{"id":"https://openalex.org/W4408506062","doi":"https://doi.org/10.1093/gpbjnl/qzaf024","title":"scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants","display_name":"scPlantLLM: A Foundation Model for Exploring Single-cell Expression Atlases in Plants","publication_year":2025,"publication_date":"2025-03-17","ids":{"openalex":"https://openalex.org/W4408506062","doi":"https://doi.org/10.1093/gpbjnl/qzaf024","pmid":"https://pubmed.ncbi.nlm.nih.gov/40094454"},"language":"en","primary_location":{"id":"doi:10.1093/gpbjnl/qzaf024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzaf024","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf024/62429563/qzaf024.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; 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/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf024/62429563/qzaf024.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059020870","display_name":"Guangshuo Cao","orcid":"https://orcid.org/0000-0002-2290-2748"},"institutions":[{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Guangshuo Cao","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011990443","display_name":"Haoyu Chao","orcid":"https://orcid.org/0000-0002-5475-0443"},"institutions":[{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyu Chao","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China","State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]},{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119607084","display_name":"Wenqi Zheng","orcid":"https://orcid.org/0009-0001-4849-9707"},"institutions":[{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenqi Zheng","raw_affiliation_strings":["Kuang Yaming Honors School, Nanjing University , Nanjing 210023,","Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"Kuang Yaming Honors School, Nanjing University , Nanjing 210023,","institution_ids":["https://openalex.org/I881766915"]},{"raw_affiliation_string":"Kuang Yaming Honors School, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034910608","display_name":"Yangming Lan","orcid":"https://orcid.org/0000-0002-8551-6705"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Yangming Lan","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023,","State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023,","institution_ids":["https://openalex.org/I881766915","https://openalex.org/I4210160211"]},{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055849925","display_name":"Kaiyan Lu","orcid":"https://orcid.org/0000-0002-9392-9585"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Kaiyan Lu","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023,","State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023,","institution_ids":["https://openalex.org/I881766915","https://openalex.org/I4210160211"]},{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010218141","display_name":"Yueyi Wang","orcid":"https://orcid.org/0000-0001-8613-2239"},"institutions":[{"id":"https://openalex.org/I4210160211","display_name":"Pharmaceutical Biotechnology (Czechia)","ror":"https://ror.org/051tvr365","country_code":"CZ","type":"company","lineage":["https://openalex.org/I4210160211"]},{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN","CZ"],"is_corresponding":false,"raw_author_name":"Yueyi Wang","raw_affiliation_strings":["State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023,","State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University , Nanjing 210023,","institution_ids":["https://openalex.org/I881766915","https://openalex.org/I4210160211"]},{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100423292","display_name":"Ming Chen","orcid":"https://orcid.org/0000-0002-9677-1699"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ming Chen","raw_affiliation_strings":["Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100420105","display_name":"He Zhang","orcid":"https://orcid.org/0000-0001-9294-1403"},"institutions":[{"id":"https://openalex.org/I146620803","display_name":"Wenzhou University","ror":"https://ror.org/020hxh324","country_code":"CN","type":"education","lineage":["https://openalex.org/I146620803"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"He Zhang","raw_affiliation_strings":["Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China"],"affiliations":[{"raw_affiliation_string":"Zhejiang Provincial Key Lab for Subtropical Water Environment and Marine Biological Resources Protection, College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China","institution_ids":["https://openalex.org/I146620803"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073035070","display_name":"Dijun Chen","orcid":"https://orcid.org/0000-0002-7456-2511"},"institutions":[{"id":"https://openalex.org/I881766915","display_name":"Nanjing University","ror":"https://ror.org/01rxvg760","country_code":"CN","type":"education","lineage":["https://openalex.org/I881766915"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dijun Chen","raw_affiliation_strings":["Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China","State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China"],"affiliations":[{"raw_affiliation_string":"Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]},{"raw_affiliation_string":"State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China","institution_ids":["https://openalex.org/I881766915"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5059020870"],"corresponding_institution_ids":["https://openalex.org/I881766915"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":2.5275,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.87985877,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"23","issue":"3","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":0.9994999766349792,"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":0.9994999766349792,"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":0.9975000023841858,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9853000044822693,"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/annotation","display_name