{"id":"https://openalex.org/W7204267049","doi":"https://doi.org/10.64898/2026.08.25.746940","title":"In the same cell, the proteome defines cellular state and the transcriptome marks transitions","display_name":"In the same cell, the proteome defines cellular state and the transcriptome marks transitions","publication_year":2026,"publication_date":"2026-08-26","ids":{"openalex":"https://openalex.org/W7204267049","doi":"https://doi.org/10.64898/2026.08.25.746940"},"language":"en","primary_location":{"id":"doi:10.64898/2026.08.25.746940","doi":"https://doi.org/10.64898/2026.08.25.746940","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.25.746940","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/26/2026.08.25.746940.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":"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/2026/08/26/2026.08.25.746940.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010489600","display_name":"Marvin Thielert","orcid":"https://orcid.org/0000-0003-3639-2221","observed_orcids":["https://orcid.org/0000-0003-3639-2221"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marvin Thielert","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0003-3639-2221","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026361455","display_name":"Enes Ugur","orcid":"https://orcid.org/0000-0003-1950-8712","observed_orcids":["https://orcid.org/0000-0003-1950-8712"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]},{"id":"https://openalex.org/I860889466","display_name":"Friedrich Miescher Institute","ror":"https://ror.org/01bmjkv45","country_code":"CH","type":"facility","lineage":["https://openalex.org/I860889466"]}],"countries":["CH","DE"],"is_corresponding":false,"raw_author_name":"Enes Ugur","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","ETH Z\u00fcrich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland","Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056 Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-1950-8712","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]},{"raw_affiliation_string":"ETH Z\u00fcrich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I860889466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054251836","display_name":"Maximilian Zwiebel","orcid":"https://orcid.org/0000-0002-7005-5619","observed_orcids":["https://orcid.org/0000-0002-7005-5619"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Maximilian Zwiebel","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7005-5619","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055843241","display_name":"Marc Oeller","orcid":"https://orcid.org/0000-0003-0597-5950","observed_orcids":["https://orcid.org/0000-0003-0597-5950"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Marc Oeller","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0003-0597-5950","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019609870","display_name":"Constantin Diekmann","orcid":"https://orcid.org/0000-0002-4779-3541","observed_orcids":["https://orcid.org/0000-0002-4779-3541"]},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Constantin Diekmann","raw_affiliation_strings":["Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0002-4779-3541","affiliations":[{"raw_affiliation_string":"Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5128929272","display_name":"Nils Eikmeier","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nils Eikmeier","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000127861","display_name":"Simon Suppinger","orcid":"https://orcid.org/0000-0001-6426-402X","observed_orcids":["https://orcid.org/0000-0001-6426-402X"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I860889466","display_name":"Friedrich Miescher Institute","ror":"https://ror.org/01bmjkv45","country_code":"CH","type":"facility","lineage":["https://openalex.org/I860889466"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Simon Suppinger","raw_affiliation_strings":["ETH Z\u00fcrich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland","Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056 Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0001-6426-402X","affiliations":[{"raw_affiliation_string":"ETH Z\u00fcrich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I860889466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119618188","display_name":"Lucas Diedrich","orcid":"https://orcid.org/0009-0007-4884-1422","observed_orcids":["https://orcid.org/0009-0007-4884-1422"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Lucas Diedrich","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0009-0007-4884-1422","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086047679","display_name":"Sophia Steigerwald","orcid":"https://orcid.org/0000-0002-7513-1131","observed_orcids":["https://orcid.org/0000-0002-7513-1131"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sophia Steigerwald","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0002-7513-1131","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5139117373","display_name":"Ankit Sinha","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I2802619606","display_name":"TUM Klinikum","ror":"https://ror.org/04jc43x05","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802619606","https://openalex.org/I62916508"]},{"id":"https://openalex.org/I4210127591","display_name":"German Centre for Cardiovascular Research","ror":"https://ror.org/031t5w623","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210127591","https://openalex.org/I4405256427"]},{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]},{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ankit Sinha","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany","Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]},{"raw_affiliation_string":"German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Berlin, Germany","institution_ids":["https://openalex.org/I4210127591"]},{"raw_affiliation_string":"Institute of Molecular Vascular Medicine, TUM University Hospital, Technical University