{"doi":"10.1101/2022.10.19.512942","title":"GrapHiC: An integrative graph based approach for imputing missing Hi-C reads","abstract":"Abstract Hi-C experiments allow researchers to study and understand the 3D genome organization and its regulatory function. Unfortunately, sequencing costs and technical constraints severely restrict access to high-quality Hi-C data for many cell types. Existing frameworks rely on a sparse Hi-C dataset or cheaper-to-acquire ChIP-seq data to predict Hi-C contact maps with high read coverage. However, these methods fail to generalize to sparse or cross-cell-type inputs because they do not account for the contributions of epigenomic features or the impact of the structural neighborhood in predicting Hi-C reads. We propose GrapHiC, which combines Hi-C and ChIP-seq in a graph representation, allowing more accurate embedding of structural and epigenomic features. Each node represents a binned genomic region, and we assign edge weights using the observed Hi-C reads. Additionally, we embed ChIP-seq and relative positional information as node attributes, allowing our representation to capture structural neighborhoods and the contributions of proteins and their modifications for predicting Hi-C reads. Our evaluations show that GrapHiC generalizes better than the current state-of-the-art on cross-cell-type settings and sparse Hi-C inputs. Moreover, we can utilize our framework to impute Hi-C reads even when no Hi-C contact map is available, thus making high-quality Hi-C data more accessible for many cell types. Availability https://github.com/rsinghlab/GrapHiC ACM Reference Format Ghulam Murtaza, Justin Wagner, Justin M. Zook, and Ritambhara Singh. 2018. GrapHiC: An integrative graph based approach for imputing missing Hi-C reads. In Proceedings of 22nd International Workshop on Data Mining in Bioinformatics (BioKDD ‘23) . ACM, New York, NY, USA, 16 pages. https://doi.org/XXXXXXX.XXXXXXX","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":304638,"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":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9413,"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":280975,"name":"Justin Wagner","orcid":"0009-0003-8903-0504","position":1,"is_corresponding":false},{"id":109458,"name":"Justin M. Zook","orcid":"0000-0003-2309-8402","position":2,"is_corresponding":false},{"id":347248,"name":"Ritambhara Singh","orcid":"0000-0002-7523-160X","position":3,"is_corresponding":false},{"id":997548,"name":"Ghulam Murtaza","orcid":"0000-0002-1803-1134","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":null,"created_at":"2026-07-19T00:32:32.651796Z","pmid":null,"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":[]}