{"id":"https://openalex.org/W7214536278","doi":"https://doi.org/10.64898/2026.09.21.753369","title":"A meta-interaction basis for cell-cell communication in tissues","display_name":"A meta-interaction basis for cell-cell communication in tissues","publication_year":2026,"publication_date":"2026-09-27","ids":{"openalex":"https://openalex.org/W7214536278","doi":"https://doi.org/10.64898/2026.09.21.753369","pmid":"https://pubmed.ncbi.nlm.nih.gov/42818244","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13622179"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.21.753369","doi":"https://doi.org/10.64898/2026.09.21.753369","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.21.753369","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/27/2026.09.21.753369.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-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","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/27/2026.09.21.753369.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5147584889","display_name":"Junjie Tang","orcid":"https://orcid.org/0009-0007-0612-2497","observed_orcids":["https://orcid.org/0009-0007-0612-2497"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junjie Tang","raw_affiliation_strings":["Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":"https://orcid.org/0009-0007-0612-2497","affiliations":[{"raw_affiliation_string":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055060386","display_name":"Shaoheng Liang","orcid":"https://orcid.org/0000-0002-9575-1522","observed_orcids":["https://orcid.org/0000-0002-9575-1522"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shaoheng Liang","raw_affiliation_strings":["Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":"https://orcid.org/0000-0002-9575-1522","affiliations":[{"raw_affiliation_string":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000345634","display_name":"Shahul Alam","orcid":"https://orcid.org/0000-0002-4821-7079","observed_orcids":["https://orcid.org/0000-0002-4821-7079"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shahul Alam","raw_affiliation_strings":["Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074045070","display_name":"Wenduo Cheng","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenduo Cheng","raw_affiliation_strings":["Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5153111116","display_name":"Yang Zhang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100626893","display_name":"Jian Ma","orcid":"https://orcid.org/0000-0002-4202-5834","observed_orcids":["https://orcid.org/0000-0002-4202-5834"]},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jian Ma","raw_affiliation_strings":["Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4202-5834","affiliations":[{"raw_affiliation_string":"Ray and Stephanie Lane Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA","institution_ids":["https://openalex.org/I74973139"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100626893"],"corresponding_institution_ids":["https://openalex.org/I74973139"],"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":0.9965999722480774,"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":0.9965999722480774,"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":0.000699999975040555,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00039999998989515007,"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/intercellular-communication","display_name":"intercellular communication","score":0.9769999980926514},{"id":"https://openalex.org/keywords/spatial-transcriptomics","display_name":"spatial transcriptomics","score":0.843999981880188},{"id":"https://openalex.org/keywords/representation-learning","display_name":"representation learning","score":0.8420000076293945},{"id":"https://openalex.org/keywords/ligand-receptor-signaling","display_name":"ligand-receptor signaling","score":0.8270000219345093},{"id":"https://openalex.org/keywords/ovarian-cancer","display_name":"ovarian cancer","score":0.47600001096725464},{"id":"https://openalex.org/keywords/melanoma","display_name":"melanoma","score":0.878000020980835},{"id":"https://openalex.org/keywords/t-cell-response","display_name":"T cell response","score":0.722000002861023},{"id":"https://openalex.org/keywords/brain-aging","display_name":"brain aging","score":0.8939999938011169},{"id":"https://openalex.org/keywords/collagen","display_name":"collagen","score":0.8299999833106995},{"id":"https://openalex.org/keywords/immunotherapy-response","display_name":"immunotherapy response","score":0.8140000104904175},{"id":"https://openalex.org/keywords/tumor-microenvironment","display_name":"tumor microenvironment","score":0.4440000057220459},{"id":"https://openalex.org/keywords/monocytes","display_name":"monocytes","score":0.5920000076293945},{"id":"https://openalex.org/keywords/fibroblasts","display_name":"fibroblasts","score":0.652999997138977}],"concepts":[{"id":"https://openalex.org/C74318829","wikidata":"https://www.wikidata.org/wiki/Q36458","display_name":"Multicellular