{"id":"https://openalex.org/W4412454213","doi":"https://doi.org/10.1093/bioinformatics/btaf194","title":"Refinement strategies for Tangram for reliable single-cell to spatial mapping","display_name":"Refinement strategies for Tangram for reliable single-cell to spatial mapping","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454213","doi":"https://doi.org/10.1093/bioinformatics/btaf194","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662790"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf194","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i552/63745368/btaf194.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i552/63745368/btaf194.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5116058948","display_name":"Merle Stahl","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Merle Stahl","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,"],"raw_orcid":"https://orcid.org/0009-0005-8652-2356","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116058949","display_name":"Lena J. Stra\u00dfer","orcid":"https://orcid.org/0009-0007-7881-6818"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Lena J Stra\u00dfer","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","Munich Data Science Institute (MDSI), Technical University of Munich , Garching 85748,"],"raw_orcid":"https://orcid.org/0009-0007-7881-6818","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Munich Data Science Institute (MDSI), Technical University of Munich , Garching 85748,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073630101","display_name":"Chit Tong Lio","orcid":"https://orcid.org/0000-0003-2297-831X"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Chit Tong Lio","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,"],"raw_orcid":"https://orcid.org/0000-0003-2297-831X","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032713341","display_name":"Judith Bernett","orcid":"https://orcid.org/0000-0001-5812-8013"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Judith Bernett","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,"],"raw_orcid":"https://orcid.org/0000-0001-5812-8013","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087115605","display_name":"Richard H. Roettger","orcid":"https://orcid.org/0000-0003-4490-5947"},"institutions":[{"id":"https://openalex.org/I177969490","display_name":"University of Southern Denmark","ror":"https://ror.org/03yrrjy16","country_code":"DK","type":"education","lineage":["https://openalex.org/I177969490"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Richard R\u00f6ttger","raw_affiliation_strings":["Department of Mathematics and Computer Science, University of Southern Denmark , Odense 5230,"],"raw_orcid":"https://orcid.org/0000-0003-4490-5947","affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, University of Southern Denmark , Odense 5230,","institution_ids":["https://openalex.org/I177969490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035928806","display_name":"Markus List","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Markus List","raw_affiliation_strings":["Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","Munich Data Science Institute (MDSI), Technical University of Munich , Garching 85748,"],"raw_orcid":"https://orcid.org/0000-0002-0941-4168","affiliations":[{"raw_affiliation_string":"Data Science in Systems Biology, TUM School of Life Sciences, Technical University of Munich , Freising 85354,","institution_ids":["https://openalex.org/I62916508"]},{"raw_affiliation_string":"Munich Data Science Institute (MDSI), Technical University of Munich , Garching 85748,","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5116058948","https://openalex.org/A5116058949"],"corresponding_institution_ids":["https://openalex.org/I62916508"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.2189,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.78375833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i552","last_page":"i560"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994000196456909,"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":0.9994000196456909,"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":9.999999747378752e-05,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":0.0,"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/computer-science","display_name":"Computer science","score":0.766472578048706},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.713294506072998},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.49740174412727356},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.4797191023826599}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.766472578048706},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.713294506072998},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.49740174412727356},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.4797191023826599},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","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":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","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":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf194","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i552/63745368/btaf194.