{"id":"https://openalex.org/W7135390696","doi":"https://doi.org/10.1093/bioinformatics/btag110","title":"Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches","display_name":"Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches","publication_year":2026,"publication_date":"2026-02-28","ids":{"openalex":"https://openalex.org/W7135390696","doi":"https://doi.org/10.1093/bioinformatics/btag110","pmid":"https://pubmed.ncbi.nlm.nih.gov/41826793"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag110","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bioinformatics/btag110","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5129135303","display_name":"Brydon P G Wall","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brydon P G Wall","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016013375","display_name":"Jonathan Ogata","orcid":"https://orcid.org/0000-0002-8082-7395"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan D Ogata","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039697461","display_name":"Matthew Nguyen","orcid":"https://orcid.org/0000-0001-8826-8658"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"My Nguyen","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000376105","display_name":"Amy L. Olex","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Amy L Olex","raw_affiliation_strings":["C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"C. Kenneth and Diane Wright Center for Clinical and Translational Research, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049700214","display_name":"Konstantinos V. Floros","orcid":"https://orcid.org/0000-0003-4916-2257"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Konstantinos V Floros","raw_affiliation_strings":["Department of Pediatrics, Virginia Commonwealth University , Richmond, VA 23298,","VCU Philips Institute, Virginia Commonwealth University School of Dentistry and Massey Comprehensive Cancer Center , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"VCU Philips Institute, Virginia Commonwealth University School of Dentistry and Massey Comprehensive Cancer Center , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054248424","display_name":"Anthony C. Faber","orcid":"https://orcid.org/0000-0002-7246-4272"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anthony C Faber","raw_affiliation_strings":["Department of Pediatrics, Virginia Commonwealth University , Richmond, VA 23298,","VCU Philips Institute, Virginia Commonwealth University School of Dentistry and Massey Comprehensive Cancer Center , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"VCU Philips Institute, Virginia Commonwealth University School of Dentistry and Massey Comprehensive Cancer Center , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048505341","display_name":"Joseph L. McClay","orcid":"https://orcid.org/0000-0002-3628-2447"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joseph L McClay","raw_affiliation_strings":["Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Pharmacotherapy and Outcomes Science, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5129199146","display_name":"J Chuck Harrell","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J Chuck Harrell","raw_affiliation_strings":["Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284,","Massey Comprehensive Cancer Center, Virginia Commonwealth University , Richmond, VA 23298,"],"affiliations":[{"raw_affiliation_string":"Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284,","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Massey Comprehensive Cancer Center, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5129160057","display_name":"Mikhail G Dozmorov","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mikhail G Dozmorov","raw_affiliation_strings":["Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,","Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284,"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23298,","institution_ids":["https://openalex.org/I184840846"]},{"raw_affiliation_string":"Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284,","institution_ids":["https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5129135303"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.64128828,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.08569999784231186,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.08569999784231186,"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":0.06759999692440033,"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/T11841","display_name":"Nuclear Structure and Function","score":0.05820000171661377,"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/set","display_name":"Set (abstract data type)","score":0.6284000277519226},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.36399999260902405},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.3472999930381775}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6833000183105469},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.6284000277519226},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.36399999260902405},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.3490000069141388},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.3472999930381775},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32440000772476196},{"id":"https://openalex.org/C112930515","wikidata":"https://www.wikidata.org/wiki/Q4389547","display_name":"Risk analysis (engineering)","level":1,"score":0.3109999895095825},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.30660000443458557},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2946999967098236},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.28949999809265137}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag110","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41826793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41826793","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:13020910","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13020910/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btag110","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag110","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.8313654661178589,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G1496344271","display_name":null,"funder_award_id":"R01CA246182","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3530699230","display_name":null,"funder_award_id":"R21CA273779","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3793792095","display_name":null,"funder_award_id":"UM1TR004360","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3850740208","display_name":null,"funder_award_id":"R56 MH107879","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5066933232","display_name":null,"funder_award_id":"1R01CA272710-01A1","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5584438681","display_name":null,"funder_award_id":"U54CA283762","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G6810423065","display_name":null,"funder_award_id":"UM1TR004360","funder_id":"https://openalex.org/F4320316438","funder_display_name":"Georgia Clinical and Translational Science Alliance"},{"id":"https://openalex.org/G7612863740","display_name":null,"funder_award_id":"R01CA246182","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7866118492","display_name":null,"funder_award_id":"HT9425-23\u20131-1017","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W1996203485","https://openalex.org/W2035618305","https://openalex.org/W2055801225","https://openalex.org/W2082238938","https://openalex.org/W2095150428","https://openalex.org/W2102904139","https://openalex.org/W2103441770","https://openalex.org/W2109714489","https://openalex.org/W2124799197","https://openalex.org/W2125636389","https://openalex.org/W2131478115","https://openalex.org/W2135993011","https://openalex.org/W2158789637","https://openalex.org/W2160697532","https://openalex.org/W2169456326","https://openalex.org/W2170551349","https://openalex.org/W2170830174","https://openalex.org/W2171808845","https://openalex.org/W2259938310","https://openalex.org/W2345356016","https://openalex.org/W2580989000","https://openalex.org/W2900675193","https://openalex.org/W2904964655","https://openalex.org/W2945678788","https://openalex.org/W2952738383","https://openalex.org/W2953622121","https://openalex.org/W2980318882","https://openalex.org/W2989061519","https://openalex.org/W2997255191","https://openalex.org/W3008816049","https://openalex.org/W3102112318","https://openalex.org/W3108485699","https://openalex.org/W3117820463","https://openalex.org/W3131055609","https://openalex.org/W4200554623","https://openalex.org/W4220999759","https://openalex.org/W4225379371","https://openalex.org/W4296782027","https://openalex.org/W4323314626","https://openalex.org/W4362521490","https://openalex.org/W4366083654","https://openalex.org/W4376133202","https://openalex.org/W4380685758","https://openalex.org/W4385663057","https://openalex.org/W4385720261","https://openalex.org/W4405056905","https://openalex.org/W4415923563"],"related_works":[],"abstract_inverted_index":{"We":[0,28,50],"examined":[1],"the":[2,31,53,56,107,115,118,123],"widely":[3],"used":[4],"Blacklist":[5],"software":[6],"and":[7,25,44,113,136],"found":[8],"that":[9,69],"pre-generated":[10],"exclusion":[11,82,111],"sets":[12,83],"were":[13],"difficult":[14],"to":[15,18,20,66,80],"reproduce":[16],"due":[17],"sensitivity":[19],"input":[21],"data,":[22],"aligner":[23],"choice,":[24],"read":[26],"length.":[27],"further":[29],"explored":[30],"use":[32,116],"of":[33,55,109,117],"\"sponge\"":[34,127],"sequences-unassembled":[35],"genomic":[36],"regions":[37],"such":[38],"as":[39,129],"satellite":[40],"DNA,":[41,43],"ribosomal":[42],"mitochondrial":[45],"DNA-as":[46],"an":[47,130],"alternative":[48],"approach.":[49],"additionally":[51],"investigated":[52],"effect":[54],"T2T-CHM13":[57,119],"genome":[58,68,125],"assembly":[59,120],"on":[60,94],"improving":[61,137],"biological":[62,86],"signals.":[63],"Aligning":[64],"reads":[65],"a":[67],"includes":[70],"sponge":[71],"sequences":[72,128],"reduced":[73],"signal":[74],"correlation":[75],"in":[76],"ChIP-seq":[77],"data":[78],"comparably":[79],"Blacklist-derived":[81],"while":[84],"preserving":[85],"signal.":[87],"Sponge-based":[88],"alignment":[89],"also":[90],"had":[91],"minimal":[92],"impact":[93],"RNA-seq":[95],"gene":[96],"counts,":[97],"suggesting":[98],"broader":[99],"applicability":[100],"beyond":[101],"chromatin":[102],"profiling.":[103],"These":[104],"results":[105],"highlight":[106],"limitations":[108],"fixed":[110],"sets,":[112],"recommend":[114],"or,":[121],"for":[122,133],"hg38":[124],"assembly,":[126],"alignment-guided":[131],"strategy":[132],"reducing":[134],"artifacts":[135],"functional":[138],"genomics":[139],"analyses.":[140]},"counts_by_year":[],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2026-03-15T00:00:00"}
