{"id":"https://openalex.org/W4411623034","doi":"https://doi.org/10.1093/bib/bbaf296","title":"iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics","display_name":"iGTP: learning interpretable cellular embedding for inferring biological mechanisms underlying single-cell transcriptomics","publication_year":2025,"publication_date":"2025-05-01","ids":{"openalex":"https://openalex.org/W4411623034","doi":"https://doi.org/10.1093/bib/bbaf296","pmid":"https://pubmed.ncbi.nlm.nih.gov/40551620"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf296","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf296","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf296/63562669/bbaf296.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/26/3/bbaf296/63562669/bbaf296.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031171460","display_name":"Kang\u2010Lin Hsieh","orcid":"https://orcid.org/0000-0002-2043-5605"},"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":"Kang-Lin Hsieh","raw_affiliation_strings":["Division of Cancer Medicine, Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center , 1515 Holcombe Blvd, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Cancer Medicine, Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center , 1515 Holcombe Blvd, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023152324","display_name":"Kai Zhang","orcid":"https://orcid.org/0000-0002-4519-609X"},"institutions":[{"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":"Kai Zhang","raw_affiliation_strings":["Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038003327","display_name":"Yan Chu","orcid":"https://orcid.org/0000-0002-7866-0821"},"institutions":[{"id":"https://openalex.org/I1320553840","display_name":"Amgen (United States)","ror":"https://ror.org/03g03ge92","country_code":"US","type":"company","lineage":["https://openalex.org/I1320553840"]},{"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"]},{"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":"Yan Chu","raw_affiliation_strings":["Center for Artificial Intelligence and Genome Informatics, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, Houston, TX 77030 ,","Center for Design and Analysis, Amgen , One Amgen Center Drive, Thousand Oaks, CA 91320 ,","Division of Radiation Oncology, Department of Radiation Physics, UT MD Anderson Cancer Center , 1400 Pressler St, Houston, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence and Genome Informatics, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"Center for Design and Analysis, Amgen , One Amgen Center Drive, Thousand Oaks, CA 91320 ,","institution_ids":["https://openalex.org/I1320553840"]},{"raw_affiliation_string":"Division of Radiation Oncology, Department of Radiation Physics, UT MD Anderson Cancer Center , 1400 Pressler St, Houston, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036642357","display_name":"Lishan Yu","orcid":"https://orcid.org/0000-0002-7245-7806"},"institutions":[{"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":"Lishan Yu","raw_affiliation_strings":["Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102724022","display_name":"Xiaoyang Li","orcid":"https://orcid.org/0000-0001-8711-7567"},"institutions":[{"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":"Xiaoyang Li","raw_affiliation_strings":["Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston , 1200 Pressler St, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston , 1200 Pressler St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112013625","display_name":"Na Hu","orcid":"https://orcid.org/0000-0003-0946-5552"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]},{"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":"Nuo Hu","raw_affiliation_strings":["Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","Department of Statistics, Rice University , 6100 Main St MS 364, Houston, TX 77005 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"Department of Statistics, Rice University , 6100 Main St MS 364, Houston, TX 77005 ,","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115077236","display_name":"Isha Kawosa","orcid":null},"institutions":[{"id":"https://openalex.org/I91045830","display_name":"Texas A&M University","ror":"https://ror.org/01f5ytq51","country_code":"US","type":"education","lineage":["https://openalex.org/I91045830"]},{"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":"Isha Kawosa","raw_affiliation_strings":["Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","Department of Computer Science and Engineering, Texas A&M University , 435 Nagle St, College Station, TX 77843 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Texas A&M University , 435 Nagle St, College Station, TX 77843 ,","institution_ids":["https://openalex.org/I91045830"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022629958","display_name":"Patrick G. Pili\u00e9","orcid":"https://orcid.org/0000-0001-8759-0020"},"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":"Patrick G Pili\u00e9","raw_affiliation_strings":["Division of Cancer Medicine, Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center , 1515 Holcombe Blvd, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Cancer Medicine, Department of Genitourinary Medical Oncology, UT MD Anderson Cancer Center , 1515 Holcombe Blvd, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034240658","display_name":"Pratip K. Bhattacharya","orcid":"https://orcid.org/0000-0002-0625-252X"},"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":"Pratip K Bhattacharya","raw_affiliation_strings":["Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012354604","display_name":"Degui Zhi","orcid":"https://orcid.org/0000-0001-7754-1890"},"institutions":[{"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":"Degui Zhi","raw_affiliation_strings":["Center for Artificial Intelligence and Genome Informatics, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Artificial Intelligence and Genome Informatics, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055458864","display_name":"Xiaoqian Jiang","orcid":"https://orcid.org/0000-0001-9933-2205"},"institutions":[{"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":"Xiaoqian Jiang","raw_affiliation_strings":["Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Secure Artificial