{"id":"https://openalex.org/W7124747730","doi":"https://doi.org/10.5167/uzh-282420","title":"Harnessing the potential of spatial statistics for spatial omics data with $pasta$","display_name":"Harnessing the potential of spatial statistics for spatial omics data with $pasta$","publication_year":2025,"publication_date":"2025-09-05","ids":{"openalex":"https://openalex.org/W7124747730","doi":"https://doi.org/10.5167/uzh-282420"},"language":"en","primary_location":{"id":"doi:10.5167/uzh-282420","doi":"https://doi.org/10.5167/uzh-282420","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-282420","pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.5167/uzh-282420","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5094039996","display_name":"Martin Emons","orcid":"https://orcid.org/0009-0000-5219-5311","observed_orcids":["https://orcid.org/0009-0000-5219-5311"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Emons, Martin","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064673302","display_name":"Samuel Gunz","orcid":"https://orcid.org/0000-0002-8909-0932","observed_orcids":["https://orcid.org/0000-0002-8909-0932"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gunz, Samuel","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025531524","display_name":"Helena Lucia Crowell","orcid":"https://orcid.org/0000-0002-4801-1767","observed_orcids":["https://orcid.org/0000-0002-4801-1767"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Crowell, Helena L","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020781057","display_name":"Izaskun Mallona","orcid":"https://orcid.org/0000-0002-2853-7526","observed_orcids":["https://orcid.org/0000-0002-2853-7526"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mallona, Izaskun","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027149328","display_name":"Malte B. Kuehl","orcid":"https://orcid.org/0000-0003-4167-2498","observed_orcids":["https://orcid.org/0000-0003-4167-2498"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kuehl, Malte","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016890115","display_name":"Reinhard Furrer","orcid":"https://orcid.org/0000-0002-6319-2332","observed_orcids":["https://orcid.org/0000-0002-6319-2332"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Furrer, Reinhard","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-6319-2332","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5029455059","display_name":"Mark D. Robinson","orcid":"https://orcid.org/0000-0002-3048-5518","observed_orcids":["https://orcid.org/0000-0002-3048-5518","https://orcid.org/0000-0001-5677-3078"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robinson, Mark","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-3048-5518","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9189000129699707,"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":0.9189000129699707,"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/T11830","display_name":"Point processes and geometric inequalities","score":0.04839999973773956,"subfield":{"id":"https://openalex.org/subfields/2604","display_name":"Applied Mathematics"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11911","display_name":"Spatial and Panel Data Analysis","score":0.017400000244379044,"subfield":{"id":"https://openalex.org/subfields/2002","display_name":"Economics and Econometrics"},"field":{"id":"https://openalex.org/fields/20","display_name":"Economics, Econometrics and Finance"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/spatial-statistics","display_name":"spatial statistics","score":0.8899999856948853},{"id":"https://openalex.org/keywords/spatial-omics","display_name":"spatial omics","score":1.0},{"id":"https://openalex.org/keywords/spatial-point-pattern-analysis","display_name":"point pattern analysis","score":0.7400000095367432},{"id":"https://openalex.org/keywords/lattice-data","display_name":"lattice data","score":0.9520000219345093},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"breast cancer","score":0.6380000114440918},{"id":"https://openalex.org/keywords/gene-co-expression","display_name":"gene co-expression","score":0.9520000219345093},{"id":"https://openalex.org/keywords/homogeneity","display_name":"homogeneity","score":0.7509999871253967},{"id":"https://openalex.org/keywords/tissue-organization","display_name":"tissue organization","score":0.8109999895095825},{"id":"https://openalex.org/keywords/spatial-gene-expression","display_name":"spatial gene expression","score":0.47999998927116394}],"concepts":[{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.7038000226020813},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5498999953269958},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5296000242233276},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5195000171661377},{"id":"https://openalex.org/C158709400","wikidata":"https://www.wikidata.org/wiki/Q3578586","display_name":"Spatial