{"id":"https://openalex.org/W4400420052","doi":"https://doi.org/10.1093/bib/bbae329","title":"Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster","display_name":"Accurately deciphering spatial domains for spatially resolved transcriptomics with stCluster","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4400420052","doi":"https://doi.org/10.1093/bib/bbae329","pmid":"https://pubmed.ncbi.nlm.nih.gov/38975895"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae329","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae329/58469384/bbae329.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/25/4/bbae329/58469384/bbae329.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5115596151","display_name":"Tao Wang","orcid":"https://orcid.org/0000-0003-4140-8734"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tao Wang","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I890469752"]},{"raw_affiliation_string":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110306113","display_name":"Han Shu","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Han Shu","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I890469752"]},{"raw_affiliation_string":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018634374","display_name":"Jialu Hu","orcid":"https://orcid.org/0000-0002-3351-8020"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jialu Hu","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I890469752"]},{"raw_affiliation_string":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026250850","display_name":"Yongtian Wang","orcid":"https://orcid.org/0000-0001-9422-0888"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongtian Wang","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I890469752"]},{"raw_affiliation_string":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102730078","display_name":"Jing Chen","orcid":"https://orcid.org/0000-0003-1894-335X"},"institutions":[{"id":"https://openalex.org/I4210131919","display_name":"Xi'an University of Technology","ror":"https://ror.org/038avdt50","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210131919"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jing Chen","raw_affiliation_strings":["School of Computer Science and Engineering, Xi'an University of Technology , No.5 South Jinhua rd., Xi'an 710048 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Xi'an University of Technology , No.5 South Jinhua rd., Xi'an 710048 , China","institution_ids":["https://openalex.org/I4210131919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084343474","display_name":"Jiajie Peng","orcid":"https://orcid.org/0000-0002-3857-7927"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiajie Peng","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I890469752"]},{"raw_affiliation_string":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I890469752","display_name":"Ministry of Industry and Information Technology","ror":"https://ror.org/0385nmy68","country_code":"CN","type":"government","lineage":["https://openalex.org/I890469752"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I890469752"]},{"raw_affiliation_string":"Northwestern Polytechnical University , Ministry of Industry and Information Technology, , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Rd., Xi'an 710072 , China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Key Laboratory of Big Data Storage and Management, Ministry of Industry and Information Technology, Northwestern Polytechnical University, 1 Dongxiang Rd., Xi'an 710072, China","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I890469752"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5009944817","https://openalex.org/A5084343474","https://openalex.org/A5102730078","https://openalex.org/A5115596151"],"corresponding_institution_ids":["https://openalex.org/I17145004","https://openalex.org/I4210131919","https://openalex.org/I890469752"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":5.5985,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.96934723,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"25","issue":"4","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/T10885","display_name":"Gene expression and cancer classification","score":0.9718999862670898,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.9495999813079834,"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":0.7455950379371643},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7224128246307373},{"id":"https://openalex.org/keywords/discriminative-model","display_name":"Discriminative model","score":0.6201683878898621},{"id":"https://openalex.org/keywords/spatial-contextual-awareness","display_name":"Spatial contextual awareness","score":0.6097104549407959},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.6065646409988403},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5441729426383972},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.524071455001831},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4838660955429077},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.45779141783714294},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4414491355419159},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3726983070373535},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1570504605770111},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1330420970916748}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7455950379371643},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7224128246307373},{"id":"https://openalex.org/C97931131","wikidata":"https://www.wikidata.org/wiki/Q5282087","display_name":"Discriminative model","level":2,"score":0.6201683878898621},{"id":"https://openalex.org/C64754055","wikidata":"https://www.wikidata.org/wiki/Q7574053","display_name":"Spatial contextual awareness","level":2,"score":0.6097104549407959},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.6065646409988403},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5441729426383972},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.524071455001831},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4838660955429077},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.45779141783714294},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4414491355419159},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3726983070373535},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1570504605770111},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1330420970916748},{"id":"https://openalex.org/C62649853","wikidata":"https://www.wikidata.org/wiki/Q199687","display_name":"Remote sensing","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C127313418","wikidata":"https://www.wikidata.org/wiki/Q1069","display_name":"Geology","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"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":"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":"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":"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":"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":"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":"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":"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":"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},{"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/bib/bbae329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae329","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae329/58469384/bbae329.