{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T01:53:54Z","timestamp":1782179634631,"version":"3.54.5"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T00:00:00Z","timestamp":1688083200000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ruth L. Kirschtein Predoctoral Fellowship"},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["F31CA24690"],"award-info":[{"award-number":["F31CA24690"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["R25 CA233208"],"award-info":[{"award-number":["R25 CA233208"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"La Caixa Junior Leader Fellowship","award":["LCF\/BQ\/PI20\/11760006"],"award-info":[{"award-number":["LCF\/BQ\/PI20\/11760006"]}]},{"name":"FERO-ASEICA","award":["BFERO2021"],"award-info":[{"award-number":["BFERO2021"]}]},{"name":"Department of Defense Pancreatic Cancer Research Program","award":["W81XWH-22-1-0814"],"award-info":[{"award-number":["W81XWH-22-1-0814"]}]},{"DOI":"10.13039\/501100004837","name":"Spanish Ministry of Science and Innovation","doi-asserted-by":"publisher","award":["PID2021-128102OA-I00"],"award-info":[{"award-number":["PID2021-128102OA-I00"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000011","name":"Howard Hughes Medical Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000011","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Geoffrey Beene Chair for Cancer Biology"},{"name":"Howard Hughes Medical Institute, Alan and Sandra Gerry Endowed Chair"},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","award":["CA209975"],"award-info":[{"award-number":["CA209975"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NCI Cancer Center Support","award":["P30 CA008748"],"award-info":[{"award-number":["P30 CA008748"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,6,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Transcriptional dynamics are governed by the action of regulatory proteins and are fundamental to systems ranging from normal development to disease. RNA velocity methods for tracking phenotypic dynamics ignore information on the regulatory drivers of gene expression variability through time.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce scKINETICS (Key regulatory Interaction NETwork for Inferring Cell Speed), a dynamical model of gene expression change which is fit with the simultaneous learning of per-cell transcriptional velocities and a governing gene regulatory network. Fitting is accomplished through an expectation\u2013maximization approach designed to learn the impact of each regulator on its target genes, leveraging biologically motivated priors from epigenetic data, gene\u2013gene coexpression, and constraints on cells\u2019 future states imposed by the phenotypic manifold. Applying this approach to an acute pancreatitis dataset recapitulates a well-studied axis of acinar-to-ductal transdifferentiation whilst proposing novel regulators of this process, including factors with previously appreciated roles in driving pancreatic tumorigenesis. In benchmarking experiments, we show that scKINETICS successfully extends and improves existing velocity approaches to generate interpretable, mechanistic models of gene regulatory dynamics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>All python code and an accompanying Jupyter notebook with demonstrations are available at http:\/\/github.com\/dpeerlab\/scKINETICS.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad267","type":"journal-article","created":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T08:16:04Z","timestamp":1688112964000},"page":"i394-i403","source":"Crossref","is-referenced-by-count":29,"title":["scKINETICS: inference of regulatory velocity with single-cell transcriptomics data"],"prefix":"10.1093","volume":"39","author":[{"given":"Cassandra","family":"Burdziak","sequence":"first","affiliation":[{"name":"Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute , 408 E 69th Street , New York, NY 10021, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chujun Julia","family":"Zhao","sequence":"additional","affiliation":[{"name":"Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute , 408 E 69th Street , New York, NY 10021, United States"},{"name":"Department of Biomedical Engineering, Columbia University , 1210 Amsterdam Ave , New York, NY 10027, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Doron","family":"Haviv","sequence":"additional","affiliation":[{"name":"Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute , 408 E 69th Street , New York, NY 10021, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Direna","family":"Alonso-Curbelo","sequence":"additional","affiliation":[{"name":"Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST) , Carrer de Baldiri Reixac, 10 , Barcelona 08028, Spain"},{"name":"Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute , 408 E 69th Street , New York, NY 10021, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott W","family":"Lowe","sequence":"additional","affiliation":[{"name":"Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute , 408 E 69th Street , New York, NY 10021, United States"},{"name":"Howard Hughes Medical Institute , 4000 Jones Bridge Road , Chevy Chase, Maryland 20815, United 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