{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,24]],"date-time":"2026-03-24T20:14:33Z","timestamp":1774383273025,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,8,23]],"date-time":"2022-08-23T00:00:00Z","timestamp":1661212800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["HL148865"],"award-info":[{"award-number":["HL148865"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Digestive Health Center","award":["DK078392"],"award-info":[{"award-number":["DK078392"]}]},{"name":"National Cooperative Reprogrammed Cell Research Program","award":["MH104172"],"award-info":[{"award-number":["MH104172"]}]},{"name":"Center of Excellence in Molecular Hematology","award":["DK126108"],"award-info":[{"award-number":["DK126108"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,20]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Cells and tissues respond to perturbations in multiple ways that can be sensitively reflected in the alterations of gene expression. Current approaches to finding and quantifying the effects of perturbations on cell-level responses over time disregard the temporal consistency of identifiable gene programs. To leverage the occurrence of these patterns for perturbation analyses, we developed CellDrift (https:\/\/github.com\/KANG-BIOINFO\/CellDrift), a generalized linear model-based functional data analysis method that is capable of identifying covarying temporal patterns of various cell types in response to perturbations. As compared to several other approaches, CellDrift demonstrated superior performance in the identification of temporally varied perturbation patterns and the ability to impute missing time points. We applied CellDrift to multiple longitudinal datasets, including COVID-19 disease progression and gastrointestinal tract development, and demonstrated its ability to identify specific gene programs associated with sequential biological processes, trajectories and outcomes.<\/jats:p>","DOI":"10.1093\/bib\/bbac324","type":"journal-article","created":{"date-parts":[[2022,8,23]],"date-time":"2022-08-23T19:28:21Z","timestamp":1661282901000},"source":"Crossref","is-referenced-by-count":12,"title":["CellDrift: inferring perturbation responses in temporally sampled single-cell data"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5638-040X","authenticated-orcid":false,"given":"Kang","family":"Jin","sequence":"first","affiliation":[{"name":"Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center , Cincinnati, OH 45229, USA"},{"name":"Department of Biomedical Informatics, University of Cincinnati , Cincinnati, OH 45229, 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, Cincinnati, OH 45229, USA"},{"name":"Department of Biomedical Informatics, University of Cincinnati , Cincinnati, OH 45229, USA"},{"name":"Department of Pediatrics, University of Cincinnati School of Medicine , Cincinnati, OH 45256, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"V B Surya","family":"Prasath","sequence":"additional","affiliation":[{"name":"Division of Biomedical Informatics, Cincinnati Children\u2019s Hospital Medical Center , Cincinnati, OH 45229, USA"},{"name":"Department of Biomedical Informatics, University of Cincinnati , Cincinnati, OH 45229, USA"},{"name":"Department of Electrical Engineering and Computer Science, University of Cincinnati , OH 45256, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rhonda","family":"Szczesniak","sequence":"additional","affiliation":[{"name":"Division of Biostatistics and Epidemiology, Cincinnati Children\u2019s Hospital Medical Center , OH 45229, 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