":"Annotation","score":0.6771742701530457},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6708475351333618},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6474641561508179},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6295793056488037},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.47372666001319885},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.46853700280189514},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.458456426858902},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41634005308151245},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.400410920381546},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.37076589465141296},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22693637013435364}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6771742701530457},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6708475351333618},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6474641561508179},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6295793056488037},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.47372666001319885},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.46853700280189514},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.458456426858902},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41634005308151245},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.400410920381546},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37076589465141296},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22693637013435364},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018506","descriptor_name":"Gene Expression Regulation, Plant","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/gpbjnl/qzaf024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzaf024","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf024/62429563/qzaf024.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40094454","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40094454","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12417071","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12417071/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genomics Proteomics Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/gpbjnl/qzaf024","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzaf024","pdf_url":"https://academic.oup.com/gpb/advance-article-pdf/doi/10.1093/gpbjnl/qzaf024/62429563/qzaf024.pdf","source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4408506062.pdf"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1910735071","https://openalex.org/W1987971958","https://openalex.org/W2065358406","https://openalex.org/W2107328658","https://openalex.org/W2169803017","https://openalex.org/W2171012097","https://openalex.org/W2587657604","https://openalex.org/W2896457183","https://openalex.org/W2913398225","https://openalex.org/W2951175428","https://openalex.org/W2965552103","https://openalex.org/W2997591727","https://openalex.org/W3108118546","https://openalex.org/W3136916445","https://openalex.org/W3194665116","https://openalex.org/W4235169531","https://openalex.org/W4378838672","https://openalex.org/W4386208756","https://openalex.org/W4387966379","https://openalex.org/W4390885669","https://openalex.org/W4392168151","https://openalex.org/W4399387478"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W4405124681","https://openalex.org/W1533177136","https://openalex.org/W2295598435"],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"provides":[4],"unprecedented":[5,179],"insights":[6],"into":[7],"plant":[8,60,133,174,190],"cellular":[9,126,183],"diversity":[10],"by":[11],"enabling":[12],"high-resolution":[13],"analyses":[14],"of":[15,25,59,105],"gene":[16,37],"expression":[17,176],"at":[18,200],"the":[19,23,114],"single-cell":[20,61,83,175],"level.":[21],"However,":[22],"complexity":[24],"scRNA-seq":[26],"data,":[27],"including":[28],"challenges":[29],"in":[30,94,109,142,195],"batch":[31,100],"integration,":[32,101],"cell":[33,74,96],"type":[34,75,97],"annotation,":[35,98],"and":[36,73,81,99,124,155,164,185],"regulatory":[38,186],"network":[39],"(GRN)":[40],"inference,":[41],"demands":[42],"advanced":[43],"computational":[44],"approaches.":[45],"To":[46],"address":[47],"these":[48],"challenges,":[49],"we":[50],"developed":[51],"scPlantLLM,":[52],"a":[53,65,169],"Transformer":[54],"model":[55,115,171],"trained":[56],"on":[57],"millions":[58],"data":[62,84],"points.":[63],"Using":[64],"sequential":[66],"pretraining":[67],"strategy":[68],"incorporating":[69],"masked":[70],"language":[71],"modeling":[72],"annotation":[76],"tasks,":[77],"scPlantLLM":[78,92,140,167],"generates":[79],"robust":[80],"interpretable":[82],"embeddings.":[85],"When":[86],"applied":[87],"to":[88,107,119,131,137,181],"Arabidopsis":[89],"thaliana":[90],"datasets,":[91],"excels":[93],"clustering,":[95],"achieving":[102],"an":[103,117],"accuracy":[104,163],"up":[106],"0.91":[108],"zero-shot":[110],"learning":[111],"scenarios.":[112],"Furthermore,":[113],"demonstrates":[116],"ability":[118],"identify":[120],"biologically":[121],"meaningful":[122],"GRNs":[123],"subtle":[125],"subtypes,":[127],"showcasing":[128],"its":[129,160],"potential":[130],"advance":[132],"biology":[134],"research.":[135],"Compared":[136],"traditional":[138],"methods,":[139],"outperforms":[141],"key":[143],"metrics":[144],"such":[145],"as":[146],"adjusted":[147],"rand":[148],"index":[149],"(ARI),":[150],"normalized":[151],"mutual":[152],"information":[153],"(NMI),":[154],"silhouette":[156],"score":[157],"(SIL),":[158],"highlighting":[159],"superior":[161],"clustering":[162],"biological":[165],"relevance.":[166],"represents":[168],"foundation":[170],"for":[172],"exploring":[173],"atlases,":[177],"offering":[178],"capabilities":[180],"resolve":[182],"heterogeneity":[184],"dynamics":[187],"across":[188],"diverse":[189],"systems.":[191],"The":[192],"code":[193],"used":[194],"this":[196],"study":[197],"is":[198],"available":[199],"https://github.com/compbioNJU/scPlantLLM.":[201]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-03-17T00:00:00"}