Intelligence for Healthcare, School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006688612","display_name":"Zhongming Zhao","orcid":"https://orcid.org/0000-0002-3477-0914"},"institutions":[{"id":"https://openalex.org/I901861585","display_name":"Vanderbilt University Medical Center","ror":"https://ror.org/05dq2gs74","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210162197","https://openalex.org/I901861585"]},{"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":"Zhongming Zhao","raw_affiliation_strings":["Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","Department of Biomedical Informatics, Vanderbilt University Medical Center , 2525 West End Av, Nashville, TN 37203 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Vanderbilt University Medical Center , 2525 West End Av, Nashville, TN 37203 ,","institution_ids":["https://openalex.org/I901861585"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043473632","display_name":"Yulin Dai","orcid":"https://orcid.org/0000-0003-1874-7893"},"institutions":[{"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":"Yulin Dai","raw_affiliation_strings":["Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston , 7000 Fannin St, Houston, TX 77030 ,","institution_ids":["https://openalex.org/I919571938"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.4868,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.63846357,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"26","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":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9965000152587891,"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/T10604","display_name":"RNA Research and Splicing","score":0.9947999715805054,"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/embedding","display_name":"Embedding","score":0.690938413143158},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.6760881543159485},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6451967358589172},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6192077398300171},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5241173505783081},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5194796323776245},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5080609321594238},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4564951956272125},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44950568675994873},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4442155659198761},{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.44309818744659424},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4324556589126587},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2713788151741028},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.14222371578216553},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10918846726417542},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1025921106338501}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.690938413143158},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.6760881543159485},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6451967358589172},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6192077398300171},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5241173505783081},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5194796323776245},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5080609321594238},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4564951956272125},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44950568675994873},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4442155659198761},{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.44309818744659424},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4324556589126587},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2713788151741028},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.14222371578216553},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10918846726417542},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1025921106338501},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"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":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"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":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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf296","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf296","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf296/63562669/bbaf296.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40551620","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40551620","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:digitalcommons.library.tmc.edu:uthshis_docs-1647","is_oa":false,"landing_page_url":"https://digitalcommons.library.tmc.edu/uthshis_docs/660","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:11013293","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12206099","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf296","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf296","pdf_url":"https://academic.oup.com/bib/article-pdf/26/3/bbaf296/63562669/bbaf296.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G174454136","display_name":null,"funder_award_id":"R01LM012806","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2443506452","display_name":null,"funder_award_id":"R03AG077191","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G2555289976","display_name":null,"funder_award_id":"U01AG079847","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3111185166","display_name":null,"funder_award_id":"R01 DE030122","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G3601259633","display_name":null,"funder_award_id":"R01DE029818","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3813486454","display_name":null,"funder_award_id":"R01LM012806","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G4171611943","display_name":null,"funder_award_id":"R21 AG087299","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G4793940158","display_name":null,"funder_award_id":"R01DE030122","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G5625665474","display_name":null,"funder_award_id":"R01DE029818","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G5651236485","display_name":null,"funder_award_id":"R01 