{"id":"https://openalex.org/W7214213245","doi":"https://doi.org/10.64898/2026.09.17.751504","title":"Extracting interpretable single-cell metabolic states with graph-guided representation learning","display_name":"Extracting interpretable single-cell metabolic states with graph-guided representation learning","publication_year":2026,"publication_date":"2026-09-24","ids":{"openalex":"https://openalex.org/W7214213245","doi":"https://doi.org/10.64898/2026.09.17.751504","pmid":"https://pubmed.ncbi.nlm.nih.gov/42818076","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13622033"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.17.751504","doi":"https://doi.org/10.64898/2026.09.17.751504","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.17.751504","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.17.751504.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":"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/2026/09/24/2026.09.17.751504.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085845625","display_name":"Daniel P. Lewinsohn","orcid":"https://orcid.org/0000-0002-4868-7847","observed_orcids":["https://orcid.org/0000-0002-4868-7847"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Daniel P. Lewinsohn","raw_affiliation_strings":["Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0002-4868-7847","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5152672749","display_name":"Nicolas Dias","orcid":"https://orcid.org/0000-0003-0873-7245","observed_orcids":["https://orcid.org/0000-0003-0873-7245"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicolas Dias","raw_affiliation_strings":["Department of Genetics and the Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT, USA"],"raw_orcid":"https://orcid.org/0000-0003-0873-7245","affiliations":[{"raw_affiliation_string":"Department of Genetics and the Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104205495","display_name":"Adelina Chau","orcid":"https://orcid.org/0009-0002-1691-8732","observed_orcids":["https://orcid.org/0009-0002-1691-8732"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Adelina Chau","raw_affiliation_strings":["Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034020037","display_name":"Yuko Koike","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuko Koike","raw_affiliation_strings":["UC Berkeley\u2013UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UC Berkeley\u2013UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I180670191","https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032021891","display_name":"Zachary D. Smith","orcid":"https://orcid.org/0000-0002-9283-1957","observed_orcids":["https://orcid.org/0000-0002-9283-1957","https://orcid.org/0009-0000-1709-745X"]},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210142260","display_name":"Max Planck Institute for Molecular Genetics","ror":"https://ror.org/03ate3e03","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210142260"]}],"countries":["DE","US"],"is_corresponding":false,"raw_author_name":"Zachary D. Smith","raw_affiliation_strings":["Department of Genetics and the Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT, USA","Max Planck Institute for Molecular Genetics, Berlin, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics and the Yale Stem Cell Center, Yale School of Medicine, Yale University, New Haven, CT, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Max Planck Institute for Molecular Genetics, Berlin, Germany","institution_ids":["https://openalex.org/I4210142260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063118302","display_name":"Nilah M. Ioannidis","orcid":"https://orcid.org/0000-0001-9628-8229","observed_orcids":["https://orcid.org/0000-0001-9628-8229"]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]},{"id":"https://openalex.org/I4210100286","display_name":"Chan Zuckerberg Biohub San Francisco","ror":"https://ror.org/00knt4f32","country_code":"US","type":"facility","lineage":["https://openalex.org/I180670191","https://openalex.org/I4210100286","https://openalex.org/I4210121800","https://openalex.org/I95457486","https://openalex.org/I97018004"]},{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nilah M. Ioannidis","raw_affiliation_strings":["Biohub, San Francisco, CA, USA","Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA","Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA, USA","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA"],"raw_orcid":"https://orcid.org/0000-0001-9628-8229","affiliations":[{"raw_affiliation_string":"Biohub, San Francisco, CA, USA","institution_ids":["https://openalex.org/I4210100286"]},{"raw_affiliation_string":"Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Applied Mathematics, University of California, Santa Cruz, Santa Cruz, CA, USA","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089647811","display_name":"Allon Wagner","orcid":"https://orcid.org/0000-0001-5095-6009","observed_orcids":["https://orcid.org/0000-0001-5095-6009"]},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Allon Wagner","raw_affiliation_strings":["Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA","Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA"],"raw_orcid":"https://orcid.org/0000-0001-5095-6009","affiliations":[{"raw_affiliation_string":"Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, Berkeley, CA, USA","institution_ids":["https://openalex.org/I95457486"]},{"raw_affiliation_string":"Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5085845625"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5224999785423279,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.5224999785423279,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.23000000417232513,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.17880000174045563,"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/folate-deficiency","display_name":"folate