{"id":"https://openalex.org/W4411759558","doi":"https://doi.org/10.1093/bioinformatics/btaf371","title":"Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture","display_name":"Adversarial attack of sequence-free enhancer prediction identifies chromatin architecture","publication_year":2025,"publication_date":"2025-06-24","ids":{"openalex":"https://openalex.org/W4411759558","doi":"https://doi.org/10.1093/bioinformatics/btaf371","pmid":"https://pubmed.ncbi.nlm.nih.gov/40581823"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf371","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/btaf371","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104704412","display_name":"Jamil Gafur","orcid":"https://orcid.org/0000-0002-1364-1662"},"institutions":[{"id":"https://openalex.org/I126307644","display_name":"University of Iowa","ror":"https://ror.org/036jqmy94","country_code":"US","type":"education","lineage":["https://openalex.org/I126307644"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jamil Gafur","raw_affiliation_strings":["Department of Computer Science, University of Iowa , Iowa City, IA 52242,","University of Iowa Department of Computer Science, , Iowa City, Iowa 52242,"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Iowa , Iowa City, IA 52242,","institution_ids":["https://openalex.org/I126307644"]},{"raw_affiliation_string":"University of Iowa Department of Computer Science, , Iowa City, Iowa 52242,","institution_ids":["https://openalex.org/I126307644"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041492072","display_name":"Olivia Lang","orcid":"https://orcid.org/0000-0002-5886-363X"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olivia W Lang","raw_affiliation_strings":["Department of Molecular Biology and Genetics, Cornell University , Ithaca, NY 14850,","Cornell University Department of Molecular Biology and Genetics, , Ithaca, NY 14850,"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Cornell University , Ithaca, NY 14850,","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Cornell University Department of Molecular Biology and Genetics, , Ithaca, NY 14850,","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000405432","display_name":"William Lai","orcid":"https://orcid.org/0000-0003-4351-7037"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William K M Lai","raw_affiliation_strings":["Department of Computational Biology, Cornell University , Ithaca, NY 14850,","Department of Molecular Biology and Genetics, Cornell University , Ithaca, NY 14850,","Cornell University Department of Computational Biology, , Ithaca, NY 14850,","Cornell University Department of Molecular Biology and Genetics, , Ithaca, NY 14850,"],"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Cornell University , Ithaca, NY 14850,","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Molecular Biology and Genetics, Cornell University , Ithaca, NY 14850,","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Cornell University Department of Computational Biology, , Ithaca, NY 14850,","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Cornell University Department of Molecular Biology and Genetics, , Ithaca, NY 14850,","institution_ids":["https://openalex.org/I205783295"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5104704412"],"corresponding_institution_ids":["https://openalex.org/I126307644"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14010276,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9988999962806702,"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":0.9988999962806702,"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/T10878","display_name":"CRISPR and Genetic Engineering","score":0.9932000041007996,"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":0.9887999892234802,"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/computer-science","display_name":"Computer science","score":0.7166523933410645},{"id":"https://openalex.org/keywords/epigenomics","display_name":"Epigenomics","score":0.657981276512146},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.6487669348716736},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.591740071773529},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5169686675071716},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.49580487608909607},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.47310757637023926},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40067723393440247},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3399335443973541},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23586642742156982},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.21801963448524475},{"id":"https://openalex.org/keywords/dna-methylation","display_name":"DNA methylation","score":0.15310633182525635},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1475749909877777},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.09745669364929199}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7166523933410645},{"id":"https://openalex.org/C121912465","wikidata":"https://www.wikidata.org/wiki/Q3589153","display_name":"Epigenomics","level":5,"score":0.657981276512146},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.6487669348716736},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.591740071773529},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5169686675071716},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.49580487608909607},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.47310757637023926},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40067723393440247},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3399335443973541},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23586642742156982},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.21801963448524475},{"id":"https://openalex.org/C190727270","wikidata":"https://www.wikidata.org/wiki/Q874745","display_name":"DNA methylation","level":4,"score":0.15310633182525635},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1475749909877777},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.09745669364929199},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf371","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:40581823","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40581823","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:12240468","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12240468","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/btaf371","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf371","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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1865845132","https://openalex.org/W1981030303","https://openalex.org/W1986586739","https://openalex.org/W1989373989","https://openalex.org/W2017840637","https://openalex.org/W2018363492","https://openalex.org/W2063815548","https://openalex.org/W2064675550","https://openalex.org/W2077874719","https://openalex.org/W2100088478","https://openalex.org/W2102619694","https://openalex.org/W2117757143","https://openalex.org/W2152314234","https://openalex.org/W2160003307","https://openalex.org/W2166037178","https://openalex.org/W2167776710","https://openalex.org/W2171111703","https://openalex.org/W2195190137","https://openalex.org/W2259938310","https://openalex.org/W2323326409","https://openalex.org/W2498392978","https://openalex.org/W2735707476","https://openalex.org/W2772741766","https://openalex.org/W2774699268","https://openalex.org/W2774733631","https://openalex.org/W2802802541","https://openalex.org/W2885130586","https://openalex.org/W2988126442","https://openalex.org/W2996427414","https://openalex.org/W3008816049","https://openalex.org/W3012245213","https://openalex.org/W3033842668","https://openalex.org/W3036652698","https://openalex.org/W3047825284","https://openalex.org/W3081278968","https://openalex.org/W3087265072","https://openalex.org/W3111875728","https://openalex.org/W3119883962","https://openalex.org/W3124680305","https://openalex.org/W3126352312","https://openalex.org/W3136167697","https://openalex.org/W3136200267","https://openalex.org/W3139240024","https://openalex.org/W3195349614","https://openalex.org/W3208823525","https://openalex.org/W3212964278","https://openalex.org/W4213140257","https://openalex.org/W4230875896","https://openalex.org/W4287447409","https://openalex.org/W4292174509","https://openalex.org/W4312018534","https://openalex.org/W4376132682","https://openalex.org/W6839312415","https://openalex.org/W6871164135"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W2061914098","https://openalex.org/W4393004084","https://openalex.org/W2118646732","https://openalex.org/W4309683845","https://openalex.org/W4387565139","https://openalex.org/W4389440207","https://openalex.org/W2795212387","https://openalex.org/W4378781551","https://openalex.org/W3160486573"],"abstract_inverted_index":{"All":[0],"software":[1],"and":[2,13,24],"code":[3],"for":[4],"data":[5],"downloading,":[6],"processing,":[7],"enhancer":[8],"inference,":[9],"eXplainable":[10],"AI":[11],"(XAI),":[12],"complete":[14],"figure":[15],"generation":[16],"are":[17],"publicly":[18],"available":[19],"on":[20],"GitHub":[21],"at":[22,26],"https://github.com/EpiGenomicsCode/ChromEnhancer":[23],"Zenodo":[25],"https://doi.org/10.5281/zenodo.15652797.":[27]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
