{"id":"https://openalex.org/W7128190761","doi":"https://doi.org/10.1093/bioinformatics/btaf655","title":"CeLLTra: aligning cell names with gene expression via a pathway-informed transformer","display_name":"CeLLTra: aligning cell names with gene expression via a pathway-informed transformer","publication_year":2025,"publication_date":"2025-12-04","ids":{"openalex":"https://openalex.org/W7128190761","doi":"https://doi.org/10.1093/bioinformatics/btaf655","pmid":"https://pubmed.ncbi.nlm.nih.gov/41652996"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf655","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf655","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btaf655","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101780500","display_name":"Li Zhao","orcid":"https://orcid.org/0000-0002-2544-0876"},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhao Li","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I4210159031"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5097767807","display_name":"Zaiyi Zheng","orcid":"https://orcid.org/0009-0003-0685-0057"},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zaiyi Zheng","raw_affiliation_strings":["University of Virginia Department of Electrical and Computer Engineering, , Charlottesville, VA 22903,"],"affiliations":[{"raw_affiliation_string":"University of Virginia Department of Electrical and Computer Engineering, , Charlottesville, VA 22903,","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125327632","display_name":"Rongbin Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rongbin Li","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I4210159031"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125305616","display_name":"Wenbo Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wenbo Chen","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I4210159031"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125297406","display_name":"Yuntao Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuntao Yang","raw_affiliation_strings":["University of Texas MD Anderson Cancer Center Department of Genomic Medicine, , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"University of Texas MD Anderson Cancer Center Department of Genomic Medicine, , Houston, TX 77030,","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053321555","display_name":"Meer Asif Ali","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Meer A Ali","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I4210159031"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124329590","display_name":"Jundong Li","orcid":null},"institutions":[{"id":"https://openalex.org/I51556381","display_name":"University of Virginia","ror":"https://ror.org/0153tk833","country_code":"US","type":"education","lineage":["https://openalex.org/I51556381"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jundong Li","raw_affiliation_strings":["University of Virginia Department of Electrical and Computer Engineering, , Charlottesville, VA 22903,"],"affiliations":[{"raw_affiliation_string":"University of Virginia Department of Electrical and Computer Engineering, , Charlottesville, VA 22903,","institution_ids":["https://openalex.org/I51556381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5125310618","display_name":"W Jim Zheng","orcid":null},"institutions":[{"id":"https://openalex.org/I4210159031","display_name":"The University of Texas Health Science Center","ror":"https://ror.org/05cwbxa29","country_code":"US","type":"education","lineage":["https://openalex.org/I4210159031"]},{"id":"https://openalex.org/I919571938","display_name":"The University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39","country_code":"US","type":"education","lineage":["https://openalex.org/I919571938"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W Jim Zheng","raw_affiliation_strings":["McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,"],"affiliations":[{"raw_affiliation_string":"McWilliams School of Biomedical Informatics, University of Texas Health Science Center at Houston Department of Bioinformatics & Systems Medicine, , Houston, TX 77030,","institution_ids":["https://openalex.org/I919571938","https://openalex.org/I4210159031"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5101780500"],"corresponding_institution_ids":["https://openalex.org/I4210159031","https://openalex.org/I919571938"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.65772819,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9745000004768372,"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":0.9745000004768372,"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":0.009100000374019146,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.0035000001080334187,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5178999900817871},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.4894999861717224},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4681999981403351},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4487000107765198},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.44620001316070557},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40540000796318054}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6930999755859375},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5404000282287598},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5178999900817871},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.4894999861717224},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4681999981403351},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4487000107765198},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.44620001316070557},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40540000796318054},{"id":"https://openalex.org/C62177273","wikidata":"https://www.wikidata.org/wiki/Q5531556","display_name":"Gene nomenclature","level":4,"score":0.4011000096797943},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.400299996137619},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.31859999895095825},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3028999865055084},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3019999861717224},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.29019999504089355},{"id":"https://openalex.org/C2984968299","wikidata":"https://www.wikidata.org/wiki/Q1077784","display_name":"Software tool","level":3,"score":0.2773999869823456},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2572000026702881}],"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":"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":"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":"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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"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":"D020869","descriptor_name":"Gene Expression Profiling","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf655","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf655","pdf_url":null,"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:41652996","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41652996","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:digitalcommons.library.tmc.edu:uthshis_docs-1790","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthshis_docs/814","pdf_url":null,"source":{"id":"https://openalex.org/S4306401994","display_name":"DigtalCommons @ Texas Medical Center Library (Texas Medical Center)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I867280407","host_organization_name":"The University of Texas Southwestern Medical Center","host_organization_lineage":["https://openalex.org/I867280407"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty, Staff and Student Publications","raw_type":"text"},{"id":"pmh:oai:europepmc.org:11689405","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12881829","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12881829","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12881829/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf655","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf655","pdf_url":null,"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/G1439040515","display_name":null,"funder_award_id":"5R56AG069880-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1923038014","display_name":null,"funder_award_id":"1UL1TR003167","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1962302012","display_name":null,"funder_award_id":"1UM1TR004906-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3120388081","display_name":null,"funder_award_id":"RP170668","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G6512622221","display_name":null,"funder_award_id":"1U24MH130988-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8056136029","display_name":null,"funder_award_id":"1R01AG066749","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G894622851","display_name":null,"funder_award_id":"W81XWH-22-1-0164","funder_id":"https://openalex.org/F4320306078","funder_display_name":"U.S. Department of Defense"}],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1681831155","https://openalex.org/W1978486653","https://openalex.org/W1979283544","https://openalex.org/W2010457001","https://openalex.org/W2108723074","https://openalex.org/W2119423220","https://openalex.org/W2462007197","https://openalex.org/W2753908609","https://openalex.org/W2768250222","https://openalex.org/W2800392236","https://openalex.org/W2897249806","https://openalex.org/W2907783748","https://openalex.org/W2926010705","https://openalex.org/W2936414047","https://openalex.org/W2949237386","https://openalex.org/W2959295202","https://openalex.org/W2971398276","https://openalex.org/W3130453114","https://openalex.org/W3200266566","https://openalex.org/W4223992851","https://openalex.org/W4280598116","https://openalex.org/W4283726509","https://openalex.org/W4297243391","https://openalex.org/W4378838672","https://openalex.org/W4389670555","https://openalex.org/W4392168151","https://openalex.org/W4393153069","https://openalex.org/W4393160131","https://openalex.org/W4396939663","https://openalex.org/W4399387478","https://openalex.org/W4402604581","https://openalex.org/W4403401644"],"related_works":[],"abstract_inverted_index":{"CeLLTra":[0],"is":[1],"freely":[2,30],"available":[3,26],"on":[4,32],"GitHub":[5],"(https://github.com/WJZheng-group/CeLLTra)":[6],"and":[7,19,27],"Zenodo":[8],"(https://doi.org/10.5281/zenodo.17666735).":[9],"The":[10],"datasets":[11,23],"underlying":[12],"this":[13],"article":[14],"are":[15,24],"the":[16,33],"following:":[17],"GSE201333":[18],"GSE127465.":[20],"All":[21],"these":[22],"publicly":[25],"can":[28],"be":[29],"accessed":[31],"Gene":[34],"Expression":[35],"Omnibus":[36],"repository.":[37]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-02-08T00:00:00"}