ecology","level":2,"score":0.41990000009536743},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.35510000586509705},{"id":"https://openalex.org/C194226119","wikidata":"https://www.wikidata.org/wiki/Q161779","display_name":"Spatial reference system","level":2,"score":0.3522999882698059},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35179999470710754},{"id":"https://openalex.org/C120894424","wikidata":"https://www.wikidata.org/wiki/Q1322871","display_name":"Exploratory data analysis","level":2,"score":0.35100001096725464},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3504999876022339},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.34279999136924744},{"id":"https://openalex.org/C3770464","wikidata":"https://www.wikidata.org/wiki/Q775963","display_name":"Smoothing","level":2,"score":0.3109999895095825},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3077999949455261},{"id":"https://openalex.org/C27511587","wikidata":"https://www.wikidata.org/wiki/Q2178623","display_name":"Spatial relation","level":2,"score":0.304500013589859},{"id":"https://openalex.org/C32792767","wikidata":"https://www.wikidata.org/wiki/Q1370484","display_name":"Summary statistics","level":2,"score":0.28139999508857727},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.27630001306533813},{"id":"https://openalex.org/C94747663","wikidata":"https://www.wikidata.org/wiki/Q7574086","display_name":"Spatial variability","level":2,"score":0.2581999897956848},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2542000114917755},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.25110000371932983}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.5167/uzh-282420","doi":"https://doi.org/10.5167/uzh-282420","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-282420","pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.5167/uzh-282420","doi":"https://doi.org/10.5167/uzh-282420","is_oa":true,"landing_page_url":"https://doi.org/10.5167/uzh-282420","pdf_url":null,"source":{"id":"https://openalex.org/S4306401281","display_name":"Zurich Open Repository and Archive (University of Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I202697423","host_organization_name":"University of Zurich","host_organization_lineage":["https://openalex.org/I202697423"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"JournalArticle"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W6931048904","https://openalex.org/W6981742142","https://openalex.org/W7212165987","https://openalex.org/W7135060793","https://openalex.org/W4309771166","https://openalex.org/W7124995059","https://openalex.org/W4384694392","https://openalex.org/W4399906763","https://openalex.org/W3128722151","https://openalex.org/W7160405553"],"abstract_inverted_index":{"Spatial":[0],"omics":[1],"allow":[2],"for":[3,119],"the":[4,14,33,54],"molecular":[5],"characterization":[6],"of":[7,32,56],"cells":[8],"in":[9,40,84],"their":[10,108],"spatial":[11,41,57,120],"context.":[12],"Notably,":[13],"two":[15,34],"main":[16],"technological":[17],"streams,":[18],"imaging-based":[19],"and":[20,46,90,102,106,125],"high-throughput":[21],"sequencing-based,":[22],"give":[23],"rise":[24],"to":[25,59,67,76,80],"very":[26],"different":[27],"data":[28,35],"modalities.":[29],"The":[30],"characteristics":[31],"types":[36],"are":[37],"well":[38],"known":[39],"statistics":[42,58,121],"as":[43],"point":[44],"patterns":[45],"lattice":[47],"data.":[48],"In":[49],"this":[50],"perspective,":[51],"we":[52,73],"show":[53,107],"versatility":[55],"quantify":[60],"biological":[61],"phenomena":[62],"from":[63],"local":[64],"gene":[65,91],"expression":[66],"tissue":[68],"organization.":[69],"As":[70],"an":[71,115],"example,":[72],"describe":[74],"how":[75],"use":[77],"exploratory":[78],"metrics":[79],"address":[81],"scientific":[82],"questions":[83],"breast":[85],"cancer,":[86],"including":[87],"cellular":[88],"co-localization":[89],"co-expression":[92],"analysis.":[93],"We":[94,110],"discuss":[95],"technical":[96],"concepts":[97],"like":[98],"window":[99],"sampling,":[100],"homogeneity,":[101],"weight":[103],"matrix":[104],"construction":[105],"importance.":[109],"also":[111],"provide":[112],"pasta":[113],"(https://robinsonlabuzh.github.io/pasta),":[114],"extensive":[116],"analysis":[117],"vignette":[118],"both":[122],"using":[123],"R":[124],"Python":[126],"packages":[127],"with":[128],"further":[129],"biology-driven":[130],"applications.":[131]},"counts_by_year":[],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2026-01-20T00:00:00"}