Munich, Munich, Germany","institution_ids":["https://openalex.org/I2802619606","https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053862797","display_name":"Prisca Liberali","orcid":"https://orcid.org/0000-0003-0695-6081","observed_orcids":["https://orcid.org/0000-0003-0695-6081"]},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I860889466","display_name":"Friedrich Miescher Institute","ror":"https://ror.org/01bmjkv45","country_code":"CH","type":"facility","lineage":["https://openalex.org/I860889466"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Prisca Liberali","raw_affiliation_strings":["ETH Z\u00fcrich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland","Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056 Basel, Switzerland"],"raw_orcid":"https://orcid.org/0000-0003-0695-6081","affiliations":[{"raw_affiliation_string":"ETH Z\u00fcrich, Department for Biosystems Science and Engineering (D-BSSE), Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Friedrich Miescher Institute for Biomedical Research, Fabrikstrasse 24, 4056 Basel, Switzerland","institution_ids":["https://openalex.org/I860889466"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072751630","display_name":"Christoph Ziegenhain","orcid":"https://orcid.org/0000-0003-2208-4877","observed_orcids":["https://orcid.org/0000-0003-2208-4877"]},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]}],"countries":["SE"],"is_corresponding":false,"raw_author_name":"Christoph Ziegenhain","raw_affiliation_strings":["Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden"],"raw_orcid":"https://orcid.org/0000-0003-2208-4877","affiliations":[{"raw_affiliation_string":"Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090940750","display_name":"Matthias Mann","orcid":"https://orcid.org/0000-0003-1292-4799","observed_orcids":["https://orcid.org/0000-0003-1292-4799","https://orcid.org/0000-0002-7122-6379"]},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Matthias Mann","raw_affiliation_strings":["Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":"https://orcid.org/0000-0003-1292-4799","affiliations":[{"raw_affiliation_string":"Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5090940750"],"corresponding_institution_ids":["https://openalex.org/I4210150093"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":3,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.7797999978065491,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.7797999978065491,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.16580000519752502,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00559999980032444,"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/single-cell-proteomics","display_name":"single-cell proteomics","score":0.8460000157356262},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.9649999737739563},{"id":"https://openalex.org/keywords/transcriptome-proteome-correlation","display_name":"transcriptome-proteome correlation","score":0.7699999809265137},{"id":"https://openalex.org/keywords/cell-states","display_name":"cell states","score":0.8379999995231628},{"id":"https://openalex.org/keywords/transcriptional-co-regulation","display_name":"transcriptional co-regulation","score":0.7879999876022339},{"id":"https://openalex.org/keywords/transcriptional-bursting","display_name":"transcriptional bursting","score":0.8510000109672546},{"id":"https://openalex.org/keywords/hela-cells","display_name":"HeLa cells","score":0.6899999976158142}],"concepts":[{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.8960999846458435},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.8452000021934509},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7299000024795532},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5200999975204468},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.5117999911308289},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.47369998693466187},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.4575999975204468},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4481000006198883},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4043000042438507},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.3921000063419342},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.37959998846054077},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.3725000023841858},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3375000059604645},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.29260000586509705},{"id":"https://openalex.org/C41282012","wikidata":"https://www.wikidata.org/wiki/Q3928341","display_name":"RNA-binding protein","level":4,"score":0.2793999910354614},{"id":"https://openalex.org/C3675279","wikidata":"https://www.wikidata.org/wiki/Q211935","display_name":"Protein biosynthesis","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C75934600","wikidata":"https://www.wikidata.org/wiki/Q419245","display_name":"Ribonucleoprotein","level":4,"score":0.2655999958515167},{"id":"https://openalex.org/C6856738","wikidata":"https://www.wikidata.org/wiki/Q331672","display_name":"Protein expression","level":3,"score":0.25839999318122864},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2581999897956848},{"id":"https://openalex.org/C2780887552","wikidata":"https://www.wikidata.org/wiki/Q7226087","display_name":"Poly(A)-binding protein","level":5,"score":0.25699999928474426},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2556000053882599},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.25099998712539673}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.08.25.746940","doi":"https://doi.org/10.64898/2026.08.25.746940","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.25.746940","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/26/2026.08.25.746940.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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.08.25.746940","doi":"https://doi.org/10.64898/2026.08.25.746940","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.08.25.746940","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/08/26/2026.08.25.746940.