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:40662790","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662790","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:sdu.dk:openaire_cris_publications/8c8788ec-9d97-4c0c-a43d-60bf5b2e5776","is_oa":true,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/8c8788ec-9d97-4c0c-a43d-60bf5b2e5776","pdf_url":null,"source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Stahl, M, Stra\u00dfer, L J, Lio, C T, Bernett, J, R\u00f6ttger, R & List, M 2025, 'Refinement strategies for Tangram for reliable single-cell to spatial mapping', Bioinformatics, vol. 41, no. Supplement_1, pp. 552-560. https://doi.org/10.1093/bioinformatics/btaf194","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12261478","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261478","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/btaf194","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf194","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i552/63745368/btaf194.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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/G191025471","display_name":"BioinformatikComputeServer","funder_award_id":"422216132","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323383","display_name":"Technische Universit\u00e4t M\u00fcnchen","ror":"https://ror.org/02kkvpp62"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454213.pdf","grobid_xml":"https://content.openalex.org/works/W4412454213.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W2042789810","https://openalex.org/W2052611179","https://openalex.org/W2118898434","https://openalex.org/W2126537932","https://openalex.org/W2131586477","https://openalex.org/W2399767476","https://openalex.org/W2471536144","https://openalex.org/W2899224111","https://openalex.org/W2949676527","https://openalex.org/W2950976066","https://openalex.org/W3099810371","https://openalex.org/W3196495189","https://openalex.org/W3208940117","https://openalex.org/W4210583065","https://openalex.org/W4220694418","https://openalex.org/W4221092226","https://openalex.org/W4280533477","https://openalex.org/W4316506627","https://openalex.org/W4323320361","https://openalex.org/W4328048773","https://openalex.org/W4385429267","https://openalex.org/W4387439135","https://openalex.org/W4390639744","https://openalex.org/W4404034359","https://openalex.org/W4404460660","https://openalex.org/W6713280873","https://openalex.org/W6873353504"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4238897586","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"provides":[5,84],"comprehensive":[6],"gene":[7,118,132,162,184,195],"expression":[8,119,163],"data":[9,64,107,215],"at":[10,49,242],"a":[11],"single-cell":[12,51],"level":[13,52],"but":[14,28],"lacks":[15],"spatial":[16,20,24,43,62,81],"context.":[17],"In":[18],"contrast,":[19],"transcriptomics":[21,63],"captures":[22],"both":[23,40,161],"and":[25,45,61,100,144,152,165,180,186,197,217,236],"transcriptional":[26],"information":[27],"is":[29,220],"limited":[30],"by":[31],"resolution,":[32],"sensitivity,":[33],"or":[34,226],"feasibility.":[35],"No":[36],"single":[37],"technology":[38],"combines":[39],"the":[41,50,78,102,112,117,127,172,175],"high":[42],"resolution":[44],"deep":[46],"transcriptomic":[47],"profiling":[48],"without":[53],"tradeoffs.":[54],"Spatial":[55],"mapping":[56,82,113,170],"tools":[57,225],"that":[58,74,104,111,157],"integrate":[59],"scRNA-seq":[60],"are":[65,240],"crucial":[66],"to":[67,94],"bridge":[68],"this":[69,158],"gap.":[70],"However,":[71],"we":[72,124],"found":[73],"Tangram,":[75],"one":[76],"of":[77,142,174,177,188],"most":[79],"prominent":[80],"tools,":[83],"inconsistent":[85],"results":[86],"over":[87],"repeated":[88],"runs.":[89],"RESULTS:":[90],"We":[91,109],"refine":[92],"Tangram":[93,206,227,235],"achieve":[95],"more":[96],"consistent":[97],"cell":[98,136,166,169,178],"mappings":[99],"investigate":[101],"challenges":[103],"arise":[105],"from":[106],"characteristics.":[108],"find":[110],"quality":[114],"depends":[115],"on":[116,129,150,207],"sparsity.":[120],"To":[121],"address":[122],"this,":[123],"(1)":[125],"train":[126],"model":[128],"an":[130],"informative":[131],"subset,":[133],"(2)":[134],"apply":[135],"filtering,":[137],"(3)":[138],"introduce":[139],"several":[140],"forms":[141],"regularization,":[143],"(4)":[145],"incorporate":[146],"neighborhood":[147],"information.":[148],"Evaluations":[149],"real":[151],"simulated":[153],"mouse":[154],"datasets":[155],"demonstrate":[156],"approach":[159],"improves":[160],"prediction":[164],"mapping.":[167],"Consistent":[168],"strengthens":[171],"reliability":[173],"projection":[176],"annotations":[179],"features":[181],"into":[182],"space,":[183],"imputation,":[185],"correction":[187],"low-quality":[189],"measurements.":[190],"Our":[191],"pipeline,":[192],"which":[193],"includes":[194],"set":[196],"hyperparameter":[198],"selection,":[199],"can":[200],"serve":[201],"as":[202],"guidance":[203],"for":[204,222,234],"applying":[205],"other":[208,224],"datasets,":[209],"while":[210],"our":[211,237],"benchmarking":[212,238],"framework":[213],"with":[214],"simulation":[216],"inconsistency":[218],"metrics":[219],"useful":[221],"evaluating":[223],"modifications.":[228],"AVAILABILITY":[229],"AND":[230],"IMPLEMENTATION:":[231],"The":[232],"refinements":[233],"pipeline":[239],"available":[241],"https://github.com/daisybio/Tangram_Refinement_Strategies.":[243]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
