{"doi":"10.1093/bib/bbae426","title":"SnapHiC-G: identifying long-range enhancer–promoter interactions from single-cell Hi-C data via a global background model","abstract":"Harnessing the power of single-cell genomics technologies, single-cell Hi-C (scHi-C) and its derived technologies provide powerful tools to measure spatial proximity between regulatory elements and their target genes in individual cells. Using a global background model, we propose SnapHiC-G, a computational method, to identify long-range enhancer-promoter interactions from scHi-C data. We applied SnapHiC-G to scHi-C datasets generated from mouse embryonic stem cells and human brain cortical cells. SnapHiC-G achieved high sensitivity in identifying long-range enhancer-promoter interactions. Moreover, SnapHiC-G can identify putative target genes for noncoding genome-wide association study (GWAS) variants, and the genetic heritability of neuropsychiatric diseases is enriched for single-nucleotide polymorphisms (SNPs) within SnapHiC-G-identified interactions in a cell-type-specific manner. In sum, SnapHiC-G is a powerful tool for characterizing cell-type-specific enhancer-promoter interactions from complex tissues and can facilitate the discovery of chromatin interactions important for gene regulation in biologically relevant cell types.","journal":"Briefings in Bioinformatics","year":2024,"id":477459,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9566,"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":408588,"name":"Wujuan Zhong","orcid":"0000-0002-6824-2255","position":1,"is_corresponding":false},{"id":29951,"name":"Paola Giusti‐Rodríguez","orcid":"0000-0002-1921-1305","position":2,"is_corresponding":false},{"id":446634,"name":"Zhiyun Jiang","orcid":null,"position":3,"is_corresponding":false},{"id":979582,"name":"Geoffery W. Wang","orcid":null,"position":4,"is_corresponding":false},{"id":279702,"name":"Huaigu Sun","orcid":null,"position":5,"is_corresponding":false},{"id":254661,"name":"Ming Hu","orcid":"0000-0003-0987-2916","position":6,"is_corresponding":false},{"id":24805,"name":"Yun Li","orcid":"0000-0002-9275-4189","position":7,"is_corresponding":false},{"id":254659,"name":"Weifang Liu","orcid":"0000-0003-2278-8946","position":0,"is_corresponding":true}],"reference_count":93,"raw_metadata":null,"created_at":"2026-07-19T02:06:37.812633Z","pmid":"39222061","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":[]}