{"doi":"10.1093/bib/bbae369","title":"Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data","abstract":"Deciphering the intricate relationships between transcription factors (TFs), enhancers, and genes through the inference of enhancer-driven gene regulatory networks (eGRNs) is crucial in understanding gene regulatory programs in a complex biological system. This study introduces STREAM, a novel method that leverages a Steiner forest problem model, a hybrid biclustering pipeline, and submodular optimization to infer eGRNs from jointly profiled single-cell transcriptome and chromatin accessibility data. Compared to existing methods, STREAM demonstrates enhanced performance in terms of TF recovery, TF-enhancer linkage prediction, and enhancer-gene relation discovery. Application of STREAM to an Alzheimer's disease dataset and a diffuse small lymphocytic lymphoma dataset reveals its ability to identify TF-enhancer-gene relations associated with pseudotime, as well as key TF-enhancer-gene relations and TF cooperation underlying tumor cells.","journal":"Briefings in Bioinformatics","year":2024,"id":433239,"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":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9512,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":235824,"name":"Anjun Ma","orcid":"0000-0001-6269-398X","position":1,"is_corresponding":false},{"id":1238497,"name":"Yizhong Wang","orcid":"0000-0002-9390-8864","position":2,"is_corresponding":false},{"id":1084691,"name":"Qi Guo","orcid":"0000-0002-3528-2533","position":3,"is_corresponding":false},{"id":257822,"name":"Cankun Wang","orcid":"0000-0002-0225-9855","position":4,"is_corresponding":false},{"id":257824,"name":"Hongjun Fu","orcid":"0000-0001-5346-7075","position":5,"is_corresponding":false},{"id":86820,"name":"BingQiang Liu","orcid":"0000-0002-5734-1135","position":6,"is_corresponding":false},{"id":235827,"name":"Qin Ma","orcid":"0000-0002-3264-8392","position":7,"is_corresponding":false},{"id":486530,"name":"Yang Li","orcid":"0000-0002-7677-9028","position":0,"is_corresponding":true}],"reference_count":101,"raw_metadata":null,"created_at":"2026-07-19T01:59:44.444627Z","pmid":"39082647","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":[]}