{"id":"https://openalex.org/W6968926692","doi":"https://doi.org/10.5281/zenodo.8356171","title":"Modeling fragment counts improves single-cell ATAC-seq analysis","display_name":"Modeling fragment counts improves single-cell ATAC-seq analysis","publication_year":2023,"publication_date":"2023-09-18","ids":{"openalex":"https://openalex.org/W6968926692","doi":"https://doi.org/10.5281/zenodo.8356171"},"language":"en","primary_location":{"id":"pmh:oai:zenodo.org:8356171","is_oa":true,"landing_page_url":"https://zenodo.org/record/8356171","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"type":"other","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://zenodo.org/record/8356171","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Martens, Laura D.","orcid":"https://orcid.org/0000-0001-6520-4029"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Martens, Laura D.","raw_affiliation_strings":["Technical University Munich/Helmholtz Munich"],"affiliations":[{"raw_affiliation_string":"Technical University Munich/Helmholtz Munich","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fischer, David S.","orcid":"https://orcid.org/0000-0002-1293-7656"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Fischer, David S.","raw_affiliation_strings":["Helmholtz Munich"],"affiliations":[{"raw_affiliation_string":"Helmholtz Munich","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Y\u00e9pez, Vicente A.","orcid":"https://orcid.org/0000-0001-7916-3643"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Y\u00e9pez, Vicente A.","raw_affiliation_strings":["Technical University Munich"],"affiliations":[{"raw_affiliation_string":"Technical University Munich","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Theis, Fabian J.","orcid":"https://orcid.org/0000-0002-2419-1943"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Theis, Fabian J.","raw_affiliation_strings":["Technical University Munich/ Helmholtz Munich"],"affiliations":[{"raw_affiliation_string":"Technical University Munich/ Helmholtz Munich","institution_ids":["https://openalex.org/I3018134672"]}]},{"author_position":"last","author":{"id":null,"display_name":"Gagneur, Julien","orcid":"https://orcid.org/0000-0002-8924-8365"},"institutions":[{"id":"https://openalex.org/I3018134672","display_name":"Helmholtz Zentrum M\u00fcnchen","ror":"https://ror.org/00cfam450","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I3018134672"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Gagneur, Julien","raw_affiliation_strings":["Technical University Munich/ Helmholtz Munich"],"affiliations":[{"raw_affiliation_string":"Technical University Munich/ Helmholtz Munich","institution_ids":["https://openalex.org/I3018134672"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I3018134672"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":true,"primary_topic":null,"topics":[],"keywords":[{"id":"https://openalex.org/keywords/nucleofection","display_name":"Nucleofection","score":0.46389999985694885},{"id":"https://openalex.org/keywords/gestational-period","display_name":"Gestational period","score":0.38530001044273376},{"id":"https://openalex.org/keywords/tsg101","display_name":"TSG101","score":0.3463999927043915},{"id":"https://openalex.org/keywords/diafiltration","display_name":"Diafiltration","score":0.33250001072883606},{"id":"https://openalex.org/keywords/dysgeusia","display_name":"Dysgeusia","score":0.33239999413490295},{"id":"https://openalex.org/keywords/liquation","display_name":"Liquation","score":0.32010000944137573},{"id":"https://openalex.org/keywords/triacetin","display_name":"Triacetin","score":0.3059000074863434},{"id":"https://openalex.org/keywords/emperipolesis","display_name":"Emperipolesis","score":0.30489999055862427},{"id":"https://openalex.org/keywords/fusible-alloy","display_name":"Fusible alloy","score":0.298799991607666}],"concepts":[{"id":"https://openalex.org/C144251240","wikidata":"https://www.wikidata.org/wiki/Q7068229","display_name":"Nucleofection","level":4,"score":0.46389999985694885},{"id":"https://openalex.org/C2992336715","wikidata":"https://www.wikidata.org/wiki/Q63431143","display_name":"Gestational