{"id":"https://openalex.org/W4403394580","doi":"https://doi.org/10.1093/bioinformatics/btae611","title":"Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics","display_name":"Statistical batch-aware embedded integration, dimension reduction, and alignment for spatial transcriptomics","publication_year":2024,"publication_date":"2024-10-01","ids":{"openalex":"https://openalex.org/W4403394580","doi":"https://doi.org/10.1093/bioinformatics/btae611","pmid":"https://pubmed.ncbi.nlm.nih.gov/39400541"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae611","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae611","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae611/59748034/btae611.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/advance-article-pdf/doi/10.1093/bioinformatics/btae611/59748034/btae611.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100428144","display_name":"Yanfang Li","orcid":"https://orcid.org/0000-0003-2761-0282"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanfang Li","raw_affiliation_strings":["NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","institution_ids":["https://openalex.org/I4210120485"]},{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076619069","display_name":"Shihua Zhang","orcid":"https://orcid.org/0000-0003-0192-7118"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210095018","display_name":"National Center for Mathematics and Interdisciplinary Sciences","ror":"https://ror.org/00s97k668","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210095018"]},{"id":"https://openalex.org/I4210120485","display_name":"Academy of Mathematics and Systems Science","ror":"https://ror.org/02jkmyk67","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210120485"]},{"id":"https://openalex.org/I4210126939","display_name":"ZheJiang Academy of Agricultural Sciences","ror":"https://ror.org/02qbc3192","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I4210126939"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shihua Zhang","raw_affiliation_strings":["Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , Hangzhou 310024,","NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049,","Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China","NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China","School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China"],"raw_orcid":"https://orcid.org/0000-0003-0192-7118","affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , Hangzhou 310024,","institution_ids":["https://openalex.org/I4210126939"]},{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190,","institution_ids":["https://openalex.org/I4210120485"]},{"raw_affiliation_string":"School of Mathematical Sciences, University of Chinese Academy of Sciences , Beijing 100049,","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China","institution_ids":["https://openalex.org/I4210165038"]},{"raw_affiliation_string":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China","institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485"]},{"raw_affiliation_string":"School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China","institution_ids":["https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5076619069"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210095018","https://openalex.org/I4210120485","https://openalex.org/I4210126939","https://openalex.org/I4210165038"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9528,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.86748743,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"40","issue":"10","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":0.9945999979972839,"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":0.9945999979972839,"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/T10885","display_name":"Gene expression and cancer classification","score":0.002400000113993883,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.7534191608428955},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7521750926971436},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5425553321838379},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4874551296234131},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.4549614191055298},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.45344075560569763},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4505402147769928},{"id":"https://openalex.org/keywords/reduction","display_name":"Reduction (mathematics)","score":0.42256397008895874},{"id":"https://openalex.org/keywords/markov-random-field","display_name":"Markov random field","score":0.42045944929122925},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3616945147514343},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32165390253067017},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1219019889831543},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09867560863494873}],"concepts":[{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.7534191608428955},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7521750926971436},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5425553321838379},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4874551296234131},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.4549614191055298},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.45344075560569763},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4505402147769928},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.42256397008895874},{"id":"https://openalex.org/C2778045648","wikidata":"https://www.wikidata.org/wiki/Q176827","display_name":"Markov random field","level":4,"score":0.42045944929122925},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3616945147514343},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32165390253067017},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1219019889831543},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09867560863494873},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"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/C124504099","wikidata":"https://www.wikidata.org/wiki/Q56933","display_name":"Image segmentation","level":3,"score":0.0},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D051379","descriptor_name":"Mice","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},{"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/btae611","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae611","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae611/59748034/btae611.