LM012806","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G604076272","display_name":null,"funder_award_id":"R01 DE029818","funder_id":"https://openalex.org/F4320337365","funder_display_name":"National Institute of Dental and Craniofacial Research"},{"id":"https://openalex.org/G6632181195","display_name":null,"funder_award_id":"U01 AG079847","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G6646588417","display_name":null,"funder_award_id":"CPRIT RP210045","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G6722721435","display_name":null,"funder_award_id":"R03 AG077191","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G7253053689","display_name":null,"funder_award_id":"R01DE030122","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7402308576","display_name":"UTHealth Cancer Genomics Core (UTHealth CGC)","funder_award_id":"RP240610","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G7562564013","display_name":null,"funder_award_id":"NCT04947254, NCT03748641","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7671781229","display_name":null,"funder_award_id":"R03AG077191","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8100577519","display_name":"Biomedical Informatics, Genomics, and Translational Cancer Research Training Program (BIG-TCR)","funder_award_id":"RP210045","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G8497683785","display_name":null,"funder_award_id":"CPRIT RP240610","funder_id":"https://openalex.org/F4320308129","funder_display_name":"Cancer Prevention and Research Institute of Texas"},{"id":"https://openalex.org/G8770013317","display_name":null,"funder_award_id":"RP210045","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320308129","display_name":"Cancer Prevention and Research Institute of Texas","ror":"https://ror.org/0003xa228"},{"id":"https://openalex.org/F4320313675","display_name":"University of Texas Health Science Center at Houston","ror":"https://ror.org/03gds6c39"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332521","display_name":"University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337365","display_name":"National Institute of Dental and Craniofacial Research","ror":"https://ror.org/004a2wv92"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411623034.pdf","grobid_xml":"https://content.openalex.org/works/W4411623034.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1560371681","https://openalex.org/W2022126078","https://openalex.org/W2067706259","https://openalex.org/W2070448139","https://openalex.org/W2075306207","https://openalex.org/W2123879591","https://openalex.org/W2126574774","https://openalex.org/W2321809676","https://openalex.org/W2612519453","https://openalex.org/W2624934104","https://openalex.org/W2774307122","https://openalex.org/W2775900076","https://openalex.org/W2884991984","https://openalex.org/W2901677030","https://openalex.org/W2949681238","https://openalex.org/W2951029718","https://openalex.org/W2951381561","https://openalex.org/W2952016241","https://openalex.org/W2965552103","https://openalex.org/W2969093152","https://openalex.org/W3019006262","https://openalex.org/W3024013192","https://openalex.org/W3043029189","https://openalex.org/W3048884493","https://openalex.org/W3130814454","https://openalex.org/W3137482466","https://openalex.org/W3184954235","https://openalex.org/W3196971188","https://openalex.org/W3198052269","https://openalex.org/W3199772305","https://openalex.org/W3204708585","https://openalex.org/W4210587306","https://openalex.org/W4220837089","https://openalex.org/W4220939068","https://openalex.org/W4249816251","https://openalex.org/W4280598116","https://openalex.org/W4385955324","https://openalex.org/W4388667039","https://openalex.org/W4389390583","https://openalex.org/W4401794004","https://openalex.org/W4410765873","https://openalex.org/W6640963894"],"related_works":["https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4392946183","https://openalex.org/W4405887298","https://openalex.org/W2983142544","https://openalex.org/W2891059443","https://openalex.org/W4281663961","https://openalex.org/W3208888551","https://openalex.org/W4313561566","https://openalex.org/W3208386644"],"abstract_inverted_index":{"Deep-learning":[0],"models":[1,102],"like":[2],"Variational":[3],"AutoEncoder":[4],"have":[5],"enabled":[6],"low":[7],"dimensional":[8],"cellular":[9,94,126],"embedding":[10],"representation":[11],"for":[12,146,168],"large-scale":[13],"single-cell":[14],"transcriptomes":[15],"and":[16,58,82,103,150,162,165],"shown":[17],"great":[18],"flexibility":[19],"in":[20,72,107],"downstream":[21],"tasks.":[22,110],"However,":[23],"biologically":[24],"meaningful":[25],"latent":[26,114,138],"space":[27,57],"is":[28,35],"usually":[29],"missing":[30],"if":[31],"no":[32],"specific":[33,147],"structure":[34],"designed.":[36],"Here,":[37],"we":[38,131],"engineered":[39],"a":[40,73,117,137],"novel":[41,172],"interpretable":[42],"generative":[43],"transcriptional":[44,54],"program":[45,55],"(iGTP)":[46],"framework":[47],"that":[48,154],"could":[49,123],"model":[50,140],"the":[51,68,90,113],"importance":[52],"of":[53,70,93],"(TP)":[56],"protein-protein":[59],"interactions":[60],"(PPI)":[61],"between":[62],"different":[63,83],"biological":[64,75],"states.":[65,151],"We":[66,152],"demonstrated":[67],"performance":[69],"iGTP":[71,86,122,133,155],"diverse":[74],"context":[76],"using":[77],"gene":[78],"ontology,":[79],"canonical":[80],"pathway,":[81],"PPI":[84,161],"curation.":[85],"not":[87],"only":[88],"elucidated":[89],"ground":[91],"truth":[92],"responses":[95,127,170],"but":[96],"also":[97],"surpassed":[98],"other":[99],"deep":[100],"learning":[101],"traditional":[104],"bioinformatics":[105],"methods":[106],"functional":[108],"enrichment":[109],"By":[111],"integrating":[112],"layer":[115],"with":[116,136],"graph":[118],"neural":[119],"network":[120],"framework,":[121],"effectively":[124],"infer":[125],"to":[128,141,171],"perturbations.":[129,173],"Lastly,":[130],"applied":[132],"TP":[134,163],"embeddings":[135,145],"diffusion":[139],"accurately":[142],"generate":[143],"cell":[144,148],"types":[149],"anticipate":[153],"will":[156],"offer":[157],"insights":[158],"at":[159],"both":[160],"levels":[164],"holds":[166],"promise":[167],"predicting":[169]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}