ArticleNature communications2021
Spearheading future omics analyses using dyngen, a multi-modal simulator of single cells.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
71 citing papers in PubMed.
- DiTSim: A Diffusion-Transformers Based Single-Cell ATAC-seq Data Simulator.Interdisciplinary sciences, computational life sciences · 2026Article
- Comprehensive benchmarking of RNA velocity methods across single-cell datasets.Genome biology · 2026Article
- BLASE: bulk linkage analysis for single cell experiments - teasing out the secrets of bulk transcriptomics with trajectory analysis.BMC methods · 2026Article
- FIERCE: reconstructing dynamic trajectories from the differentiation potency of single cells.Bioinformatics (Oxford, England) · 2026Article
- Prediction of parsimonious and temporally sensitive sets of cell fate engineering transcription factors with IMCell.bioRxiv : the preprint server for biology · 2026Article
- StPedf: Cell trajectory inference of spatial transcriptomics via spatial proximity embedding and spatial density-adaptive fusion.PLoS computational biology · 2026Article
- Benchmarking RNA velocity methods across 17 independent studies.Cell reports methods · 2026Article
- SCOPE: Localizing fate-decision states and their regulatory drivers in single-cell differentiation.bioRxiv : the preprint server for biology · 2026Article
- SuperGLUE facilitates an explainable training framework for multi-modal data analysis.Cell reports methods · 2025Article
- GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells.Nature communications · 2025Article
- Inferring causal trajectories from spatial transcriptomics using CASCAT.Nucleic acids research · 2025Article
- Current Bioinformatics Tools in Precision Oncology.MedComm · 2025Review
- Imputing single-cell protein abundance in multiplex tissue imaging.Nature communications · 2025Article
- ONTraC characterizes spatially continuous variations of tissue microenvironment through niche trajectory analysis.Genome biology · 2025Article
- scMultiSim: simulation of single-cell multi-omics and spatial data guided by gene regulatory networks and cell-cell interactions.Nature methods · 2025Article
- TrAGEDy-trajectory alignment of gene expression dynamics.Bioinformatics (Oxford, England) · 2025Article
- Gene-level alignment of single-cell trajectories.Nature methods · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Exploratory trajectory inference reveals convergent lineages for CD8 T cells in chronic LCMV infection.PloS one · 2025Article
- Trajectory inference from single-cell genomics data with a process time model.PLoS computational biology · 2025Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present dyngen, a multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. dyngen is more flexible than current single-cell simulation engines, and allows better method development and benchmarking, thereby stimulating development and testing of computational methods. We demonstrate its potential for spearheading computational methods on three applications: aligning cell developmental trajectories, cell-specific regulatory network inference and estimation of RNA velocity.
Indexed as
Identifiers
What OpenQuestion holds
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.