2025
Suppression of Autosomal Dominant Polycystic Kidney Disease Influences Epithelial Cell Transcription Program
Rai V, Failli M, Fiusco M, Reyna-Neyra A, Onuchic L, di Bernardo D, Craft J, Caplan M. Suppression of Autosomal Dominant Polycystic Kidney Disease Influences Epithelial Cell Transcription Program. Physiology 2025, 40: 0966. DOI: 10.1152/physiol.2025.40.s1.0966.Peer-Reviewed Original ResearchC-terminal tailCystic phenotypeTranscriptional programsAutosomal dominant polycystic kidney diseaseScRNA-seqTranscriptional differencesAmino acid C-terminal tailAcidic C-terminal tailPolycystin-1 proteinCell transcriptional programDifferentiated cell stateEpithelial cellsSingle cell RNA sequencingDoxycycline-inducible mouse modelCell RNA sequencingNovel transcriptsLibrary preparationCell transcriptional profilingChromium technologyPKD1 geneBiological replicatesRNA velocityCDNA synthesisRNA sequencingTranscriptional profiles
2022
DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations
Chen Z, King W, Hwang A, Gerstein M, Zhang J. DeepVelo: Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. Science Advances 2022, 8: eabq3745. PMID: 36449617, PMCID: PMC9710871, DOI: 10.1126/sciadv.abq3745.Peer-Reviewed Original ResearchOrdinary differential equationsDifferential equationsTranscriptome dynamicsSingle-cell gene expression measurementsNeural ordinary differential equationsSingle-cell sequencing technologiesVelocity fieldIndividual cellsGene expression changesGene expression profilesDynamical systemsGene expression measurementsTranscriptional dynamicsRNA velocityDifferent sequencing platformsChaotic propertiesSequencing technologiesCell statesPerturbation analysisRegulatory relationshipsData-Driven DiscoveryExpression changesExpression profilesSequencing platformsDriver genes
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