organism","level":3,"score":0.8144000172615051},{"id":"https://openalex.org/C198104137","wikidata":"https://www.wikidata.org/wiki/Q974688","display_name":"Communication source","level":2,"score":0.6800000071525574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5888000130653381},{"id":"https://openalex.org/C2778156585","wikidata":"https://www.wikidata.org/wiki/Q174053","display_name":"Relay","level":3,"score":0.5406000018119812},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5397999882698059},{"id":"https://openalex.org/C12426560","wikidata":"https://www.wikidata.org/wiki/Q189569","display_name":"Basis (linear algebra)","level":2,"score":0.4620000123977661},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4560000002384186},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4512999951839447},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4287000000476837},{"id":"https://openalex.org/C169760540","wikidata":"https://www.wikidata.org/wiki/Q207011","display_name":"Neuroscience","level":1,"score":0.3271999955177307},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3140999972820282},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.29919999837875366},{"id":"https://openalex.org/C5917680","wikidata":"https://www.wikidata.org/wiki/Q2621825","display_name":"Basis function","level":2,"score":0.2827000021934509},{"id":"https://openalex.org/C46312422","wikidata":"https://www.wikidata.org/wiki/Q11024","display_name":"Communication","level":1,"score":0.2750999927520752},{"id":"https://openalex.org/C101765175","wikidata":"https://www.wikidata.org/wiki/Q577764","display_name":"Communications system","level":2,"score":0.26080000400543213},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.25189998745918274}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.09.21.753369","doi":"https://doi.org/10.64898/2026.09.21.753369","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.21.753369","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/27/2026.09.21.753369.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-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"},{"id":"pmid:42818244","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42818244","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"},{"id":"pmh:oai:pubmedcentral.nih.gov:13622179","doi":null,"is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42818244/","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.64898/2026.09.21.753369","doi":"https://doi.org/10.64898/2026.09.21.753369","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.21.753369","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/27/2026.09.21.753369.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-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":[{"id":"https://openalex.org/G4992377567","display_name":"Multiscale Analyses of 4D Nucleome Structure and Function by Comprehensive Multimodal Data Integration","funder_award_id":"UM1HG011593","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G5944552820","display_name":"Computational Methods for Next-Generation Comparative Genomics","funder_award_id":"R01HG007352","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G7112737660","display_name":"Spatial omics technologies to map the senescent cell microenvironment","funder_award_id":"UH3CA268202","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7291668909","display_name":"Three-dimensional mapping and modeling of combinatorial interactions underlying biomolecular condensates in olfactory neurons","funder_award_id":"1r21da061481-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000907590","display_name":"Integrative Machine Learning for Common Fund Spatial Omics","funder_award_id":"1r03od039980-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000908455","display_name":"Computational methods for studying single-cell 3D genome","funder_award_id":"R01HG012303","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G9000908836","display_name":"WashU-Northwestern Genomic Variation and Function Data and Administrative Coordinating Center","funder_award_id":"U24HG012070","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320308774","display_name":"John Simon Guggenheim Memorial