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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2201897555","display_name":"Tissue scale coordination during crypt morphogenesis","funder_award_id":"223263","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7099346681","display_name":"Decoding the interplay of regulation and stochasticity in alternative mRNA splicing","funder_award_id":"2022-01471","funder_id":"https://openalex.org/F4320322581","funder_display_name":"Vetenskapsr\u00e5det"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320322315","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691"},{"id":"https://openalex.org/F4320322434","display_name":"Max-Planck-Gesellschaft","ror":"https://ror.org/01hhn8329"},{"id":"https://openalex.org/F4320322581","display_name":"Vetenskapsr\u00e5det","ror":"https://ror.org/03zttf063"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7204267049.pdf","grobid_xml":"https://content.openalex.org/works/W7204267049.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W1874303456","https://openalex.org/W1973268693","https://openalex.org/W1993009001","https://openalex.org/W2053460598","https://openalex.org/W2059053384","https://openalex.org/W2064186732","https://openalex.org/W2106014350","https://openalex.org/W2114870653","https://openalex.org/W2126441851","https://openalex.org/W2128551987","https://openalex.org/W2162098178","https://openalex.org/W2162640412","https://openalex.org/W2211016425","https://openalex.org/W2293782153","https://openalex.org/W2332292689","https://openalex.org/W2340761255","https://openalex.org/W2509957998","https://openalex.org/W2529263647","https://openalex.org/W2555892463","https://openalex.org/W2572662684","https://openalex.org/W2583932040","https://openalex.org/W2625834976","https://openalex.org/W2739492614","https://openalex.org/W2766437506","https://openalex.org/W2788593837","https://openalex.org/W2792650071","https://openalex.org/W2806543441","https://openalex.org/W2808845633","https://openalex.org/W2905317377","https://openalex.org/W2906180136","https://openalex.org/W2950402574","https://openalex.org/W2953170162","https://openalex.org/W2984472267","https://openalex.org/W2991106430","https://openalex.org/W3021060601","https://openalex.org/W3023198889","https://openalex.org/W3027051073","https://openalex.org/W3044145717","https://openalex.org/W3047141442","https://openalex.org/W3108179367","https://openalex.org/W3130844754","https://openalex.org/W3179871140","https://openalex.org/W3196855488","https://openalex.org/W4210607772","https://openalex.org/W4214546240","https://openalex.org/W4281965038","https://openalex.org/W4290052552","https://openalex.org/W4310942643","https://openalex.org/W4317718280","https://openalex.org/W4321367488","https://openalex.org/W4321371924","https://openalex.org/W4362521490","https://openalex.org/W4362737480","https://openalex.org/W4386019486","https://openalex.org/W4386944450","https://openalex.org/W4392091326","https://openalex.org/W4400422998","https://openalex.org/W4402902773","https://openalex.org/W4404511387","https://openalex.org/W4406473173","https://openalex.org/W4406473270","https://openalex.org/W4409108775","https://openalex.org/W4409485811","https://openalex.org/W4413395154","https://openalex.org/W4414373167","https://openalex.org/W7161118381","https://openalex.org/W7161238401","https://openalex.org/W7167884469"],"related_works":["https://openalex.org/W2030680494","https://openalex.org/W7161238401","https://openalex.org/W3199418278","https://openalex.org/W4388745365","https://openalex.org/W7147253777","https://openalex.org/W4399180024","https://openalex.org/W4317603143","https://openalex.org/W4385408313","https://openalex.org/W7222395708","https://openalex.org/W2211104821"],"abstract_inverted_index":{"Summary":[0],"Bulk":[1],"transcriptome":[2,135,155],"and":[3,33,47,60,93,118,154,161],"proteome":[4,123,141,153],"correlate":[5],"only":[6,87],"modestly,":[7],"but":[8,74,168],"this":[9],"has":[10],"not":[11,76],"been":[12],"investigated":[13],"in":[14,35],"the":[15,36,65,79,98,126,134,140,157],"same":[16,37,158],"cell":[17,70,131,167],"or":[18],"across":[19,78,171],"cell-state":[20,143],"changes.":[21],"Here":[22],"we":[23],"introduce":[24],"a":[25,69,88,166,174],"scalable":[26],"technology":[27],"that":[28],"quantifies":[29],"thousands":[30],"of":[31,90,130,176],"proteins":[32,94],"transcripts":[34,92],"cell,":[38],"separating":[39],"RNA":[40,50],"from":[41,144,156,194],"protein":[42,61,113,162],"by":[43],"tip-based":[44],"C18":[45],"capture":[46],"pairing":[48],"full-length":[49],"sequencing":[51],"with":[52],"latest-generation":[53],"mass":[54],"spectrometry.":[55],"In":[56,84],"HeLa":[57],"cells,":[58],"transcript":[59],"abundances":[62],"agree":[63],"on":[64],"broad":[66],"ranking":[67],"within":[68,165],"(r":[71,81],"=":[72,82],"0.45),":[73],"do":[75],"co-vary":[77],"population":[80],"0.038).":[83],"pluripotency":[85],"transitions,":[86],"third":[89,175],"matched":[91],"change":[95,179],"synchronously,":[96],"yet":[97,181],"transcription":[99],"factors":[100],"defining":[101,192],"each":[102],"state":[103,193],"stay":[104,184],"tightly":[105],"co-regulated.":[106],"Transcript":[107,160],"variance":[108],"is":[109,124],"several-fold":[110,188],"larger":[111],"than":[112,190],"variance,":[114],"reflecting":[115],"transcriptional":[116],"bursting":[117],"mRNA":[119],"sampling":[120],"noise.":[121],"The":[122],"thus":[125],"stable,":[127],"low-noise":[128],"definition":[129],"state,":[132],"while":[133],"marks":[136],"cellular":[137],"transitions;":[138],"consequently,":[139],"defines":[142],"far":[145,195],"fewer":[146,196],"cells.":[147],"Highlights":[148],"Multimodal":[149],"workflow":[150],"yields":[151],"deep":[152],"cells":[159,172,197],"rank":[163],"similarly":[164],"are":[169],"uncoupled":[170],"Only":[173],"RNA-protein":[177],"pairs":[178],"together,":[180],"state-defining":[182],"TFs":[183],"coupled":[185],"Protein":[186],"varies":[187],"less":[189],"mRNA,":[191]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2026-08-27T00:00:00"}