Research graph
References from GP-DHT: A dual-head transformer with supervised contrastive learning for shared-gene pretraining and single-cell GRN prediction. Local targets link to admitted publications; unresolved targets remain external evidence.
Gene regulatory network inference in single-cell biology
10.1016/j.coisb.2021.04.007 · 2021 · External reference
Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data
10.1038/s41592-019-0690-6 · 2020 · External reference
Machine learning methods for gene regulatory network inference
10.1093/bib/bbaf470 · 2025 · External reference
Graph neural networks for single-cell omics data: a review of approaches and applications
2025 · External reference
Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data
10.1038/s41540-023-00312-6 · 2023 · External reference
Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics
10.1038/s41592-023-01971-3 · 2023 · External reference
A hybrid deep learning framework for gene regulatory network inference from single-cell transcriptomic data
10.1093/bib/bbab568 · 2022 · External reference
Deep learning-based cell-specific gene regulatory networks inferred from single-cell multiome data
2025 · External reference
Modeling gene regulatory networks using neural network architectures
10.1038/s43588-021-00099-8 · 2021 · External reference
Cross-species analysis of biological networks by Bayesian alignment
10.1073/pnas.0602294103 · 2006 · External reference
Global Mapping of Human RNA-RNA Interactions
10.1016/j.molcel.2016.04.030 · 2016 · External reference
circRNA-miRNA-mRNA regulatory network in human lung cancer: an update
10.1186/s12935-020-01245-4 · 2020 · External reference
DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data
10.1093/bib/bbab325 · 2021 · External reference
Modeling gene regulatory networks using neural network architectures
10.1038/s43588-021-00099-8 · 2021 · External reference
Single-cell transcriptomics unveils gene regulatory network plasticity
10.1186/s13059-019-1713-4 · 2019 · External reference
Inferring gene regulatory network from single-cell transcriptomes with graph autoencoder model
10.1371/journal.pgen.1010942 · 2023 · External reference
scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses
10.1038/s41467-021-22197-x · 2021 · External reference
GMFGRN: a matrix factorization and graph neural network approach for gene regulatory network inference
2024 · External reference
HGATLink: single-cell gene regulatory network inference via the fusion of heterogeneous graph attention networks and transformer
10.1186/s12859-025-06071-x · 2025 · External reference
Inferring gene regulatory networks by hypergraph variational autoencoder
2024 · External reference
Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data
10.1016/j.crmeth.2022.100382 · 2023 · External reference
PMF-GRN: a variational inference approach to single-cell gene regulatory network inference using probabilistic matrix factorization
10.1186/s13059-024-03226-6 · 2024 · External reference
KEGNI: knowledge graph enhanced framework for gene regulatory network inference
10.1186/s13059-025-03780-7 · 2025 · External reference
Multi-omics single-cell data integration and regulatory inference with graph-linked embedding
10.1038/s41587-022-01284-4 · 2022 · External reference
SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks
10.1038/s41592-023-01938-4 · 2023 · External reference
Comprehensive analysis of single cell ATAC-seq data with SnapATAC
10.1038/s41467-021-21583-9 · 2021 · External reference
Expanded encyclopaedias of DNA elements in the human and mouse genomes
10.1038/s41586-020-2493-4 · 2020 · External reference
Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation
10.1038/s41467-021-27232-5 · 2021 · External reference
GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model
10.1038/s41422-024-01034-y · 2024 · External reference
Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN
10.1038/s41592-024-02191-z · 2024 · External reference
scPRINT: pre-training on 50 million cells allows robust gene network predictions
10.1038/s41467-025-58699-1 · 2025 · External reference
Region or global? A principle for negative sampling in graph-based recommendation
2022 · External reference
Evaluating graph neural networks for link prediction: Current pitfalls and new benchmarking
10.52202/075280-0169 · 2023 · External reference
scGREAT: Transformer-based deep-language model for gene regulatory network inference from single-cell transcriptomics
10.1016/j.isci.2024.109352 · 2024 · External reference
Predicting gene regulatory links from single-cell RNA-seq data using graph neural networks
2023 · External reference
Graph attention network with convolutional layer for predicting gene regulations from single-cell ribonucleic acid sequence data
10.1016/j.engappai.2024.108938 · 2024 · External reference
