{"doi":"10.1186/s13059-021-02597-4","title":"Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies","abstract":"Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.","journal":"Genome biology","year":2022,"id":280287,"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":10,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8843,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":554015,"name":"Matthew C. Hill","orcid":"0000-0003-4578-3873","position":1,"is_corresponding":false},{"id":896,"name":"Patrick T. Ellinor","orcid":"0000-0002-2067-0533","position":2,"is_corresponding":false},{"id":554016,"name":"Min Li","orcid":"0000-0002-0188-1394","position":3,"is_corresponding":false},{"id":610112,"name":"Li Tang","orcid":"0000-0003-2741-3545","position":0,"is_corresponding":true}],"reference_count":82,"raw_metadata":null,"created_at":"2026-07-19T00:28:59.341002Z","pmid":"35063001","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":[]}