{"id":"https://openalex.org/W7225001325","doi":"https://doi.org/10.64898/2026.10.30.762954","title":"SMFNet reveals principles of combinatorial transcription factor assembly","display_name":"SMFNet reveals principles of combinatorial transcription factor assembly","publication_year":2026,"publication_date":"2026-10-31","ids":{"openalex":"https://openalex.org/W7225001325","doi":"https://doi.org/10.64898/2026.10.30.762954"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.30.762954","doi":"https://doi.org/10.64898/2026.10.30.762954","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.30.762954","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.10.30.762954","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039314403","display_name":"Till Schw\u00e4mmle","orcid":"https://orcid.org/0000-0003-4650-0214","observed_orcids":["https://orcid.org/0000-0003-4650-0214"]},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Till Schw\u00e4mmle","raw_affiliation_strings":["Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4650-0214","affiliations":[{"raw_affiliation_string":"Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004655457","display_name":"Nathaniel Diamant","orcid":"https://orcid.org/0000-0002-1738-304X","observed_orcids":["https://orcid.org/0000-0002-1738-304X"]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathaniel Diamant","raw_affiliation_strings":["Department of Computer Science, School of Engineering, Stanford University","Department of Genetics, School of Medicine, Stanford University"],"raw_orcid":"https://orcid.org/0000-0002-1738-304X","affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Engineering, Stanford University","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, School of Medicine, Stanford University","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033699651","display_name":"Yuliya Badayeva","orcid":"https://orcid.org/0000-0003-2084-0763","observed_orcids":["https://orcid.org/0000-0003-2084-0763"]},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Yuliya Badayeva","raw_affiliation_strings":["Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany","Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-2084-0763","affiliations":[{"raw_affiliation_string":"Faculty of Biosciences, Collaboration for Joint PhD Degree between EMBL and Heidelberg University, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I4210138560"]},{"raw_affiliation_string":"Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088581943","display_name":"Rozemarijn Kleinendorst","orcid":"https://orcid.org/0000-0003-1803-8982","observed_orcids":["https://orcid.org/0000-0003-1803-8982"]},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rozemarijn Kleinendorst","raw_affiliation_strings":["Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1803-8982","affiliations":[{"raw_affiliation_string":"Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210138560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083952534","display_name":"Anshul Bharat Kundaje","orcid":"https://orcid.org/0000-0003-3084-2287","observed_orcids":["https://orcid.org/0000-0003-3084-2287"]},"institutions":[{"id":"https://openalex.org/I4210137306","display_name":"Stanford Medicine","ror":"https://ror.org/03mtd9a03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Anshul Kundaje","raw_affiliation_strings":["Department of Computer Science, School of Engineering, Stanford University","Department of Genetics, School of Medicine, Stanford University"],"raw_orcid":"https://orcid.org/0000-0003-3084-2287","affiliations":[{"raw_affiliation_string":"Department of Computer Science, School of Engineering, Stanford University","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Department of Genetics, School of Medicine, Stanford University","institution_ids":["https://openalex.org/I4210137306","https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020051043","display_name":"Arnaud Regis Krebs","orcid":"https://orcid.org/0000-0001-7999-6127","observed_orcids":["https://orcid.org/0000-0001-7999-6127"]},"institutions":[{"id":"https://openalex.org/I4210138560","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/03mstc592","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Arnaud R. Krebs","raw_affiliation_strings":["Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7999-6127","affiliations":[{"raw_affiliation_string":"Genome Biology Unit, EMBL Heidelberg, Meyerhofstra\u00dfe 1, 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210138560"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020051043"],"corresponding_institution_ids":["https://openalex.org/I4210138560"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"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":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9976000189781189,"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":0.9976000189781189,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.0008999999845400453,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":9.999999747378752e-05,"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/chromatin-accessibility","display_name":"chromatin accessibility","score":0.8489999771118164},{"id":"https://openalex.org/keywords/cis-regulatory-elements","display_name":"cis-regulatory elements","score":0.9459999799728394},{"id":"https://openalex.org/keywords/generative-diffusion-models","display_name":"generative diffusion models","score":0.8980000019073486},{"id":"https://openalex.org/keywords/nucleosome-positioning","display_name":"nucleosome