{"doi":"10.1101/2025.09.23.678129","title":"Exploring endothelial cell environments across organs in spatially resolved omics data","abstract":"Endothelial cells are ubiquitously present in the human body and line the luminal surface of blood and lymphatic vessels. The oxygen-dependence of cells impacts their proximity to blood vessels, and consequently, to endothelial cells depending on their functional properties and priorities. This paper presents cell-to-nearest-endothelial-cell distance distributions for various cell types using 399 spatially resolved omics datasets from 14 studies comprising 12 tissue types with a total of 47,349,496 cells. Additionally, we developed an open-source web-based interactive tool, Cell Distance Explorer, that allows researchers to interactively visualize cell graphs and linkages in 2D and 3D datasets. Finally, we present a hierarchical neighborhood analysis focused on the endothelial cell neighborhoods in small and large intestine datasets. This paper provides an open-access resource (datasets, tools, and analyses) to characterize and compare cell distances and cell neighborhoods in spatially resolved omics data.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":555757,"datarank":0.24141568686511508,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.0,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":4,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8243,"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":1455069,"name":"Jodie Jepson","orcid":null,"position":1,"is_corresponding":false},{"id":675262,"name":"Roy Chen","orcid":"0000-0002-0228-6773","position":2,"is_corresponding":false},{"id":1454598,"name":"Elizabeth Maier","orcid":"0009-0008-3801-4973","position":3,"is_corresponding":false},{"id":556229,"name":"Bruce W. Herr","orcid":"0000-0002-6703-7647","position":4,"is_corresponding":false},{"id":878655,"name":"Aleix Puig-Barbe","orcid":"0000-0001-6677-8489","position":5,"is_corresponding":false},{"id":303981,"name":"Ellen M. Quardokus","orcid":"0000-0001-7655-4833","position":6,"is_corresponding":false},{"id":1312103,"name":"Danial Qaurooni","orcid":"0000-0001-6190-073X","position":7,"is_corresponding":false},{"id":65129,"name":"Clarence Yapp","orcid":"0000-0003-1144-5710","position":8,"is_corresponding":false},{"id":1455070,"name":"Samuel L. Ewing","orcid":null,"position":9,"is_corresponding":false},{"id":553569,"name":"Archibald Enninful","orcid":"0000-0002-6350-6530","position":10,"is_corresponding":false},{"id":624272,"name":"Negin Farzad","orcid":"0009-0002-5391-9363","position":11,"is_corresponding":false},{"id":632373,"name":"Andreas Bueckle","orcid":"0000-0002-8977-498X","position":12,"is_corresponding":false},{"id":877780,"name":"Quinn T. Easter","orcid":"0000-0002-8018-0405","position":13,"is_corresponding":false},{"id":877785,"name":"Bruno Fernandes Matuck","orcid":"0000-0002-2132-3402","position":14,"is_corresponding":false},{"id":49797,"name":"Chenchen Zhu","orcid":"0000-0003-2165-9456","position":15,"is_corresponding":false},{"id":21448,"name":"Emma Monte","orcid":"0000-0003-2566-1967","position":16,"is_corresponding":false},{"id":1195605,"name":"Jeffrey M. Purkerson","orcid":"0000-0001-7636-4992","position":17,"is_corresponding":false},{"id":1455071,"name":"M. Jehrio","orcid":null,"position":18,"is_corresponding":false},{"id":561601,"name":"Ravi Misra","orcid":"0000-0002-1352-4378","position":19,"is_corresponding":false},{"id":35664,"name":"Rong Fan","orcid":"0000-0001-7805-8059","position":20,"is_corresponding":false},{"id":237253,"name":"Fiona Ginty","orcid":"0000-0001-6638-683X","position":21,"is_corresponding":false},{"id":904938,"name":"Arivarasan Karunamurthy","orcid":"0000-0002-5739-4923","position":22,"is_corresponding":false},{"id":25158,"name":"Jean Fan","orcid":"0000-0002-0212-5451","position":23,"is_corresponding":false},{"id":251270,"name":"Martha Campbell‐Thompson","orcid":"0000-0001-6878-1235","position":24,"is_corresponding":false},{"id":12155,"name":"Gloria Pryhuber","orcid":"0000-0002-9185-3994","position":25,"is_corresponding":false},{"id":347178,"name":"Kevin M. Byrd","orcid":"0000-0002-5565-0524","position":26,"is_corresponding":false},{"id":615289,"name":"John W. Hickey","orcid":"0000-0001-9961-7673","position":27,"is_corresponding":false},{"id":20958,"name":"Katy Börner","orcid":"0000-0002-3321-6137","position":28,"is_corresponding":false},{"id":666416,"name":"Yashvardhan Jain","orcid":"0000-0002-6300-5568","position":0,"is_corresponding":true}],"reference_count":55,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:55:03.976486Z","pmid":"41040203","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":[]}