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:39400541","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39400541","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:11512591","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11512591","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11512591/pdf/btae611.pdf","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/btae611","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae611","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae611/59748034/btae611.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/G1050989711","display_name":null,"funder_award_id":"2022M723328","funder_id":"https://openalex.org/F4320321543","funder_display_name":"China Postdoctoral Science Foundation"},{"id":"https://openalex.org/G579061253","display_name":null,"funder_award_id":"12126605","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G686147530","display_name":null,"funder_award_id":"2021YFA1302500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403394580.pdf"},"referenced_works_count":49,"referenced_works":["https://openalex.org/W1990885553","https://openalex.org/W2002785668","https://openalex.org/W2011832962","https://openalex.org/W2029006847","https://openalex.org/W2053675401","https://openalex.org/W2066769544","https://openalex.org/W2094650342","https://openalex.org/W2100235303","https://openalex.org/W2107665951","https://openalex.org/W2118796069","https://openalex.org/W2163488795","https://openalex.org/W2322720146","https://openalex.org/W2471536144","https://openalex.org/W2531627693","https://openalex.org/W2790675139","https://openalex.org/W2794521141","https://openalex.org/W2883806880","https://openalex.org/W2942880491","https://openalex.org/W2949177718","https://openalex.org/W2953036966","https://openalex.org/W2984472267","https://openalex.org/W3001833132","https://openalex.org/W3033919438","https://openalex.org/W3036371598","https://openalex.org/W3086790268","https://openalex.org/W3108118546","https://openalex.org/W3112563877","https://openalex.org/W3123293518","https://openalex.org/W3126958162","https://openalex.org/W3127422037","https://openalex.org/W3134766331","https://openalex.org/W3165120573","https://openalex.org/W3173882906","https://openalex.org/W3216124552","https://openalex.org/W4223515068","https://openalex.org/W4225272983","https://openalex.org/W4226192560","https://openalex.org/W4231665431","https://openalex.org/W4280494993","https://openalex.org/W4283274609","https://openalex.org/W4317215046","https://openalex.org/W4322738920","https://openalex.org/W4387440956","https://openalex.org/W4387580076","https://openalex.org/W4390814844","https://openalex.org/W4394892297","https://openalex.org/W6667361011","https://openalex.org/W6815484573","https://openalex.org/W6851849565"],"related_works":["https://openalex.org/W3176621072","https://openalex.org/W2995475466","https://openalex.org/W2356785732","https://openalex.org/W4210430843","https://openalex.org/W4239033281","https://openalex.org/W4380789568","https://openalex.org/W3105745662","https://openalex.org/W4379523021","https://openalex.org/W2146824712","https://openalex.org/W3081644756"],"abstract_inverted_index":{"MOTIVATION:":[0],"Spatial":[1],"transcriptomics":[2],"(ST)":[3],"technologies":[4],"provide":[5],"richer":[6],"insights":[7],"into":[8],"the":[9,89,138,183,195,207],"molecular":[10],"characteristics":[11],"of":[12,88,140,194,209],"cells":[13],"by":[14,225],"simultaneously":[15,132],"measuring":[16],"gene":[17],"expression":[18],"profiles":[19],"and":[20,33,53,63,76,95,102,131,149,155,157,163,174,190,200,204,216,231],"their":[21],"relative":[22],"locations.":[23],"However,":[24],"each":[25],"slice":[26],"can":[27,84,166],"only":[28],"contain":[29],"limited":[30],"biological":[31,77,96,125,177],"variation,":[32],"since":[34],"there":[35],"are":[36],"almost":[37],"always":[38],"non-negligible":[39],"batch":[40,51,121,198],"effects":[41,52],"across":[42,127,171],"different":[43,146],"slices,":[44,130],"integrating":[45,81],"numerous":[46],"slices":[47,173],"to":[48,99,119,214],"account":[49],"for":[50,73],"locations":[54],"is":[55,227],"not":[56],"straightforward.":[57],"Performing":[58],"multi-slice":[59],"integration,":[60],"dimensionality":[61],"reduction,":[62],"other":[64,184],"downstream":[65],"analyses":[66],"separately":[67],"often":[68],"results":[69],"in":[70,192],"suboptimal":[71],"embeddings":[72],"technical":[74,93],"artifacts":[75,94],"variations.":[78],"Joint":[79],"modeling":[80,211],"these":[82],"steps":[83],"enhance":[85],"our":[86],"understanding":[87],"complex":[90],"interplay":[91],"between":[92,197],"signals,":[97],"leading":[98],"more":[100],"accurate":[101],"insightful":[103],"results.":[104],"RESULTS:":[105],"In":[106,179],"this":[107],"context,":[108],"we":[109],"propose":[110],"a":[111],"hierarchical":[112],"hidden":[113],"Markov":[114],"random":[115],"field":[116],"model":[117],"STADIA":[118,141,165,181],"reduce":[120],"effects,":[122],"extract":[123],"common":[124,168],"patterns":[126],"multiple":[128,172],"ST":[129],"identify":[133],"spatial":[134,201],"domains.":[135],"We":[136],"demonstrate":[137],"effectiveness":[139],"using":[142],"five":[143],"datasets":[144],"from":[145],"species":[147],"(human":[148],"mouse),":[150],"various":[151],"organs":[152],"(brain,":[153],"skin,":[154],"liver),":[156],"diverse":[158],"platforms":[159],"(10x":[160],"Visium,":[161],"ST,":[162],"Slice-seqV2).":[164],"capture":[167],"tissue":[169],"structures":[170],"preserve":[175],"slice-specific":[176],"signals.":[178],"addition,":[180],"outperforms":[182],"three":[185],"competing":[186],"methods":[187],"(PRECAST,":[188],"fastMNN,":[189],"Harmony)":[191],"terms":[193],"balance":[196],"mixing":[199],"domain":[202],"identification,":[203],"it":[205],"demonstrates":[206],"advantage":[208],"joint":[210],"when":[212],"compared":[213],"STAGATE":[215],"GraphST.":[217],"AVAILABILITY":[218],"AND":[219],"IMPLEMENTATION:":[220],"The":[221],"source":[222],"code":[223],"implemented":[224],"R":[226],"available":[228],"at":[229],"https://github.com/zhanglabtools/STADIA":[230],"archived":[232],"with":[233],"version":[234],"1.01":[235],"on":[236],"Zenodo":[237],"https://zenodo.org/records/13637744.":[238]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":9}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
