{"id":"https://openalex.org/W4317478285","doi":"https://doi.org/10.1093/bib/bbad013","title":"DIST: spatial transcriptomics enhancement using deep learning","display_name":"DIST: spatial transcriptomics enhancement using deep learning","publication_year":2023,"publication_date":"2023-01-18","ids":{"openalex":"https://openalex.org/W4317478285","doi":"https://doi.org/10.1093/bib/bbad013","pmid":"https://pubmed.ncbi.nlm.nih.gov/36653906"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad013","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad013/49559939/bbad013.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad013/49559939/bbad013.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046275862","display_name":"Yanping Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanping Zhao","raw_affiliation_strings":["Nankai University School of Statistics and Data Science, LPMC and KLMDASR, , Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nankai University School of Statistics and Data Science, LPMC and KLMDASR, , Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100342696","display_name":"Kui Wang","orcid":"https://orcid.org/0000-0003-3503-1563"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kui Wang","raw_affiliation_strings":["Nankai University School of Statistics and Data Science, LPMC and KLMDASR, , Tianjin, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nankai University School of Statistics and Data Science, LPMC and KLMDASR, , Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072443515","display_name":"Gang Hu","orcid":"https://orcid.org/0000-0002-7134-3380"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Gang Hu","raw_affiliation_strings":["Nankai University School of Statistics and Data Science, LPMC and KLMDASR, , Tianjin, China"],"raw_orcid":"https://orcid.org/0000-0002-7134-3380","affiliations":[{"raw_affiliation_string":"Nankai University School of Statistics and Data Science, LPMC and KLMDASR, , Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5072443515"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.6873,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.90057157,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"24","issue":"2","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":0.9998999834060669,"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":0.9998999834060669,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.986299991607666,"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":0.9840999841690063,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6605742573738098},{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.5795393586158752},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5483177900314331},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5368500351905823},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5267019867897034},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5116456151008606},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5114137530326843},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5050995945930481},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4401562213897705},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4207722842693329},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.42071348428726196},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4204115867614746},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4051312804222107},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.35533764958381653},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3268616497516632},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.23503294587135315},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21265339851379395}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6605742573738098},{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.5795393586158752},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5483177900314331},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5368500351905823},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5267019867897034},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5116456151008606},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5114137530326843},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5050995945930481},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4401562213897705},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4207722842693329},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.42071348428726196},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4204115867614746},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4051312804222107},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35533764958381653},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3268616497516632},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.23503294587135315},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21265339851379395},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","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}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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":2,"locations":[{"id":"doi:10.1093/bib/bbad013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad013","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad013/49559939/bbad013.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36653906","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36653906","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bib/bbad013","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad013","pdf_url":"https://academic.oup.com/bib/article-pdf/24/2/bbad013/49559939/bbad013.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2202405192","display_name":null,"funder_award_id":"31970649","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4317478285.pdf","grobid_xml":"https://content.openalex.org/works/W4317478285.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1599195847","https://openalex.org/W2003406618","https://openalex.org/W2035122273","https://openalex.org/W2049220630","https://openalex.org/W2071102398","https://openalex.org/W2098389926","https://openalex.org/W2112138633","https://openalex.org/W2131681506","https://openalex.org/W2145204829","https://openalex.org/W2147233186","https://openalex.org/W2171439874","https://openalex.org/W2567196365","https://openalex.org/W2800392236","https://openalex.org/W2809368942","https://openalex.org/W2889453805","https://openalex.org/W2899224111","https://openalex.org/W2923300855","https://openalex.org/W2928665623","https://openalex.org/W2939929026","https://openalex.org/W2944545583","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2976494531","https://openalex.org/W2984472267","https://openalex.org/W2996171578","https://openalex.org/W2999977864","https://openalex.org/W3001833132","https://openalex.org/W3036882247","https://openalex.org/W3099768174","https://openalex.org/W3100967665","https://openalex.org/W3119671877","https://openalex.org/W3126958162","https://openalex.org/W3134766331","https://openalex.org/W3164692211","https://openalex.org/W3165120573","https://openalex.org/W3190202966","https://openalex.org/W3194004635","https://openalex.org/W3203128182","https://openalex.org/W3207315182","https://openalex.org/W3216067893","https://openalex.org/W3216124552","https://openalex.org/W3217269355","https://openalex.org/W4212991200","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4255556797","https://openalex.org/W4280494993","https://openalex.org/W4285803722","https://openalex.org/W4388624454","https://openalex.org/W6804194808"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2982720988","https://openalex.org/W4211215373","https://openalex.org/W3217094455","https://openalex.org/W3119637569","https://openalex.org/W4388725868","https://openalex.org/W2104762330","https://openalex.org/W2073305407"],"abstract_inverted_index":{"Spatially":[0],"resolved":[1],"transcriptomics":[2],"technologies":[3,19],"enable":[4],"comprehensive":[5],"measurement":[6],"of":[7,14,69],"gene":[8,40,49,89,94],"expression":[9,41,50,75,90,95],"patterns":[10],"in":[11],"the":[12,39,48,67,88,93,115],"context":[13],"intact":[15],"tissues.":[16],"However,":[17],"existing":[18],"suffer":[20],"from":[21],"either":[22],"low":[23],"resolution":[24],"or":[25],"shallow":[26],"sequencing":[27],"depth.":[28],"Here,":[29],"we":[30],"present":[31],"DIST,":[32],"a":[33],"deep":[34],"learning-based":[35],"method":[36],"that":[37,84],"imputes":[38],"profiles":[42],"on":[43],"unmeasured":[44],"locations":[45],"and":[46,56,62,77,107],"enhances":[47],"for":[51,71,96,111],"both":[52],"original":[53],"measured":[54],"spots":[55,58],"imputed":[57],"by":[59],"self-supervised":[60],"learning":[61],"transfer":[63],"learning.":[64],"We":[65],"evaluate":[66],"performance":[68],"DIST":[70,85],"imputation,":[72],"clustering,":[73],"differential":[74],"analysis":[76],"functional":[78],"enrichment":[79],"analysis.":[80],"The":[81],"results":[82],"show":[83],"can":[86],"impute":[87],"accurately,":[91],"enhance":[92],"low-quality":[97],"data,":[98],"help":[99],"detect":[100],"more":[101],"biological":[102,116],"meaningful":[103],"differentially":[104],"expressed":[105],"genes":[106],"pathways,":[108],"therefore":[109],"allow":[110],"deeper":[112],"insights":[113],"into":[114],"processes.":[117]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":4}],"updated_date":"2026-07-14T08:27:34.040176","created_date":"2025-10-10T00:00:00"}
