{"doi":"10.1145/3774976.3774995","title":"Gene Regulatory Network Inference from Pseudotime-Ordered scRNA-seq Data via Time-Lagged Divergence Measures","abstract":"Inferring cell type-specific gene regulatory networks (GRNs) from time-series single-cell RNA sequencing (scRNA-seq) data is challenging due to sparse temporal resolution, high dimensionality, and inherent cellular heterogeneity. We present a novel integrative framework, called PseudoGRN, that unifies multiple pseudotime inference methods, different time-lagged divergence measures, non-redundant penalized network inference, and partial correlation analysis to reconstruct directed GRNs from time-series scRNA-seq data. Applying our method to the real-world scRNA-seq dataset, we demonstrate its superior performance over existing approaches, offering a robust and interpretable tool for uncovering dynamic regulatory mechanisms in single-cell systems.","journal":"PubMed","year":2025,"id":586605,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9445,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1248165,"name":"Tong Si","orcid":"0000-0002-0430-7283","position":1,"is_corresponding":false},{"id":1501190,"name":"Lucas Koch","orcid":"0009-0009-3046-0685","position":2,"is_corresponding":false},{"id":1135071,"name":"Haijun Gong","orcid":"0000-0003-1666-1674","position":3,"is_corresponding":false},{"id":27178,"name":"L. Zhang","orcid":"0009-0000-4105-4564","position":0,"is_corresponding":true}],"reference_count":30,"raw_metadata":null,"created_at":"2026-07-19T02:59:32.191237Z","pmid":"41488124","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}