{"id":"https://openalex.org/W4310590875","doi":"https://doi.org/10.1093/bioinformatics/btac775","title":"Comprehensive visualization of cell\u2013cell interactions in single-cell and spatial transcriptomics with NICHES","display_name":"Comprehensive visualization of cell\u2013cell interactions in single-cell and spatial transcriptomics with NICHES","publication_year":2022,"publication_date":"2022-12-01","ids":{"openalex":"https://openalex.org/W4310590875","doi":"https://doi.org/10.1093/bioinformatics/btac775","pmid":"https://pubmed.ncbi.nlm.nih.gov/36458905"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac775","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac775","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac775/48520747/btac775.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac775/48520747/btac775.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017478777","display_name":"Micha Sam Brickman Raredon","orcid":"https://orcid.org/0000-0003-1441-6122"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Micha Sam Brickman Raredon","raw_affiliation_strings":["Department of Anesthesiology, Yale School of Medicine , New Haven, CT 06511,","Department of Biomedical Engineering, Yale University , New Haven, CT 06511,","Department of Immunobiology, Yale University , New Haven, CT 06511,","Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine , New Haven, CT 06511,","Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06511, USA","Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA","Department of Immunobiology, Yale University, New Haven, CT 06511, USA","Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA"],"raw_orcid":"https://orcid.org/0000-0003-1441-6122","affiliations":[{"raw_affiliation_string":"Department of Anesthesiology, Yale School of Medicine , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Immunobiology, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Immunobiology, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041944596","display_name":"Junchen Yang","orcid":"https://orcid.org/0000-0003-0988-1564"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junchen Yang","raw_affiliation_strings":["Interdepartmental Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06511,","Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA"],"raw_orcid":"https://orcid.org/0000-0003-0988-1564","affiliations":[{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018326083","display_name":"Neeharika Kothapalli","orcid":"https://orcid.org/0000-0002-6867-9756"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Neeharika Kothapalli","raw_affiliation_strings":["Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine , New Haven, CT 06511,","Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088279473","display_name":"Wesley Lewis","orcid":null},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wesley Lewis","raw_affiliation_strings":["Interdepartmental Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06511,","Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088823841","display_name":"Naftali Kaminski","orcid":"https://orcid.org/0000-0001-5917-4601"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naftali Kaminski","raw_affiliation_strings":["Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine , New Haven, CT 06511,","Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085748100","display_name":"Laura E. Niklason","orcid":"https://orcid.org/0000-0002-5156-504X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laura E Niklason","raw_affiliation_strings":["Department of Anesthesiology, Yale School of Medicine , New Haven, CT 06511,","Department of Biomedical Engineering, Yale University , New Haven, CT 06511,","Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06511, USA","Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Anesthesiology, Yale School of Medicine , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Anesthesiology, Yale School of Medicine, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020473435","display_name":"Yuval Kluger","orcid":"https://orcid.org/0000-0002-3035-071X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210131439","display_name":"Applied Mathematics (United States)","ror":"https://ror.org/03seew607","country_code":"US","type":"company","lineage":["https://openalex.org/I4210131439"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuval Kluger","raw_affiliation_strings":["Applied Mathematics Program, Yale University , New Haven, CT 06511,","Department of Pathology, Yale School of Medicine , New Haven, CT 06511,","Interdepartmental Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06511,","Applied Mathematics Program, Yale University, New Haven, CT 06511, USA","Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA","Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA"],"raw_orcid":"https://orcid.org/0000-0002-3035-071X","affiliations":[{"raw_affiliation_string":"Applied Mathematics Program, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Pathology, Yale School of Medicine , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, Yale University , New Haven, CT 06511,","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Applied Mathematics Program, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4210131439"]},{"raw_affiliation_string":"Department of Pathology, Yale School of Medicine, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06511, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017478777","https://openalex.org/A5020473435"],"corresponding_institution_ids":["https://openalex.org/I32971472","https://openalex.org/I4210131439"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":7.5173,"has_fulltext":true,"cited_by_count":125,"citation_normalized_percentile":{"value":0.98486053,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.000699999975040555,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6739280819892883},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.5988094806671143},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5006289482116699},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.47807884216308594},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47741711139678955},{"id":"https://openalex.org/keywords/niche","display_name":"Niche","score":0.4561727046966553},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3997686505317688},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.24917879700660706},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15283310413360596},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.1057921051979065},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07845523953437805},