ArticleNature methods2015
Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
What it found
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Who cites it
94 citing papers in PubMed.
- OscillomeR infers ultradian oscillations and targets of the Hes family.Patterns (New York, N.Y.) · 2026Article
- Deep learning models for cell cycle phase prediction from single-cell RNA sequencing data.Briefings in bioinformatics · 2026Article
- Are physiological oscillations physiological?The Journal of physiology · 2026Review
- Deciphering Cell Cycle Dynamics and Cell States in Single-cell RNA-seq data with SPAE.bioRxiv : the preprint server for biology · 2026Article
- scIRT: Imputation and Dimensionality Reduction for Single-Cell RNA-Seq Data by Combining NMF with SMOTE.International journal of molecular sciences · 2026Article
- CycleMix: Gaussian mixture modeling of the cell cycle.Bioinformatics advances · 2026Article
- Consensus spectral clustering with weighted similarity functions for single-cell RNA sequencing data.Communications in statistics: Simulation and computation · 2025Article
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- Rhythm profiling using COFE reveals multi-omic circadian rhythms in human cancers in vivo.PLoS biology · 2025Article
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- Classifying cell cycle states and a quiescent-like G0 state using single-cell transcriptomics.bioRxiv : the preprint server for biology · 2025Article
- Gene expression clock: an unsupervised deep learning approach for predicting circadian rhythmicity from whole genome expression.Neural computing & applications · 2024Article
- Cell identity revealed by precise cell cycle state mapping links data modalities.bioRxiv : the preprint server for biology · 2024Article
- Analyzing Single Cell RNA Sequencing with Topological Nonnegative Matrix Factorization.Journal of computational and applied mathematics · 2024Article
- Optimizing retinal ganglion cell nuclear staining for automated cell counting.Experimental eye research · 2024Article
- Modification of Seurat v4 for the Development of a Phase Assignment Tool Able to Distinguish between G2 and Mitotic Cells.International journal of molecular sciences · 2024Article
- Oscillatory differentiation dynamics fundamentally restricts the resolution of pseudotime reconstruction algorithms.Journal of the Royal Society, Interface · 2024Article
- Identification of genes with oscillatory expression in glioblastoma: the paradigm of SOX2.Scientific reports · 2024Article
- From G1 to M: a comparative study of methods for identifying cell cycle phases.Briefings in bioinformatics · 2024Review
- scPrisma infers, filters and enhances topological signals in single-cell data using spectral template matching.Nature biotechnology · 2023Article
34 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Oscillatory gene expression is fundamental to development, but technologies for monitoring expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applying Oscope to a number of data sets, we demonstrated its utility and also identified a potential artifact in the Fluidigm C1 platform.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.