period","level":4,"score":0.38530001044273376},{"id":"https://openalex.org/C2778283623","wikidata":"https://www.wikidata.org/wiki/Q18032200","display_name":"TSG101","level":5,"score":0.3463999927043915},{"id":"https://openalex.org/C18743360","wikidata":"https://www.wikidata.org/wiki/Q1208096","display_name":"Diafiltration","level":4,"score":0.33250001072883606},{"id":"https://openalex.org/C2777054765","wikidata":"https://www.wikidata.org/wiki/Q6402731","display_name":"Dysgeusia","level":3,"score":0.33239999413490295},{"id":"https://openalex.org/C180938184","wikidata":"https://www.wikidata.org/wiki/Q2142270","display_name":"Liquation","level":3,"score":0.32010000944137573},{"id":"https://openalex.org/C2776781215","wikidata":"https://www.wikidata.org/wiki/Q83253","display_name":"Triacetin","level":2,"score":0.3059000074863434},{"id":"https://openalex.org/C2777968768","wikidata":"https://www.wikidata.org/wiki/Q1280161","display_name":"Emperipolesis","level":4,"score":0.30489999055862427},{"id":"https://openalex.org/C133074676","wikidata":"https://www.wikidata.org/wiki/Q428729","display_name":"Fusible alloy","level":2,"score":0.298799991607666},{"id":"https://openalex.org/C104545631","wikidata":"https://www.wikidata.org/wiki/Q464858","display_name":"Demotion","level":3,"score":0.29409998655319214},{"id":"https://openalex.org/C2777935831","wikidata":"https://www.wikidata.org/wiki/Q3144949","display_name":"Hemopericardium","level":3,"score":0.29339998960494995},{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.29170000553131104},{"id":"https://openalex.org/C2777158700","wikidata":"https://www.wikidata.org/wiki/Q1419356","display_name":"Hyporeflexia","level":3,"score":0.28949999809265137},{"id":"https://openalex.org/C135979968","wikidata":"https://www.wikidata.org/wiki/Q609809","display_name":"Protein isoform","level":5,"score":0.2858000099658966},{"id":"https://openalex.org/C2777742743","wikidata":"https://www.wikidata.org/wiki/Q19904005","display_name":"Durvalumab","level":5,"score":0.28529998660087585},{"id":"https://openalex.org/C2778843634","wikidata":"https://www.wikidata.org/wiki/Q2013780","display_name":"Ocrelizumab","level":4,"score":0.27869999408721924},{"id":"https://openalex.org/C2779645999","wikidata":"https://www.wikidata.org/wiki/Q1858477","display_name":"Frugality","level":2,"score":0.2750999927520752},{"id":"https://openalex.org/C2781032047","wikidata":"https://www.wikidata.org/wiki/Q938793","display_name":"Articular cartilage damage","level":5,"score":0.2732999920845032},{"id":"https://openalex.org/C2779627259","wikidata":"https://www.wikidata.org/wiki/Q779763","display_name":"Pretext","level":3,"score":0.2727000117301941},{"id":"https://openalex.org/C2909186138","wikidata":"https://www.wikidata.org/wiki/Q1500373","display_name":"Hyperlactatemia","level":2,"score":0.26989999413490295},{"id":"https://openalex.org/C2775917601","wikidata":"https://www.wikidata.org/wiki/Q1424050","display_name":"Sclerodactyly","level":4,"score":0.2685000002384186},{"id":"https://openalex.org/C2780904289","wikidata":"https://www.wikidata.org/wiki/Q426498","display_name":"Tantalum carbide","level":3,"score":0.2651999890804291},{"id":"https://openalex.org/C2776356786","wikidata":"https://www.wikidata.org/wiki/Q1048573","display_name":"Tubulopathy","level":3,"score":0.2581000030040741},{"id":"https://openalex.org/C2778128915","wikidata":"https://www.wikidata.org/wiki/Q3782613","display_name":"Contractualism","level":2,"score":0.2531999945640564}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:zenodo.org:8356171","is_oa":true,"landing_page_url":"https://zenodo.org/record/8356171","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},{"id":"doi:10.5281/zenodo.8356171","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.8356171","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:zenodo.org:8356171","is_oa":true,"landing_page_url":"https://zenodo.org/record/8356171","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/other"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.43684402108192444,"id":"https://metadata.un.org/sdg/17"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"ATAC-sequencing":[1],"(scATAC-seq)":[2],"coverage":[3],"in":[4],"regulatory":[5,49],"regions":[6],"is":[7,21],"typically":[8],"binarized":[9],"as":[10],"an":[11,22],"indicator":[12],"of":[13],"open":[14],"chromatin.":[15],"Here":[16],"we":[17],"show":[18],"that":[19,25],"binarization":[20],"unnecessary":[23],"step":[24],"neither":[26],"improves":[27],"goodness-of-fit,":[28],"clustering,":[29],"cell":[30],"type":[31],"identification,":[32],"nor":[33],"batch":[34],"integration.":[35],"Fragment":[36],"counts,":[37,41],"but":[38],"not":[39],"read":[40],"should":[42],"instead":[43],"be":[44],"modeled,":[45],"which":[46],"preserves":[47],"quantitative":[48],"information.":[50],"These":[51],"results":[52],"have":[53],"immediate":[54],"implications":[55],"for":[56],"scATAC-seq":[57],"analysis.":[58]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