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.061565101146698}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6739280819892883},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.5988094806671143},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5006289482116699},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.47807884216308594},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47741711139678955},{"id":"https://openalex.org/C153991713","wikidata":"https://www.wikidata.org/wiki/Q17142856","display_name":"Niche","level":2,"score":0.4561727046966553},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3997686505317688},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.24917879700660706},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15283310413360596},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.1057921051979065},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07845523953437805},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.061565101146698}],"mesh":[{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac775","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac775","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac775/48520747/btac775.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36458905","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36458905","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9825783","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9825783","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac775","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac775","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac775/48520747/btac775.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1040404194","display_name":null,"funder_award_id":"R01 GM131642","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G1044130170","display_name":null,"funder_award_id":"UL1TR001863\u00d0","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G1316390211","display_name":null,"funder_award_id":"U54AG076043","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G1358700859","display_name":null,"funder_award_id":"P50 CA121974","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1439563269","display_name":null,"funder_award_id":"F30 HL143906","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G218820949","display_name":null,"funder_award_id":"UM1DA051410","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G2810379811","display_name":"Reverse Engineering the Pulmonary Microvasculature","funder_award_id":"5f30hl143906-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5209238363","display_name":null,"funder_award_id":"U01 DA053628","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G7660318146","display_name":null,"funder_award_id":"T32GM086287","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320308380","display_name":"Yale University","ror":"https://ror.org/03v76x132"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4310590875.pdf","grobid_xml":"https://content.openalex.org/works/W4310590875.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1016059894","https://openalex.org/W2129357971","https://openalex.org/W2743344672","https://openalex.org/W2785854718","https://openalex.org/W2786421413","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2801762127","https://openalex.org/W2912065541","https://openalex.org/W2916020270","https://openalex.org/W2951158909","https://openalex.org/W2964691289","https://openalex.org/W2986910456","https://openalex.org/W2992151131","https://openalex.org/W2995703197","https://openalex.org/W3007935255","https://openalex.org/W3012498554","https://openalex.org/W3017023874","https://openalex.org/W3022882652","https://openalex.org/W3028489281","https://openalex.org/W3039465315","https://openalex.org/W3082597692","https://openalex.org/W3099810371","https://openalex.org/W3123592252","https://openalex.org/W3130232612","https://openalex.org/W3132661792","https://openalex.org/W3138055079","https://openalex.org/W3184931457","https://openalex.org/W4221038504","https://openalex.org/W4281716326"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2068608913","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W2095253586","https://openalex.org/W2393629471","https://openalex.org/W3150324899","https://openalex.org/W4392059188","https://openalex.org/W3169186547"],"abstract_inverted_index":{"MOTIVATION:":[0],"Recent":[1],"years":[2],"have":[3],"seen":[4],"the":[5,31,35,57],"release":[6],"of":[7,34,65,105,120],"several":[8],"toolsets":[9],"that":[10],"reveal":[11],"cell-cell":[12,121],"interactions":[13],"from":[14],"single-cell":[15,32,59,113,124],"data.":[16,37],"However,":[17],"all":[18],"existing":[19,112],"approaches":[20],"leverage":[21],"mean":[22],"celltype":[23],"gene":[24],"expression":[25],"values,":[26],"and":[27,44,80,115,142],"do":[28],"not":[29],"preserve":[30],"fidelity":[33],"original":[36],"Here,":[38],"we":[39],"present":[40],"NICHES":[41,62,90,99,129],"(Niche":[42],"Interactions":[43],"Communication":[45],"Heterogeneity":[46],"in":[47,135],"Extracellular":[48],"Signaling),":[49],"a":[50],"tool":[51],"to":[52,69,86,94],"explore":[53],"extracellular":[54],"signaling":[55,72,107,122],"at":[56,123,146,152,160],"truly":[58],"level.":[60],"RESULTS:":[61],"allows":[63,116],"embedding":[64],"ligand-receptor":[66,106],"signal":[67],"proxies":[68],"visualize":[70],"heterogeneous":[71],"archetypes":[73],"within":[74],"cell":[75,78],"clusters,":[76],"between":[77],"clusters":[79],"across":[81],"experimental":[82],"conditions.":[83],"When":[84],"applied":[85],"spatial":[87],"transcriptomic":[88],"data,":[89],"can":[91,100],"be":[92],"used":[93],"reflect":[95],"local":[96],"cellular":[97],"microenvironment.":[98],"operate":[101],"with":[102,111],"any":[103],"list":[104],"mechanisms,":[108],"is":[109,130,144],"compatible":[110],"packages,":[114],"rapid,":[117],"flexible":[118],"analysis":[119],"resolution.":[125],"AVAILABILITY":[126],"AND":[127],"IMPLEMENTATION:":[128],"an":[131],"open-source":[132],"software":[133],"implemented":[134],"R":[136],"under":[137],"academic":[138],"free":[139],"license":[140],"v3.0":[141],"it":[143],"available":[145,151,159],"http://github.com/msraredon/NICHES.":[147],"Use-case":[148],"vignettes":[149],"are":[150,158],"https://msraredon.github.io/NICHES/.":[153],"SUPPLEMENTARY":[154],"INFORMATION:":[155],"Supplementary":[156],"data":[157],"Bioinformatics":[161],"online.":[162]},"counts_by_year":[{"year":2026,"cited_by_count":29},{"year":2025,"cited_by_count":42},{"year":2024,"cited_by_count":37},{"year":2023,"cited_by_count":13},{"year":2022,"cited_by_count":4}],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
