{"id":"https://openalex.org/W7204098015","doi":"https://doi.org/10.64898/2026.08.18.745447","title":"Implicit Hierarchical Tensor Decomposition of Single-Cell Four-Omics Data Reveals Cell-Type-Associated Enhancer\u2013Promoter Regulatory Programs","display_name":"Implicit Hierarchical Tensor Decomposition of Single-Cell Four-Omics Data Reveals Cell-Type-Associated Enhancer\u2013Promoter Regulatory Programs","publication_year":2026,"publication_date":"2026-08-23","ids":{"openalex":"https://openalex.org/W7204098015","doi":"https://doi.org/10.64898/2026.08.18.745447"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.18.745447","doi":"https://doi.org/10.64898/2026.08.18.745447","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.18.745447","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/23/2026.08.18.745447.full.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/23/2026.08.18.745447.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045603108","display_name":"Y\u2010h. Taguchi","orcid":"https://orcid.org/0000-0003-0867-8986","observed_orcids":["https://orcid.org/0000-0003-0867-8986"]},"institutions":[{"id":"https://openalex.org/I96679780","display_name":"Chuo University","ror":"https://ror.org/03qvqb743","country_code":"JP","type":"education","lineage":["https://openalex.org/I96679780"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Y-H Taguchi","raw_affiliation_strings":["Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan"],"raw_orcid":"https://orcid.org/0000-0003-0867-8986","affiliations":[{"raw_affiliation_string":"Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan","institution_ids":["https://openalex.org/I96679780"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5007548463","display_name":"Turki Turki","orcid":"https://orcid.org/0000-0002-9491-2435","observed_orcids":["https://orcid.org/0000-0002-9491-2435"]},"institutions":[{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Turki Turki","raw_affiliation_strings":["Department of Computer Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5045603108"],"corresponding_institution_ids":["https://openalex.org/I96679780"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8198000192642212,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.8198000192642212,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.1429000049829483,"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/T12303","display_name":"Tensor decomposition and applications","score":0.007699999958276749,"subfield":{"id":"https://openalex.org/subfields/2605","display_name":"Computational Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/single-cell-multi-omics","display_name":"single-cell multi-omics","score":0.8069999814033508},{"id":"https://openalex.org/keywords/enhancer-promoter-interactions","display_name":"enhancer-promoter interactions","score":0.7870000004768372},{"id":"https://openalex.org/keywords/3d-genome-organization","display_name":"3D genome organization","score":0.7789999842643738},{"id":"https://openalex.org/keywords/chromatin-accessibility","display_name":"chromatin accessibility","score":0.6389999985694885},{"id":"https://openalex.org/keywords/h3k27ac","display_name":"H3K27ac","score":0.9869999885559082},{"id":"https://openalex.org/keywords/cell-type-specific-gene-regulation","display_name":"cell type-specific gene regulation","score":0.6230000257492065},{"id":"https://openalex.org/keywords/mouse-brain","display_name":"mouse brain","score":0.6439999938011169},{"id":"https://openalex.org/keywords/developmental-gene-regulation","display_name":"developmental gene regulation","score":0.40299999713897705}],"concepts":[{"id":"https://openalex.org/C155281189","wikidata":"https://www.wikidata.org/wiki/Q3518150","display_name":"Tensor (intrinsic definition)","level":2,"score":0.6338000297546387},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.557699978351593},{"id":"https://openalex.org/C2164484","wikidata":"https://www.wikidata.org/wiki/Q5170150","display_name":"Core (optical fiber)","level":2,"score":0.5019999742507935},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.5005999803543091},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4973999857902527},{"id":"https://openalex.org/C139676723","wikidata":"https://www.wikidata.org/wiki/Q1193832","display_name":"Sign (mathematics)","level":2,"score":0.48919999599456787},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48660001158714294},{"id":"https://openalex.org/C2780226545","wikidata":"https://www.wikidata.org/wiki/Q6888030","display_name":"Modality (human\u2013computer interaction)","level":2,"score":0.46459999680519104},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4043999910354614},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40369999408721924},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.38370001316070557},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.38179999589920044},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.38029998540878296},{"id":"https://openalex.org/C42704193","wikidata":"https://www.wikidata.org/wiki/Q7851097","display_name":"Tucker