deficiency","score":0.9700000286102295},{"id":"https://openalex.org/keywords/de-novo-purine-synthesis","display_name":"de novo purine synthesis","score":0.8790000081062317},{"id":"https://openalex.org/keywords/neural-tube-defects","display_name":"neural tube defects","score":0.9909999966621399},{"id":"https://openalex.org/keywords/t-cell-metabolism","display_name":"T cell metabolism","score":0.902999997138977},{"id":"https://openalex.org/keywords/cytokines","display_name":"cytokines","score":0.8389999866485596},{"id":"https://openalex.org/keywords/t-cell-exhaustion","display_name":"T cell exhaustion","score":0.9909999966621399},{"id":"https://openalex.org/keywords/cancer-therapy-response","display_name":"cancer therapy response","score":0.8180000185966492},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.718999981880188}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7379999756813049},{"id":"https://openalex.org/C192989942","wikidata":"https://www.wikidata.org/wiki/Q68685","display_name":"Metabolic pathway","level":3,"score":0.6804999709129333},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.6212000250816345},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5311999917030334},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5206999778747559},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.42800000309944153},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.42570000886917114},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.42320001125335693},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.413100004196167},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.38760000467300415},{"id":"https://openalex.org/C169586020","wikidata":"https://www.wikidata.org/wiki/Q3780159","display_name":"Purine metabolism","level":3,"score":0.38760000467300415},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.37940001487731934},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35670000314712524},{"id":"https://openalex.org/C2993927895","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolic activity","level":2,"score":0.3481999933719635},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.34119999408721924},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.32249999046325684},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.31779998540878296},{"id":"https://openalex.org/C2992768293","wikidata":"https://www.wikidata.org/wiki/Q623293","display_name":"Metabolic rate","level":2,"score":0.3093999922275543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27900001406669617},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.27379998564720154},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.26820001006126404},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.26409998536109924},{"id":"https://openalex.org/C48103436","wikidata":"https://www.wikidata.org/wiki/Q599031","display_name":"State (computer science)","level":2,"score":0.2542000114917755}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.64898/2026.09.17.751504","doi":"https://doi.org/10.64898/2026.09.17.751504","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.17.751504","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.17.751504.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":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:42818076","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42818076","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:13622033","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13622033/","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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"bioRxiv","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.64898/2026.09.17.751504","doi":"https://doi.org/10.64898/2026.09.17.751504","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.17.751504","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/24/2026.09.17.751504.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":"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/G5141625836","display_name":"Epigenetic and environmental impact on early embryonic development","funder_award_id":"DP2HD108774","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"}],"funders":[{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214213245.pdf","grobid_xml":"https://content.openalex.org/works/W7214213245.grobid-xml"},"referenced_works_count":92,"referenced_works":["https://openalex.org/W1535641839","https://openalex.org/W1597619535","https://openalex.org/W1918238463","https://openalex.org/W1959608418","https://openalex.org/W1988391018","https://openalex.org/W2045274781","https://openalex.org/W2070050178","https://openalex.org/W2076272449","https://openalex.org/W2089375110","https://openalex.org/W2094973077","https://openalex.org/W2111642621","https://openalex.org/W2128265910","https://openalex.org/W2130410032","https://openalex.org/W2151936673","https://openalex.org/W2159707944","https://openalex.org/W2167482691","https://openalex.org/W2332292689","https://openalex.org/W2530067632","https://openalex.org/W2561754210","https://openalex.org/W2616