ArticleNature methods2023
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed, 100 citations in OpenAlex.
- MIGC: Pseudotime differentially expressed genes detection with mutual information.Quantitative biology (Beijing, China) · 2026Article
- CauTrigger: deciphering biological system state transitions by hierarchical causal decomposition.Nature methods · 2026Article
- Artificial Intelligence for Plant Gene Regulatory Networks.International journal of molecular sciences · 2026Review
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- Joint inference of paired dynamical gene regulatory networks reveals distinct cell-state landscapes of neutrophil reprogramming.bioRxiv : the preprint server for biology · 2026Article
- Article
- Deciphering global transcriptional dynamics coordinated by gene-gene regulatory interactions using single-cell data.Molecular systems biology · 2026Article
- Multiscale learning of gene network-driven phenotypic dynamics of single cells.Molecular systems biology · 2026Article
- T-ChroNet: Time-aware chromatin network reconstruction to detect dynamic regulatory programs in longitudinal epigenetic dataset.NAR genomics and bioinformatics · 2026Article
- Gene regulatory networks: from correlative models to causal explanations.Nature reviews. Genetics · 2026Review
- CeSpGRN: inferring cell-specific gene regulatory networks from single-cell multi-omics and spatial data.Bioinformatics (Oxford, England) · 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
- Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet.Genome research · 2026Article
- Inference of marker genes of subtle cell state changes via iLR: iterative logistic regression.Bioinformatics (Oxford, England) · 2026Article
- Modulation of Network Plasticity Opens Novel Therapeutic Possibilities in Cancer, Diabetes, and Neurodegeneration.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
- GP-DHT: A dual-head transformer with supervised contrastive learning for shared-gene pretraining and single-cell GRN prediction.PloS one · 2026Article
- Gene regulatory network inference with popInfer reveals the dynamic regulation of hematopoietic stem cell quiescence.iScience · 2025Article
- Building dynamical models of multi-step state transitions from single cell gene expression trajectories.bioRxiv : the preprint server for biology · 2025Article
- Airqtl dissects cell state-specific causal gene regulatory networks with efficient single-cell eQTL mapping.Nature communications · 2025Article
8 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease. Despite decades of advancement, challenges remain in GRN inference, including dynamic rewiring, causal inference, feedback loop modeling and context specificity. To address these challenges, we develop Dictys, a dynamic GRN inference and analysis method that leverages multiomic single-cell assays of chromatin accessibility and gene expression, context-specific transcription factor footprinting, stochastic process network and efficient probabilistic modeling of single-cell RNA-sequencing read counts. Dictys improves GRN reconstruction accuracy and reproducibility and enables the inference and comparative analysis of context-specific and dynamic GRNs across developmental contexts. Dictys' network analyses recover unique insights in human blood and mouse skin development with cell-type-specific and dynamic GRNs. Its dynamic network visualizations enable time-resolved discovery and investigation of developmental driver transcription factors and their regulated targets. Dictys is available as a free, open-source and user-friendly Python package.
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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.