed":[80],"this":[82],"type":[83],"data":[85],"some":[89],"that":[90],"repurposed":[93],"it.":[95],"also":[97],"investigate":[98,129],"variations":[99],"these":[101],"methods,":[102,140],"three":[105],"particularly":[106],"promising":[107],"(a":[109],"chromVAR-limma":[110],"workflow":[111],"critical":[113],"adjustments,":[114],"monaLisa":[115],"GC":[120],"smooth":[121],"quantile":[122],"normalization":[123],"multivariate":[125],"modeling).":[126],"further":[128],"specific":[131],"use":[132,151],"nucleosome-free":[134],"fragments,":[135],"top":[139,154],"impact":[143,163],"technical":[145],"variation.":[146],"Finally,":[147],"illustrate":[149],"novel":[158],"dataset":[159],"characterize":[161],"DNA":[165],"TRAnscription":[168],"Factor":[169],"TArgeting":[170],"Chimeras":[171],"(TRAFTAC),":[172],"which":[173],"deplete":[175],"TFs-in":[176],"our":[177],"case":[178],"NFkB-at":[179],"protein":[181],"level.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