positioning","score":0.8820000290870667},{"id":"https://openalex.org/keywords/transcription-factor-binding-motifs","display_name":"transcription factor binding motifs","score":0.7630000114440918},{"id":"https://openalex.org/keywords/prism","display_name":"PRISM","score":0.5950000286102295},{"id":"https://openalex.org/keywords/cell-type-specific-gene-expression","display_name":"cell type-specific gene expression","score":0.8019999861717224},{"id":"https://openalex.org/keywords/chromatin-opening","display_name":"chromatin opening","score":0.5820000171661377}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.9099000096321106},{"id":"https://openalex.org/C84772758","wikidata":"https://www.wikidata.org/wiki/Q271794","display_name":"Nucleosome","level":4,"score":0.6535000205039978},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6266999840736389},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5796999931335449},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5644999742507935},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.5418999791145325},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5325000286102295},{"id":"https://openalex.org/C176619506","wikidata":"https://www.wikidata.org/wiki/Q5065899","display_name":"ChIP-sequencing","level":5,"score":0.5130000114440918},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4016000032424927},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3774000108242035},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.3698999881744385},{"id":"https://openalex.org/C56262557","wikidata":"https://www.wikidata.org/wiki/Q3931949","display_name":"Scaffold/matrix attachment region","level":5,"score":0.36329999566078186},{"id":"https://openalex.org/C167227067","wikidata":"https://www.wikidata.org/wiki/Q5113739","display_name":"Chromatin remodeling","level":4,"score":0.3481999933719635},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3260999917984009},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.322299987077713},{"id":"https://openalex.org/C137365298","wikidata":"https://www.wikidata.org/wiki/Q7833928","display_name":"Transcription coregulator","level":5,"score":0.29980000853538513},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.29649999737739563},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.28220000863075256},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.26489999890327454},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.26100000739097595},{"id":"https://openalex.org/C94966510","wikidata":"https://www.wikidata.org/wiki/Q2252764","display_name":"DNA-binding protein","level":4,"score":0.2603999972343445},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.26019999384880066},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.25360000133514404},{"id":"https://openalex.org/C191608507","wikidata":"https://www.wikidata.org/wiki/Q7815764","display_name":"ChIP-on-chip","level":5,"score":0.25279998779296875}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.30.762954","doi":"https://doi.org/10.64898/2026.10.30.762954","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.30.762954","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.10.30.762954","doi":"https://doi.org/10.64898/2026.10.30.762954","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.30.762954","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":116,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1928213240","https://openalex.org/W1971451591","https://openalex.org/W1971578941","https://openalex.org/W1978125302","https://openalex.org/W1982323384","https://openalex.org/W1987289112","https://openalex.org/W1998000745","https://openalex.org/W2002873026","https://openalex.org/W2005501593","https://openalex.org/W2008047506","https://openalex.org/W2014677321","https://openalex.org/W2017886758","https://openalex.org/W2026690931","https://openalex.org/W2029785188","https://openalex.org/W2033169664","https://openalex.org/W2039053594","https://openalex.org/W2042392223","https://openalex.org/W2045362835","https://openalex.org/W2051875167","https://openalex.org/W2068478010","https://openalex.org/W2071525868","https://openalex.org/W2086468671","https://openalex.org/W2105512180","https://openalex.org/W2108234281","https://openalex.org/W2111846924","https://openalex.org/W2142410561","https://openalex.org/W2144578935","https://openalex.org/W2156933633","https://openalex.org/W2161350677","https://openalex.org/W2170551349","https://openalex.org/W2171302228","https://openalex.org/W2171808845","https://openalex.org/W2198606573","https://openalex.org/W2219596071","https://openalex.org/W2342249984","https://openalex.org/W2345512687","https://openalex.org/W2546519000","https://openalex.org/W2573731673","https://openalex.org/W2575110262","https://openalex.org/W2601243251","https://openalex.org/W2738668193","https://openalex.org/W2760103357","https://openalex.org/W2779662045","https://openalex.org/W2911252985","https://openalex.org/W2937299982","https://openalex.org/W2951091094","https://openalex.org/W2951212842","https://openalex.org/W2990427812","https://openalex.org/W3004849394","https://openalex.org/W3035965352","https://openalex.org/W3037519049","https://openalex.org/W3045910546","https://openalex.org/W3046196569","https://openalex.org/W3046345618","https://openalex.org/W3083240949","https://openalex.org/W3109792160","https://openalex.org/W3111715132","https://openalex.org/W3126820803","https://openalex.org/W3130819465","https://openalex.org/W3131443014","https://openalex.org/W3163257742","https://openalex.org/W3177586536","https://openalex.org/W3203588026","https://openalex.org/W3212486106","https://openalex.org/W4200456075","https://openalex.org/W4205345182","https://openalex.org/W4213140257","https://openalex.org/W4225938290","https://openalex.org/W4280563114","https://openalex.org/W4282918068","https://openalex.org/W4311666135","https://openalex.org/W4312121367","https://openalex.org/W4318027593","https://openalex.org/W4319593304","https://openalex.org/W4320806770","https://openalex.org/W4362694632","https://openalex.org/W4386609944","https://openalex.org/W4389613138","https://openalex.org/W4391112869","https://openalex.org/W4392763126","https://openalex.org/W4395447546","https://openalex.org/W4399256283","https://openalex.org/W4399893662","https://openalex.org/W4400729643","https://openalex.org/W4401454363","https://openalex.org/W4401951406","https://openalex.org/W4404566620","https://openalex.org/W4405506478","https://openalex.org/W4405514987","https://openalex.org/W4405829527","https://openalex.org/W4406178430","https://openalex.org/W4406693602","https://openalex.org/W4409312366","https://openalex.org/W4410334277","https://openalex.org/W4410926447","https://openalex.org/W4414849153","https://openalex.org/W4416097143","https://openalex.org/W4416702275","https://openalex.org/W4416772976","https://openalex.org/W4416889480","https://openalex.org/W4416943542","https://openalex.org/W7125967877","https://openalex.org/W7127576249","https://openalex.org/W7128603322","https://openalex.org/W7135042669","https://openalex.org/W7147749522","https://openalex.org/W7151931292","https://openalex.org/W7158816791","https://openalex.org/W7160159865","https://openalex.org/W7160384206","https://openalex.org/W7171940685","https://openalex.org/W7172502384","https://openalex.org/W7202280781","https://openalex.org/W7204162191","https://openalex.org/W7221037795"],"related_works":["https://openalex.org/W6922224700","https://openalex.org/W4225831698","https://openalex.org/W4385197384","https://openalex.org/W7140273819","https://openalex.org/W4321478759","https://openalex.org/W2582038667","https://openalex.org/W2951890754","https://openalex.org/W4405829527","https://openalex.org/W2737959952","https://openalex.org/W2806575716"],"abstract_inverted_index":{"Combinatorial":[0],"assembly":[1,244],"of":[2,20,33,47,97,137,195,215,241],"transcription":[3],"factors":[4],"(TFs)":[5],"opens":[6],"chromatin":[7,57,69,99,126,155,174,196,206,230,246],"at":[8,128,222],"cis-regulatory":[9],"elements":[10],"(cREs)":[11],"to":[12,68,121,165,173],"establish":[13],"cell-type-specific":[14],"gene":[15],"expression.":[16],"Dissecting":[17],"the":[18,31,53,141],"role":[19],"individual":[21,113,168],"TFs":[22,177],"and":[23,49,105,169,186,202,210],"their":[24,149],"collective":[25],"function":[26],"has":[27],"been":[28],"limited":[29],"by":[30,146],"diversity":[32],"TF":[34,48,61,81,132,171,208,216,243],"binding-site":[35],"arrangements":[36],"across":[37],"cREs.":[38],"A":[39],"single":[40,124],"regulatory":[41,66],"sequence":[42,67,109],"can":[43],"support":[44],"multiple":[45],"configurations":[46,153],"nucleosome":[50,211],"occupancy,":[51],"raising":[52],"possibility":[54],"that":[55,94,226],"distinct":[56,73,179],"states":[58,75,127,143],"reflect":[59],"different":[60],"assemblies.":[62],"Predictive":[63],"models":[64],"linking":[65],"accessibility":[70,100,231],"collapse":[71],"these":[72,117,138],"molecular":[74,114],"into":[76],"population":[77],"averages,":[78],"obscuring":[79],"how":[80],"assemblies":[82],"shape":[83,229],"accessible":[84],"chromatin.":[85],"Here,":[86],"we":[87],"introduce":[88],"SMFNet,":[89,147],"a":[90],"generative":[91],"diffusion":[92],"model":[93],"predicts":[95],"distributions":[96],"single-molecule":[98],"profiles":[101],"from":[102],"DNA":[103],"sequence,":[104],"PRISM,":[106],"which":[107],"identifies":[108],"features":[110],"associated":[111,191],"with":[112,130,192],"states.":[115],"Together,":[116,235],"approaches":[118],"enable":[119],"us":[120],"systematically":[122,166],"associate":[123],"molecule":[125],"cREs":[129],"specific":[131],"binding":[133,217],"motifs.":[134],"Experimental":[135],"perturbation":[136,214],"motifs":[139,199],"redistributes":[140],"corresponding":[142],"as":[144,151],"predicted":[145],"supporting":[148],"interpretation":[150],"TF-dependent":[152],"underlying":[154],"opening.":[156,175,247],"We":[157],"then":[158],"use":[159],"controlled":[160],"in":[161,183,232],"silico":[162],"motif":[163],"screens":[164],"dissect":[167],"combinatorial":[170,242],"contributions":[172],"Individual":[176],"show":[178],"chromatin-opening":[180],"signatures,":[181],"differing":[182],"accessible-region":[184],"width":[185],"nucleosome-positioning":[187],"precision":[188],"even":[189],"when":[190],"similar":[193],"levels":[194],"accessibility.":[197],"Combining":[198],"reveals":[200],"partner-":[201],"spacing-dependent":[203],"effects":[204],"on":[205],"accessibility,":[207],"occupancy":[209],"positioning.":[212],"Genetic":[213],"sites":[218],"using":[219],"natural":[220],"variation":[221],"endogenous":[223],"cRE":[224],"confirms":[225],"TF-specific":[227],"properties":[228],"vivo":[233],".":[234],"our":[236],"findings":[237],"reveal":[238],"sequence-encoded":[239],"principles":[240],"during":[245]},"counts_by_year":[],"updated_date":"2026-11-05T12:25:35.769452","created_date":"2026-11-01T00:00:00"}