922646","https://openalex.org/W2753908609","https://openalex.org/W2901677030","https://openalex.org/W2942678593","https://openalex.org/W2950975031","https://openalex.org/W2965552103","https://openalex.org/W2992151131","https://openalex.org/W3007935255","https://openalex.org/W3010473572","https://openalex.org/W3012280517","https://openalex.org/W3015450697","https://openalex.org/W3082731516","https://openalex.org/W3093858607","https://openalex.org/W3106615577","https://openalex.org/W3132661792","https://openalex.org/W3133076643","https://openalex.org/W3133221794","https://openalex.org/W3174064560","https://openalex.org/W3174551568","https://openalex.org/W3184580818","https://openalex.org/W3196650609","https://openalex.org/W3210028685","https://openalex.org/W3212661219","https://openalex.org/W4200249439","https://openalex.org/W4200468913","https://openalex.org/W4206027424","https://openalex.org/W4206662285","https://openalex.org/W4210587306","https://openalex.org/W4214503098","https://openalex.org/W4220652655","https://openalex.org/W4220798004","https://openalex.org/W4225278475","https://openalex.org/W4226455535","https://openalex.org/W4283588821","https://openalex.org/W4294216483","https://openalex.org/W4307497973","https://openalex.org/W4309944312","https://openalex.org/W4318217624","https://openalex.org/W4318981406","https://openalex.org/W4362657851","https://openalex.org/W4366982140","https://openalex.org/W4375955255","https://openalex.org/W4378953806","https://openalex.org/W4382632237","https://openalex.org/W4385638616","https://openalex.org/W4385955324","https://openalex.org/W4386923465","https://openalex.org/W4386923889","https://openalex.org/W4387576070","https://openalex.org/W4389390583","https://openalex.org/W4391567286","https://openalex.org/W4394764901","https://openalex.org/W4401978437","https://openalex.org/W4402826744","https://openalex.org/W4403619489","https://openalex.org/W4403629504","https://openalex.org/W4405893365","https://openalex.org/W4408896223","https://openalex.org/W4410416432","https://openalex.org/W4410961058","https://openalex.org/W4411023060","https://openalex.org/W4411047102","https://openalex.org/W4411069266","https://openalex.org/W4411226928","https://openalex.org/W4412160990","https://openalex.org/W4412615070","https://openalex.org/W4414014302","https://openalex.org/W4415101863","https://openalex.org/W4416704627","https://openalex.org/W4417500776","https://openalex.org/W7128425265","https://openalex.org/W7148582669","https://openalex.org/W7204052357"],"related_works":["https://openalex.org/W4399708278","https://openalex.org/W7168250360","https://openalex.org/W7160827121","https://openalex.org/W4417500776","https://openalex.org/W4396966031","https://openalex.org/W3184580818","https://openalex.org/W4410416432","https://openalex.org/W4285201328","https://openalex.org/W3082658663","https://openalex.org/W2900477098"],"abstract_inverted_index":{"Summary":[0],"Metabolism":[1],"shapes":[2],"cellular":[3],"function":[4],"and":[5,43,69,123,131,162,213],"state,":[6],"yet":[7],"measuring":[8],"single-cell":[9,47,149],"metabolic":[10,30,41,63,85,90,125,146,156,164,176,186,207,215],"states":[11],"at":[12],"scale":[13],"remains":[14],"a":[15,23,33,97,142],"challenge.":[16],"We":[17],"present":[18],"Metabolic":[19],"Representation":[20],"Net":[21],"(MeRN),":[22],"graph-guided":[24],"variational":[25],"autoencoder":[26],"that":[27,171],"leverages":[28,154],"prior":[29],"knowledge":[31],"as":[32,141],"topology":[34,157],"graph":[35],"to":[36,83,106,158,195],"learn":[37],"latent":[38],"representations":[39],"of":[40,52,58,71,127,148,179,189,209],"state":[42],"reaction":[44,53],"activity":[45,54],"from":[46],"transcriptomes.":[48,150],"MeRN\u2019s":[49],"scalable":[50],"estimation":[51],"enables":[55,167],"the":[56,79,93,155],"definition":[57],"data-driven":[59,168],"pathways":[60,169],"(DDPs):":[61],"context-specific":[62],"modules":[64],"supported":[65,174],"by":[66],"transcriptomic":[67],"evidence":[68],"agnostic":[70,178],"standard":[72,180],"pathway":[73,181],"definitions.":[74],"Using":[75],"DDPs,":[76],"we":[77],"introduce":[78],"weakest":[80],"link":[81],"analysis":[82,147],"identify":[84,185],"network":[86,187],"rewiring.":[87],"MeRN":[88,140,153,166,203],"recovers":[89],"zonation":[91],"in":[92,101,134],"mouse":[94],"intestine,":[95],"links":[96],"folate":[98,196],"deficiency-induced":[99],"break":[100],"de":[102,190],"novo":[103,191],"purine":[104,192],"synthesis":[105,193],"embryonic":[107,199],"neural":[108,200],"tube":[109,201],"defects,":[110],"shows":[111],"cytokines":[112],"with":[113],"similar":[114],"non-metabolic":[115],"effects":[116],"can":[117],"elicit":[118],"divergent":[119],"T":[120,128,210],"cell":[121,129,211],"metabolism,":[122],"identifies":[124,204],"drivers":[126,208],"exhaustion":[130,212],"therapy":[132],"response":[133],"human":[135,205],"cancers.":[136],"Our":[137],"results":[138],"establish":[139],"unified":[143],"method":[144],"for":[145],"Research":[151],"highlights":[152],"comprehensively":[159],"predict":[160],"reaction-":[161],"pathway-level":[163],"activities":[165],"(DDPs)":[170],"capture":[172],"empirically":[173],"cell-type-specific":[175],"modules,":[177],"definitions":[182],"MeRN-based":[183],"DDPs":[184],"rewiring":[188],"due":[194],"deficiency":[197],"during":[198],"development":[202],"pan-cancer":[206],"Treg-specific":[214],"adaptations":[216]},"counts_by_year":[],"updated_date":"2026-10-30T12:39:25.321706","created_date":"2026-09-25T00:00:00"}