{"id":"https://openalex.org/W7214945382","doi":"https://doi.org/10.64898/2026.09.25.754372","title":"ProxiNet transfers spatially learned cellular proximity to dissociated single-cell transcriptomes","display_name":"ProxiNet transfers spatially learned cellular proximity to dissociated single-cell transcriptomes","publication_year":2026,"publication_date":"2026-09-30","ids":{"openalex":"https://openalex.org/W7214945382","doi":"https://doi.org/10.64898/2026.09.25.754372","pmid":"https://pubmed.ncbi.nlm.nih.gov/42856154","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13648456"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.25.754372","doi":"https://doi.org/10.64898/2026.09.25.754372","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.25.754372","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.25.754372.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.25.754372.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101233734","display_name":"Yuxiang Zhan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210157710","display_name":"Whitehead Institute for Biomedical Research","ror":"https://ror.org/04vqm6w82","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210157710","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuxiang Zhan","raw_affiliation_strings":["Whitehead Institute for Biomedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Whitehead Institute for Biomedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210157710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104344595","display_name":"Binwei Yan","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Binwei Yan","raw_affiliation_strings":["MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4405258931"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035743359","display_name":"Ao Zhang","orcid":"https://orcid.org/0000-0002-0825-1264","observed_orcids":["https://orcid.org/0000-0002-0825-1264","https://orcid.org/0009-0005-8518-9010"]},"institutions":[{"id":"https://openalex.org/I183935753","display_name":"King's College London","ror":"https://ror.org/0220mzb33","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I183935753"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ao Zhang","raw_affiliation_strings":["Department of Biostatistics and Health Informatics, King\u2019s College London, London, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Health Informatics, King\u2019s College London, London, UK","institution_ids":["https://openalex.org/I183935753"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108044601","display_name":"M Kellis","orcid":"https://orcid.org/0000-0001-7113-9630","observed_orcids":["https://orcid.org/0000-0001-7113-9630"]},"institutions":[{"id":"https://openalex.org/I107606265","display_name":"Broad Institute","ror":"https://ror.org/05a0ya142","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I107606265"]},{"id":"https://openalex.org/I4405258931","display_name":"MIT Computer Science and Artificial Intelligence Laboratory","ror":"https://ror.org/01e85r662","country_code":"US","type":"facility","lineage":["https://openalex.org/I4405258931","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manolis Kellis","raw_affiliation_strings":["Broad Institute of MIT and Harvard, Cambridge, MA, USA","MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Broad Institute of MIT and Harvard, Cambridge, MA, USA","institution_ids":["https://openalex.org/I107606265"]},{"raw_affiliation_string":"MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4405258931"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100406414","display_name":"Na Sun","orcid":"https://orcid.org/0009-0008-5785-5495","observed_orcids":["https://orcid.org/0009-0008-5785-5495"]},"institutions":[{"id":"https://openalex.org/I4210157710","display_name":"Whitehead Institute for Biomedical Research","ror":"https://ror.org/04vqm6w82","country_code":"US","type":"facility","lineage":["https://openalex.org/I4210157710","https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Na Sun","raw_affiliation_strings":["Whitehead Institute for Biomedical Research, Cambridge, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Whitehead Institute for Biomedical Research, Cambridge, MA, USA","institution_ids":["https://openalex.org/I4210157710"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100406414"],"corresponding_institution_ids":["https://openalex.org/I4210157710"],"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":1.0,"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":1.0,"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":0.0,"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/T13127","display_name":"Biotin and Related Studies","score":0.0,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/spatial-transcriptomics","display_name":"spatial transcriptomics","score":0.8309999704360962},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.7699999809265137},{"id":"https://openalex.org/keywords/zero-shot-transfer","display_name":"zero-shot transfer","score":0.7990000247955322},{"id":"https://openalex.org/keywords/intercellular-communication","display_name":"intercellular communication","score":0.8479999899864197},{"id":"https://openalex.org/keywords/alzheimer-s-disease","display_name":"Alzheimer's disease","score":0.9520000219345093},{"id":"https://openalex.org/keywords/astrocytes","display_name":"astrocytes","score":0.7250000238418579},{"id":"https://openalex.org/keywords/neurons","display_name":"neurons","score":0.7310000061988831},{"id":"https://openalex.org/keywords/cell-type-composition","display_name":"cell type