Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions
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Summary
Monocle is described, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points that revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation.
- Type
- article
- Published
- 2014-03-23
- Cited by
- 5,423
- References
- 44
- Access
- Open access
- OpenAlex
- https://openalex.org/W1984883254
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:195679512
Keywords
Transcriptome, Gene expression, Cellular differentiation, Biology, Computational biology
References
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- Discovering Biological Progression Underlying Microarray Samples
- Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis
- Extracting a Cellular Hierarchy from High-dimensional Cytometry Data with SPADE
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- Computational morphology of curves
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
- Estimation of Relationships for Limited Dependent Variables
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- A Bead-Based Microfluidic Approach to Integrated Single-Cell Gene Expression Analysis by Quantitative RT-PCR
- SINCERA: A Pipeline for Single-Cell RNA-Seq Profiling Analysis
- Multipotent pancreas progenitors: Inconclusive but pivotal topic.
- Inference of differentiation time for single cell transcriptomes using cell population reference data
- scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
- DCARS: Differential correlation across ranked samples
- Revealing cellular and molecular transitions in neonatal germ cell differentiation using single cell RNA sequencing
- Systematic Comparison of High-throughput Single-Cell and Single-Nucleus Transcriptomes during Cardiomyocyte Differentiation
- A Single-Cell Characterization of Human Post-implantation Embryos Cultured In Vitro Delineates Morphogenesis in Primary Syncytialization
- Single-cell analysis of the aging female mouse hypothalamus
- Combined Single‐Cell and Spatial Transcriptomics Reveal the Metabolic Evolvement of Breast Cancer during Early Dissemination
- Methionine restriction reduced growth performance and exacerbated lipid deposition in hybrid grouper (Epinephelus fuscoguttatus ♀ × E. lanceolatus ♂) under high-lipid diets by suppressing the lipid degradation pathways with the single-cell RNA-seq analysis.
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- Lessons from reverse-genetic studies of lncRNAs.
- Scalable Optimization Algorithms for High-throughput Genomic Data
- CD8+ T cell diversification by asymmetric cell division
- Multiplex Single Cell Profiling of Chromatin Accessibility by Combinatorial Cellular Indexing
- A hyper-dynamic nature of bivalent promoter states underlies coordinated developmental gene expression modules
- Human and Mouse Mononuclear Phagocyte Networks: A Tale of Two Species?
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