Foundation","ror":"https://ror.org/0407tnq23"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214536278.pdf","grobid_xml":"https://content.openalex.org/works/W7214536278.grobid-xml"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1967449699","https://openalex.org/W1970924670","https://openalex.org/W2015583498","https://openalex.org/W2069518226","https://openalex.org/W2094863064","https://openalex.org/W2096234619","https://openalex.org/W2125061065","https://openalex.org/W2164928285","https://openalex.org/W2299181842","https://openalex.org/W2512899508","https://openalex.org/W2557833574","https://openalex.org/W2572293469","https://openalex.org/W2796207838","https://openalex.org/W2800392236","https://openalex.org/W2899204048","https://openalex.org/W2912137016","https://openalex.org/W2924317925","https://openalex.org/W2945711076","https://openalex.org/W2973690026","https://openalex.org/W3003058300","https://openalex.org/W3014940784","https://openalex.org/W3131183594","https://openalex.org/W3132661792","https://openalex.org/W3162215872","https://openalex.org/W3190202966","https://openalex.org/W4206140576","https://openalex.org/W4214881895","https://openalex.org/W4221123198","https://openalex.org/W4233698560","https://openalex.org/W4294216483","https://openalex.org/W4307233008","https://openalex.org/W4307432965","https://openalex.org/W4307497973","https://openalex.org/W4317757307","https://openalex.org/W4322768301","https://openalex.org/W4324046169","https://openalex.org/W4383342368","https://openalex.org/W4385520050","https://openalex.org/W4390974497","https://openalex.org/W4391262585","https://openalex.org/W4392198237","https://openalex.org/W4392343318","https://openalex.org/W4392748138","https://openalex.org/W4401406616","https://openalex.org/W4401736092","https://openalex.org/W4401798287","https://openalex.org/W4401894636","https://openalex.org/W4402171757","https://openalex.org/W4404040230","https://openalex.org/W4405375104","https://openalex.org/W4405515030","https://openalex.org/W4405640528","https://openalex.org/W4405854492","https://openalex.org/W4408363679","https://openalex.org/W4408823181","https://openalex.org/W4408959691","https://openalex.org/W4409382793","https://openalex.org/W4411100466","https://openalex.org/W7138942596","https://openalex.org/W7139970162","https://openalex.org/W7203444486"],"related_works":["https://openalex.org/W7163010629","https://openalex.org/W7220185075","https://openalex.org/W4414465018","https://openalex.org/W7139970162","https://openalex.org/W4223952512","https://openalex.org/W7167817881","https://openalex.org/W4294555560","https://openalex.org/W4413128015","https://openalex.org/W4402222433","https://openalex.org/W4402171757"],"abstract_inverted_index":{"Abstract":[0],"Tissue":[1],"function":[2],"depends":[3],"on":[4],"signals":[5,160],"exchanged":[6],"between":[7,199],"cells":[8,138],"and":[9,58,64,80,88,94,115,136,152,158,165,186,202,212],"the":[10],"responses":[11,147],"they":[12],"elicit.":[13],"Yet":[14],"whether":[15],"diverse":[16],"cell-cell":[17,44],"interactions":[18,201],"in":[19,98,101,113,178,216],"situ":[20,217],"form":[21],"recurrent":[22,170],"sender-receiver":[23],"programs":[24,38,112],"remains":[25],"un-clear.":[26],"We":[27],"present":[28],"SpiderNet,":[29],"an":[30,130,140],"interpretable":[31],"representation-learning":[32],"framework":[33,207],"that":[34,161],"discovers":[35],"such":[36],"directed":[37],"as":[39,194],"a":[40,154,169,195,206],"compact":[41],"basis":[42],"of":[43],"meta-interactions":[45],"(MIs)":[46],"from":[47],"spatial":[48],"transcriptomics.":[49],"SpiderNet":[50,90,128,190],"jointly":[51],"learns":[52],"which":[53],"sender":[54],"regulators,":[55],"ligand-receptor":[56],"pairs,":[57],"receiver":[59],"targets":[60],"define":[61],"each":[62,66],"MI":[63],"where":[65],"program":[67,157,174],"is":[68,181],"active":[69],"across":[70,163],"neighboring":[71],"cell":[72,84],"pairs.":[73],"The":[74],"resulting":[75],"representation":[76],"traces":[77],"multicellular":[78,214],"relays":[79],"links":[81],"communication":[82],"to":[83,148,188,208],"states,":[85],"perturbation":[86],"responses,":[87],"phenotypes.":[89],"recovers":[91],"ground-truth":[92],"MIs":[93,193],"their":[95],"molecular":[96,200],"components":[97],"simulations":[99],"and,":[100],"real":[102],"tissues,":[103],"shows":[104],"stronger":[105],"direction-specific":[106],"agreement":[107],"with":[108,183],"independently":[109],"curated":[110],"regulatory":[111],"senders":[114],"receivers":[116],"than":[117,122],"alternative":[118],"methods.":[119],"Across":[120],"more":[121],"5.8":[123],"million":[124],"spatially":[125],"profiled":[126],"cells,":[127],"resolves":[129],"SPP1-THBS":[131],"relay":[132],"linking":[133],"monocytes,":[134],"fibroblasts,":[135],"tumor":[137],"within":[139],"immune-suppressive":[141],"ovarian":[142],"cancer":[143],"niche,":[144],"predicts":[145],"T-cell":[146],"held-out":[149],"melanoma-cell":[150],"perturbations,":[151],"identifies":[153],"T-cell-associated":[155],"brain-aging":[156],"age-predictive":[159],"transfer":[162],"regions":[164],"platforms.":[166],"It":[167],"reveals":[168],"pan-cancer":[171],"COLLAGEN-linked":[172],"fibroblast-tumor":[173],"whose":[175],"projected":[176],"abundance":[177],"independent":[179],"cohorts":[180],"associated":[182],"poorer":[184],"survival":[185],"non-response":[187],"immunotherapy.":[189],"thus":[191],"establishes":[192],"reusable":[196],"organizational":[197],"layer":[198],"tissue":[203],"phenotypes,":[204],"providing":[205],"resolve,":[209],"compare,":[210],"trace,":[211],"perturb":[213],"regulation":[215],".":[218]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-28T00:00:00"}