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38975895","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38975895","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},{"id":"pmh:oai:pubmedcentral.nih.gov:11771244","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11771244","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11771244/pdf/bbae329.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":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae329","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae329","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae329/58469384/bbae329.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","score":0.7599999904632568,"display_name":"Reduced inequalities"}],"awards":[{"id":"https://openalex.org/G3128057212","display_name":null,"funder_award_id":"62102319","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"},{"id":"https://openalex.org/F4320325627","display_name":"Education Department of Shaanxi Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4400420052.pdf","grobid_xml":"https://content.openalex.org/works/W4400420052.grobid-xml"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W48830290","https://openalex.org/W1967320885","https://openalex.org/W2074466695","https://openalex.org/W2125287331","https://openalex.org/W2131099349","https://openalex.org/W2131681506","https://openalex.org/W2222512263","https://openalex.org/W2247585390","https://openalex.org/W2299467264","https://openalex.org/W2471536144","https://openalex.org/W2519132385","https://openalex.org/W2800392236","https://openalex.org/W2889326414","https://openalex.org/W2950372712","https://openalex.org/W2951429788","https://openalex.org/W2952383043","https://openalex.org/W2963285578","https://openalex.org/W2964074409","https://openalex.org/W2997681568","https://openalex.org/W2999905431","https://openalex.org/W3035705215","https://openalex.org/W3036371598","https://openalex.org/W3095746859","https://openalex.org/W3099810371","https://openalex.org/W3108118546","https://openalex.org/W3126958162","https://openalex.org/W3154503084","https://openalex.org/W3201206168","https://openalex.org/W4212867045","https://openalex.org/W4225381889","https://openalex.org/W4226192560","https://openalex.org/W4229033508","https://openalex.org/W4283165220","https://openalex.org/W4283791586","https://openalex.org/W4285723986","https://openalex.org/W4290154117","https://openalex.org/W4294042823","https://openalex.org/W4306406844","https://openalex.org/W4309334544","https://openalex.org/W4309341717","https://openalex.org/W4309667063","https://openalex.org/W4313261772","https://openalex.org/W4322738920","https://openalex.org/W4388035146","https://openalex.org/W4390814844","https://openalex.org/W4391529870","https://openalex.org/W6678276164","https://openalex.org/W6678914141","https://openalex.org/W6679686813","https://openalex.org/W6681648400","https://openalex.org/W6732085715","https://openalex.org/W6801325971","https://openalex.org/W6846495618","https://openalex.org/W6848190953","https://openalex.org/W6858454745"],"related_works":["https://openalex.org/W3148227991","https://openalex.org/W1486593826","https://openalex.org/W2771174107","https://openalex.org/W1536965844","https://openalex.org/W2344941099","https://openalex.org/W4322212724","https://openalex.org/W2106788855","https://openalex.org/W3081561710","https://openalex.org/W2477413883","https://openalex.org/W2463773089"],"abstract_inverted_index":{"Spatial":[0],"transcriptomics":[1],"provides":[2],"valuable":[3],"insights":[4],"into":[5],"gene":[6,53,135,175],"expression":[7,54,136,176],"within":[8],"the":[9,125,145,173,180],"native":[10],"tissue":[11,26,43],"context,":[12,30],"effectively":[13,171],"merging":[14],"molecular":[15],"data":[16,55],"with":[17,56,84],"spatial":[18,33,57,70,92,97,138,155,174,181],"information":[19],"to":[20,87,107,127,130],"uncover":[21],"intricate":[22],"cellular":[23,32,40],"relationships":[24,133],"and":[25,42,66,137,160,165,178],"organizations.":[27],"In":[28],"this":[29],"deciphering":[31],"domains":[34,156],"becomes":[35],"essential":[36],"for":[37,91],"revealing":[38],"complex":[39,132,154],"dynamics":[41],"structures.":[44],"However,":[45],"current":[46],"methods":[47],"encounter":[48],"challenges":[49],"in":[50,60,69,151],"seamlessly":[51],"integrating":[52],"information,":[58],"resulting":[59],"less":[61],"informative":[62,89],"representations":[63,90,110,126],"of":[64,112,187],"spots":[65],"suboptimal":[67],"accuracy":[68],"domain":[71,98],"identification.":[72,99],"We":[73],"introduce":[74],"stCluster,":[75],"a":[76],"novel":[77],"method":[78],"that":[79],"integrates":[80],"graph":[81,103],"contrastive":[82,104],"learning":[83,86,105],"multi-task":[85],"refine":[88],"transcriptomic":[93],"data,":[94],"consequently":[95],"improving":[96],"stCluster":[100,122,169,188],"first":[101],"leverages":[102],"technology":[106],"obtain":[108],"discriminative":[109],"capable":[111],"recognizing":[113],"spatially":[114],"coherent":[115],"patterns.":[116],"Through":[117],"jointly":[118],"optimizing":[119],"multiple":[120],"tasks,":[121],"further":[123],"fine-tunes":[124],"be":[128],"able":[129],"capture":[131],"between":[134],"organization.":[139],"Benchmarked":[140],"against":[141],"six":[142],"state-of-the-art":[143],"methods,":[144],"experimental":[146],"results":[147],"reveal":[148],"its":[149],"proficiency":[150],"accurately":[152],"identifying":[153],"across":[157],"various":[158],"datasets":[159],"platforms,":[161],"spanning":[162],"tissue,":[163],"organ,":[164],"embryo":[166],"levels.":[167],"Moreover,":[168],"can":[170],"denoise":[172],"patterns":[177],"enhance":[179],"trajectory":[182],"inference.":[183],"The":[184],"source":[185],"code":[186],"is":[189],"freely":[190],"available":[191],"at":[192],"https://github.com/hannshu/stCluster.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
