{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:03:08Z","timestamp":1792785788893,"version":"4.5.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T00:00:00Z","timestamp":1788912000000},"content-version":"vor","delay-in-days":251,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Radiation Effects Research Foundation","award":["1\u201323-3"],"award-info":[{"award-number":["1\u201323-3"]}],"id":[{"id":"https:\/\/ror.org\/01fmtas32","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Japanese Ministry of Health, Labour and Welfare and the United States Department of Energy","id":[{"id":"https:\/\/ror.org\/03mwa7s65","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Low-dimensional representations are central to single-cell RNA sequencing analysis, yet perturbation-associated geometry is often interpreted visually without explicit assessment of estimator, sampling, or representation dependence. We introduce ScGeo, a representation-aware framework that treats embeddings as quantitative objects and reports robust state displacement, biological-sample uncertainty, local geometric preservation, cross-representation stability, distributional change, and agreement between condition-dependent displacement and independently supplied dynamics estimates. In GSE280305 post-irradiation hematopoietic recovery, ScGeo identified heterogeneous D8-to-D21 cluster displacement and partial agreement between geometric shifts and RNA velocity, while avoiding interpretation of time-point mixing as proof of valid integration. A prespecified synthetic benchmark showed that robust center estimators reduced outlier sensitivity, global representation corruption was detectable, and fine-grained localization of local distortion remained limited. A GSE132188-derived pancreatic-development workflow provided descriptive geometry-dynamics validation. In GSE249479, inflammatory effects in hematopoietic stem and progenitor cells were broadly stable across the primary representation ensemble but remained descriptive because biological-replicate identity was unavailable. In replicate-aware GSE211713 lung-radiation analysis, early 17\u2009Gy effects were representation-sensitive, whereas late remodeling was stable in five of six major compartments. ScGeo provides an auditable downstream layer for distinguishing stable, neutral, insufficient-coverage, and representation-sensitive interpretations rather than assuming any single latent space is biologically definitive.<\/jats:p>","DOI":"10.1093\/bioadv\/vbag266","type":"journal-article","created":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T11:37:04Z","timestamp":1788867424000},"source":"Crossref","is-referenced-by-count":0,"title":["ScGeo reveals non-canonical trajectories beyond RNA velocity in radiation-induced hematopoietic recovery"],"prefix":"10.1093","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2750-0182","authenticated-orcid":false,"given":"Yu-Chen","family":"Liu","sequence":"first","affiliation":[{"name":"Radiation Effects Research Foundation (RERF) , Hiroshima, 5-2 Hijiyama Park, Minami-ku , 732-0815,","place":["Japan"]},{"name":"Laboratory for Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center (IFReC), Osaka University , Osaka, 565-0871,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kengo","family":"Yoshida","sequence":"additional","affiliation":[{"name":"Radiation Effects Research Foundation (RERF) , Hiroshima, 5-2 Hijiyama Park, Minami-ku , 732-0815,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,9,9]]},"reference":[{"key":"2026092610240841000_vbag266-B1","doi-asserted-by":"publisher","first-page":"1832","DOI":"10.1101\/gr.279886.124","article-title":"Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated","volume":"35","author":"Antonsson","year":"2025","journal-title":"Genome Res"},{"key":"2026092610240841000_vbag266-B2","doi-asserted-by":"publisher","DOI":"10.1242\/dev.173849","article-title":"Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic 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