decomposition","level":4,"score":0.37540000677108765},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.36419999599456787},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35089999437332153},{"id":"https://openalex.org/C42355184","wikidata":"https://www.wikidata.org/wiki/Q1361088","display_name":"Matrix decomposition","level":3,"score":0.3359000086784363},{"id":"https://openalex.org/C156273044","wikidata":"https://www.wikidata.org/wiki/Q4913766","display_name":"Bin","level":2,"score":0.33219999074935913},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32010000944137573},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.30889999866485596},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.305400013923645},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.2847999930381775},{"id":"https://openalex.org/C144986985","wikidata":"https://www.wikidata.org/wiki/Q871236","display_name":"Hierarchical database model","level":2,"score":0.27250000834465027},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.257099986076355},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.25189998745918274}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.18.745447","doi":"https://doi.org/10.64898/2026.08.18.745447","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.18.745447","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/23/2026.08.18.745447.full.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.18.745447","doi":"https://doi.org/10.64898/2026.08.18.745447","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.18.745447","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/23/2026.08.18.745447.full.pdf","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204098015.pdf","grobid_xml":"https://content.openalex.org/works/W7204098015.grobid-xml"},"referenced_works_count":4,"referenced_works":["https://openalex.org/W2013912476","https://openalex.org/W2100761975","https://openalex.org/W2128049108","https://openalex.org/W3175752499"],"related_works":["https://openalex.org/W4405420013","https://openalex.org/W4225278475","https://openalex.org/W4415205355","https://openalex.org/W7211879957","https://openalex.org/W4403235965","https://openalex.org/W7147139203","https://openalex.org/W7207860542","https://openalex.org/W3200063971","https://openalex.org/W4383186693","https://openalex.org/W4388961299"],"abstract_inverted_index":{"Abstract":[0],"Single-cell":[1],"multi-omics":[2],"provides":[3],"complementary":[4],"views":[5],"of":[6],"gene":[7],"regulation,":[8],"but":[9],"integrating":[10],"modalities":[11,183],"with":[12],"natural":[13],"features":[14],"comprising":[15],"enhancers,":[16,65],"genes,":[17,67],"and":[18,34,52,72,85,150,159],"three-dimensional":[19],"(3D)":[20],"genomic":[21],"loci":[22],"remains":[23],"challenging.":[24],"This":[25],"study":[26],"developed":[27],"an":[28,88],"implicit":[29,89],"hierarchical":[30],"tensor":[31],"decomposition":[32],"framework":[33,173],"applied":[35],"it":[36],"to":[37,82,87,147],"the":[38,103,113,140,175],"CHARM":[39],"single-cell":[40],"four-omics":[41],"mouse":[42],"brain":[43],"data":[44],"(GSE303006)":[45],"by":[46],"jointly":[47],"analyzing":[48],"ATAC,":[49,157],"H3K27ac,":[50,158],"RNA,":[51],"reconstructed":[53],"3D":[54,160],"enhancer\u2013promoter":[55],"(E\u2013P)":[56],"distances.":[57],"After":[58],"quality":[59],"control,":[60],"730,969":[61,90],"E\u2013P":[62,152],"pairs,":[63,71],"42,669":[64],"16,239":[66],"391,435":[68],"20-kb":[69],"bin":[70],"4,258":[73,92],"cells":[74],"were":[75,170],"retained.":[76],"Each":[77],"modality":[78],"was":[79,99],"independently":[80],"reduced":[81],"20":[83,94],"components":[84,110],"mapped":[86],"\u00d7":[91,93,95,130],"4":[96],"tensor,":[97],"which":[98],"decomposed":[100],"without":[101],"materializing":[102],"full":[104],"array.":[105],"All":[106],"12":[107],"distinct":[108,186],"cell":[109,145],"represented":[111],"among":[112],"100":[114],"largest":[115],"Tucker":[116],"core":[117,138],"elements":[118],"showed":[119,155],"greater":[120],"cell-type":[121],"effects":[122,125,161,169],"than":[123],"replicate":[124],"(":[126],"P":[127],"=":[128],"2.44":[129],"10":[131],"\u22124":[132],",":[133],"sign":[134],"test).":[135],"A":[136],"representative":[137],"linked":[139],"Inh":[141],"Ndnf/Lamp5\u2013Ex":[142],"L3/4":[143],"IT":[144],"axis":[146],"contrasting":[148],"presynaptic-transmission":[149],"developmental/morphogenetic":[151],"programs.":[153],"Backprojection":[154],"reproducible":[156],"across":[162,181],"three":[163],"biological":[164],"replicates,":[165],"whereas":[166],"module-level":[167],"RNA":[168],"weaker.":[171],"The":[172],"reveals":[174],"regulatory":[176],"structure":[177],"that":[178],"is":[179],"shared":[180],"molecular":[182,190],"while":[184],"remaining":[185],"from":[187],"any":[188],"single":[189],"modality.":[191]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-08-25T00:00:00"}
