ArticleNature biotechnology2022
CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Computational approaches for multimodal lineage tracing.Nature reviews. Genetics · 2026Review
- FlowMap: Geometry-Dynamics Consistent Embedding of RNA Velocity for Interpretable Cellular Trajectories.bioRxiv : the preprint server for biology · 2026Article
- Cell-level random splits leak group-owned answers in single-cell benchmarks.bioRxiv : the preprint server for biology · 2026Article
- A single-cell lens into the co-evolution of genotypes and phenotypes in cancer.Nature reviews. Cancer · 2026Review
- Sensitivity analysis of cell fate trajectories from single-cell transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.Nature methods · 2026Article
- Lineage-aware stochastic modeling reveals gene-expression dynamics in development and disease.bioRxiv : the preprint server for biology · 2026Article
- Computational blueprints for cell fate programming.Stem cell reports · 2026Review
- barbieQ: an R software package for analysing barcode count data from clonal tracking experiments.Bioinformatics (Oxford, England) · 2026Article
- Charting single-cell lineages with synthetic and natural barcodes.Nature reviews. Genetics · 2026Review
- Leveraging Lineage Barcodes as Natural Augmentations for Contrastive Learning of Cell Fate in scRNA-seq Data.bioRxiv : the preprint server for biology · 2026Article
- Clonal embeddings allow exploratory analysis of lineage-resolved single-cell data.bioRxiv : the preprint server for biology · 2026Article
- Robust identification of cell-cell communication heterogeneity in single cells.bioRxiv : the preprint server for biology · 2026Article
- Interpretation, extrapolation and perturbation of single cells.Nature reviews. Genetics · 2026Review
- Trajectory inference for a branching SDE model of cell differentiation via lineage tracing.Journal of mathematical biology · 2026Article
- DestinyNet: A deep-learning framework for cell-fate analysis from lineage-tracing single-cell RNA sequencing data.Patterns (New York, N.Y.) · 2026Article
- SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation.bioRxiv : the preprint server for biology · 2026Article
- Single-Cell Mitochondrial Lineage Tracing Decodes Fate Decision and Spatial Clonal Architecture in Human Hematopoietic Organoids.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- DNA methylation meets lineage tracing: History, recent progress, and future directions.Quantitative biology (Beijing, China) · 2026Article
- Single-cell mitochondrial lineage tracing: Opportunities and challenges.Quantitative biology (Beijing, China) · 2026Review
3 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
A goal of single-cell genome-wide profiling is to reconstruct dynamic transitions during cell differentiation, disease onset and drug response. Single-cell assays have recently been integrated with lineage tracing, a set of methods that identify cells of common ancestry to establish bona fide dynamic relationships between cell states. These integrated methods have revealed unappreciated cell dynamics, but their analysis faces recurrent challenges arising from noisy, dispersed lineage data. In this study, we developed coherent, sparse optimization (CoSpar) as a robust computational approach to infer cell dynamics from single-cell transcriptomics integrated with lineage tracing. Built on assumptions of coherence and sparsity of transition maps, CoSpar is robust to severe downsampling and dispersion of lineage data, which enables simpler experimental designs and requires less calibration. In datasets representing hematopoiesis, reprogramming and directed differentiation, CoSpar identifies early fate biases not previously detected, predicting transcription factors and receptors implicated in fate choice. Documentation and detailed examples for common experimental designs are available at https://cospar.readthedocs.io/ .
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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.