{"doi":"10.1093/nargab/lqaf098","title":"Loopsim: enrichment analysis of chromosome conformation capture with fast empirical distribution simulation","abstract":"Gene regulation is intricately influenced by the three-dimensional organization of the genome. In particular, chromatin can exist in loop structures that enable long-range regulatory interactions. By utilizing chromosome conformation capture techniques such as Hi-C, valuable information regarding the organization of these loop structures in 3D space can be obtained. Although functional/feature enrichment is now a common downstream analysis for various genomic platforms to provide biological context, tools specifically designed for high-throughput assays that capture chromosome conformation remain relatively limited. Here, we present Loopsim, a command-line application that performs enrichment analysis on Hi-C loop profiles against user-defined regions (available on GitHub at https://github.com/CutaneousBioinf/Loopsim). Loopsim efficiently simulates a background distribution using a distinctive sampling approach that considers loop size, intervals, loop-loop distances, and structure; it then computes statistics based on the empirical null distribution.","journal":"NAR Genomics and Bioinformatics","year":2025,"id":570699,"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":0.938,"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":350590,"name":"Haihan Zhang","orcid":"0000-0002-5902-7289","position":1,"is_corresponding":false},{"id":1159919,"name":"Zhaolin Zhang","orcid":"0000-0003-1978-8160","position":2,"is_corresponding":false},{"id":379383,"name":"Jiayu Zhou","orcid":"0000-0003-4336-6777","position":3,"is_corresponding":false},{"id":12829,"name":"Jóhann E. Guðjónsson","orcid":"0000-0002-0080-0812","position":4,"is_corresponding":false},{"id":1476581,"name":"James T Elder","orcid":null,"position":5,"is_corresponding":false},{"id":249271,"name":"Matthew T. Patrick","orcid":"0000-0002-6174-9002","position":6,"is_corresponding":false},{"id":12819,"name":"Lam C. Tsoi","orcid":"0000-0003-1627-5722","position":7,"is_corresponding":false},{"id":1476247,"name":"Gideon M. Shaked","orcid":"0000-0001-5822-3010","position":0,"is_corresponding":true}],"reference_count":27,"raw_metadata":null,"created_at":"2026-07-19T02:57:11.713851Z","pmid":"40686570","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":[]}