composition","score":0.6890000104904175},{"id":"https://openalex.org/keywords/gradient-based-attribution","display_name":"gradient-based attribution","score":0.640999972820282}],"concepts":[{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.7139999866485596},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6003999710083008},{"id":"https://openalex.org/C175779824","wikidata":"https://www.wikidata.org/wiki/Q7574078","display_name":"Spatial organization","level":2,"score":0.5494999885559082},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4609000086784363},{"id":"https://openalex.org/C78885561","wikidata":"https://www.wikidata.org/wiki/Q189055","display_name":"Cellular compartment","level":3,"score":0.42660000920295715},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.40630000829696655},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.40610000491142273},{"id":"https://openalex.org/C2780196419","wikidata":"https://www.wikidata.org/wiki/Q1762173","display_name":"Nerve net","level":2,"score":0.34139999747276306},{"id":"https://openalex.org/C3018011982","wikidata":"https://www.wikidata.org/wiki/Q7316120","display_name":"Functional connectivity","level":2,"score":0.3327000141143799},{"id":"https://openalex.org/C153646914","wikidata":"https://www.wikidata.org/wiki/Q535695","display_name":"Cellular network","level":2,"score":0.32019999623298645},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.31200000643730164},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2971000075340271},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.28290000557899475},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2752000093460083},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.274399995803833},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.2718000113964081},{"id":"https://openalex.org/C147025567","wikidata":"https://www.wikidata.org/wiki/Q16335140","display_name":"Cellular model","level":3,"score":0.2599000036716461},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.25119999051094055}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.09.25.754372","doi":"https://doi.org/10.64898/2026.09.25.754372","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.25.754372","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.25.754372.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:pubmedcentral.nih.gov:13648456","doi":null,"is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42856154/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13648456/pdf/nihpp-2026.09.25.754372v1.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmid:42856154","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42856154","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,"listed_in":[],"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":"bioRxiv : the preprint server for biology","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.64898/2026.09.25.754372","doi":"https://doi.org/10.64898/2026.09.25.754372","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.25.754372","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/30/2026.09.25.754372.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214945382.pdf","grobid_xml":"https://content.openalex.org/works/W7214945382.grobid-xml"},"referenced_works_count":2,"referenced_works":["https://openalex.org/W4412825866","https://openalex.org/W4417230386"],"related_works":["https://openalex.org/W4223904764","https://openalex.org/W7155367179","https://openalex.org/W4288758477","https://openalex.org/W4376275195","https://openalex.org/W4407708874","https://openalex.org/W4293074653","https://openalex.org/W7154935976","https://openalex.org/W4393307128","https://openalex.org/W7117627098","https://openalex.org/W4399211696"],"abstract_inverted_index":{",":[0],"a":[1],"spatially":[2,79,145],"supervised":[3],"framework":[4],"that":[5],"learns":[6],"transcriptomic":[7],"signatures":[8],"of":[9,72,107],"pairwise":[10,134],"cellular":[11,27,59,87,135],"proximity":[12,28,50,75,136],"from":[13],"spatial":[14,33,53,70],"reference":[15],"datasets":[16,54],"and":[17,32,39,44,65,93,121,125,140],"transfers":[18],"these":[19,131],"relationships":[20],"to":[21,82,149],"dissociated":[22,83,150],"single-cell":[23,151],"transcriptomes.":[24,152],"ProxiNet":[25,102],"predicted":[26],"across":[29],"brain":[30],"regions":[31],"technologies,":[34],"including":[35,110],"zero-shot":[36],"cross-technology":[37],"transfer,":[38],"gradient-based":[40],"attribution":[41],"identified":[42,104],"genes":[43],"broader":[45],"transcriptional":[46,123],"programs":[47],"associated":[48],"with":[49,55,89],"predictions.":[51],"In":[52,97],"known":[56],"coordinates,":[57],"ProxiNet-derived":[58],"neighborhoods":[60,88],"recovered":[61],"reproducible":[62],"tissue":[63,147],"organization":[64,148],"anatomical":[66],"structure,":[67],"providing":[68],"independent":[69],"validation":[71],"the":[73,78],"inferred":[74,108],"relationships.":[76],"Applying":[77],"calibrated":[80],"model":[81],"scRNA-seq":[84],"revealed":[85],"heterogeneous":[86],"distinct":[90,119],"cell-type":[91],"compositions":[92],"candidate":[94,126],"communication":[95,128],"programs.":[96,129],"an":[98,111,138],"Alzheimer's":[99],"disease":[100],"dataset,":[101],"further":[103],"age-associated":[105],"remodeling":[106],"neighborhoods,":[109],"AD-associated":[112],"neighborhood":[113],"at":[114],"8":[115],"months":[116],"characterized":[117],"by":[118],"astrocyte":[120],"neuronal":[122],"states":[124],"intercellular":[127],"Together,":[130],"results":[132],"establish":[133],"as":[137],"interpretable":[139],"transferable":[141],"representation":[142],"for":[143],"extending":[144],"learned":[146]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-10-01T00:00:00"}
