Inferring absolute cell proliferation and death rates from non-longitudinal single-cell transcriptomics

Inferring absolute cell proliferation and death rates from non-longitudinal single-cell transcriptomics | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Article Inferring absolute cell proliferation and death rates from non-longitudinal single-cell transcriptomics Jean Hausser, Jakob Rosenbauer, Sofie Blahova, Michael Hagemann-Jensen, and 3 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8252082/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Cell proliferation and death rates are central to tissue biology but measuring them in vivo remains a persistent challenge. Here we present tissue dynamics inference (TIDYI), which quantifies absolute cell proliferation and death rates from non-longitudinal single-cell RNAseq snapshots. TIDYI expands the capability of single-cell RNAseq to extracting the cell dynamics of healthy and pathological tissues in vivo. Biological sciences/Biological techniques/Gene expression analysis Biological sciences/Computational biology and bioinformatics/Machine learning Biological sciences/Systems biology/Software Biological sciences/Stem cells/Self-renewal Full Text Additional Declarations There is NO Competing Interest. Supplementary Files TIDYISupplement.pdf Supplementary material Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8252082","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":576500071,"identity":"e90e2ec0-3207-45e4-953e-8623722ccf4e","order_by":0,"name":"Jean Hausser","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA2ElEQVRIiWNgGAWjYBACxgYYAQIfDkiQqIVxBjFaEPqAgJnnABGqmdubnz1g3GGXOL//8LHPNmcsGOTbG/BrYew5Zm7AeCY5ccONtOTZOTckGAzOELCKcUaCmQRjG3PiBgkeY+acD0AtEgkEtMx//g2opR7osPOfmS2AWuTnPyBkCw/IlsOJDQdymJkZgA5juIFfB9AvOWUSiW3HjYF+MWbsOSPBY3CGgMMM249vk/jYVi0LDLHHDD+O1cnJtx8goKUBSCAby0PAWQwM8gRVjIJRMApGwSgAAM77Q+NzcPzPAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-3321-7199","institution":"Karolinska Institute \u0026 SciLifeLab","correspondingAuthor":true,"prefix":"","firstName":"Jean","middleName":"","lastName":"Hausser","suffix":""},{"id":576500072,"identity":"5517f89e-a32a-45e4-8717-83bb0080c5b6","order_by":1,"name":"Jakob Rosenbauer","email":"","orcid":"","institution":"Karolinska Institute \u0026 SciLifeLab","correspondingAuthor":false,"prefix":"","firstName":"Jakob","middleName":"","lastName":"Rosenbauer","suffix":""},{"id":576500073,"identity":"4a856b5c-b5c3-4aaf-b1e2-60ca5efb60c9","order_by":2,"name":"Sofie Blahova","email":"","orcid":"https://orcid.org/0009-0007-2328-6231","institution":"Karolinska Institute \u0026 SciLifeLab","correspondingAuthor":false,"prefix":"","firstName":"Sofie","middleName":"","lastName":"Blahova","suffix":""},{"id":576500074,"identity":"b815a5b3-6214-46ca-a3ed-f2e55e49d847","order_by":3,"name":"Michael Hagemann-Jensen","email":"","orcid":"https://orcid.org/0000-0002-6423-8216","institution":"Karolinska Institute","correspondingAuthor":false,"prefix":"","firstName":"Michael","middleName":"","lastName":"Hagemann-Jensen","suffix":""},{"id":576500075,"identity":"c21c74a3-be11-46c6-b138-9ca279f85752","order_by":4,"name":"Alper Eroglu","email":"","orcid":"https://orcid.org/0000-0001-9473-3317","institution":"Karolinska Institute \u0026 SciLifeLab","correspondingAuthor":false,"prefix":"","firstName":"Alper","middleName":"","lastName":"Eroglu","suffix":""},{"id":576500076,"identity":"a1b4e343-7aff-462a-91ed-fbcb0773f7c0","order_by":5,"name":"Rickard Sandberg","email":"","orcid":"https://orcid.org/0000-0001-6473-1740","institution":"Karolinska Institute","correspondingAuthor":false,"prefix":"","firstName":"Rickard","middleName":"","lastName":"Sandberg","suffix":""},{"id":576500077,"identity":"bb742030-d859-42b0-9545-6ff32b137a97","order_by":6,"name":"Antony Cougnoux","email":"","orcid":"","institution":"Karolinska Institute \u0026 SciLifeLab","correspondingAuthor":false,"prefix":"","firstName":"Antony","middleName":"","lastName":"Cougnoux","suffix":""}],"badges":[],"createdAt":"2025-12-01 15:36:52","currentVersionCode":1,"declarations":{"humanSubjects":false,"vertebrateSubjects":false,"conflictsOfInterestStatement":false,"humanSubjectEthicalGuidelines":false,"humanSubjectConsent":false,"humanSubjectClinicalTrial":false,"humanSubjectCaseReport":false,"vertebrateSubjectEthicalGuidelines":false},"doi":"10.21203/rs.3.rs-8252082/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8252082/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":109405277,"identity":"4cf450dc-231c-456a-b6a7-c61149b54fee","added_by":"auto","created_at":"2026-05-17 13:15:49","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":881708,"visible":true,"origin":"","legend":"Article File","description":"","filename":"TIDYImanuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8252082/v1_covered_c935e640-45ef-4ddf-a4a9-798fa4fb80de.pdf"},{"id":102266550,"identity":"92e18623-9c87-4245-aa81-13460c7d6a24","added_by":"auto","created_at":"2026-02-10 02:48:26","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":3643006,"visible":true,"origin":"","legend":"Supplementary material","description":"","filename":"TIDYISupplement.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8252082/v1/8c523a853dbaa2640d07e243.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"Inferring absolute cell proliferation and death rates from non-longitudinal single-cell transcriptomics","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":true,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-8252082/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8252082/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Cell proliferation and death rates are central to tissue biology but measuring them in vivo remains a persistent challenge. Here we present tissue dynamics inference (TIDYI), which quantifies absolute cell proliferation and death rates from non-longitudinal single-cell RNAseq snapshots. TIDYI expands the capability of single-cell RNAseq to extracting the cell dynamics of healthy and pathological tissues in vivo.","manuscriptTitle":"Inferring absolute cell proliferation and death rates from non-longitudinal single-cell transcriptomics","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-02-10 02:48:21","doi":"10.21203/rs.3.rs-8252082/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"14a595f3-7c69-4ba9-bf29-02c088b5750a","owner":[],"postedDate":"February 10th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[{"id":61334328,"name":"Biological sciences/Biological techniques/Gene expression analysis"},{"id":61334329,"name":"Biological sciences/Computational biology and bioinformatics/Machine learning"},{"id":61334330,"name":"Biological sciences/Systems biology/Software"},{"id":61334331,"name":"Biological sciences/Stem cells/Self-renewal"}],"tags":[],"updatedAt":"2026-05-14T14:20:37+00:00","versionOfRecord":[],"versionCreatedAt":"2026-02-10 02:48:21","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8252082","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8252082","identity":"rs-8252082","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}