{"id":"https://openalex.org/W4383757091","doi":"https://doi.org/10.1371/journal.pcbi.1011300","title":"LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity","display_name":"LRT: Integrative analysis of scRNA-seq and scTCR-seq data to investigate clonal differentiation heterogeneity","publication_year":2023,"publication_date":"2023-07-10","ids":{"openalex":"https://openalex.org/W4383757091","doi":"https://doi.org/10.1371/journal.pcbi.1011300","pmid":"https://pubmed.ncbi.nlm.nih.gov/37428794"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011300","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011300&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011300&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065427036","display_name":"Juan Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Juan Xie","raw_affiliation_strings":["The Interdisciplinary Program in Biostatistics, The Ohio State University, Columbus, Ohio, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Interdisciplinary Program in Biostatistics, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041958648","display_name":"Hyeongseon Jeon","orcid":"https://orcid.org/0000-0002-3539-4332"},"institutions":[{"id":"https://openalex.org/I2799885155","display_name":"The Ohio State University Comprehensive Cancer Center \u2013 Arthur G. James Cancer Hospital and Richard J. Solove Research Institute","ror":"https://ror.org/028t46f04","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799885155"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hyeongseon Jeon","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America","Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100698888","display_name":"Gang Xin","orcid":"https://orcid.org/0000-0003-1963-505X"},"institutions":[{"id":"https://openalex.org/I2799885155","display_name":"The Ohio State University Comprehensive Cancer Center \u2013 Arthur G. James Cancer Hospital and Richard J. Solove Research Institute","ror":"https://ror.org/028t46f04","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799885155"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Gang Xin","raw_affiliation_strings":["Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America","Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Microbial Infection and Immunity, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022408570","display_name":"Qin Ma","orcid":"https://orcid.org/0000-0002-3264-8392"},"institutions":[{"id":"https://openalex.org/I2799885155","display_name":"The Ohio State University Comprehensive Cancer Center \u2013 Arthur G. James Cancer Hospital and Richard J. Solove Research Institute","ror":"https://ror.org/028t46f04","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799885155"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qin Ma","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America","Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-3264-8392","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080810068","display_name":"Dongjun Chung","orcid":"https://orcid.org/0000-0002-8072-5671"},"institutions":[{"id":"https://openalex.org/I2799885155","display_name":"The Ohio State University Comprehensive Cancer Center \u2013 Arthur G. James Cancer Hospital and Richard J. Solove Research Institute","ror":"https://ror.org/028t46f04","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799885155"]},{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dongjun Chung","raw_affiliation_strings":["Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America","Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8072-5671","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I52357470"]},{"raw_affiliation_string":"Pelotonia Institute for Immuno-Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, United States of America","institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5022408570","https://openalex.org/A5041958648","https://openalex.org/A5065427036","https://openalex.org/A5080810068","https://openalex.org/A5100698888"],"corresponding_institution_ids":["https://openalex.org/I2799885155","https://openalex.org/I52357470"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.163,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.78641797,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"19","issue":"7","first_page":"e1011300","last_page":"e1011300"},"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/T10031","display_name":"T-cell and B-cell Immunology","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11020","display_name":"Immune Cell Function and Interaction","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7060697078704834},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6398100852966309},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.5374600887298584},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.46797898411750793},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.3722827434539795},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.30762672424316406},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27801382541656494},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1897726058959961},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15779438614845276},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.12640663981437683}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7060697078704834},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6398100852966309},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5374600887298584},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.46797898411750793},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3722827434539795},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30762672424316406},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27801382541656494},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1897726058959961},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15779438614845276},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.12640663981437683}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002999","descriptor_name":"Clone Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011948","descriptor_name":"Receptors, Antigen, T-Cell","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1011300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011300","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011300&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37428794","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37428794","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10358952","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10358952","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10358952/pdf/pcbi.1011300.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:RePEc:plo:pcbi00:1011300","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011300","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011300","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011300","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011300&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1043988785","display_name":null,"funder_award_id":"NSF1945971","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2041606102","display_name":null,"funder_award_id":"GM122078","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2266666766","display_name":null,"funder_award_id":"R01 GM122078","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3282092998","display_name":null,"funder_award_id":"U01 DA045300","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G3310236632","display_name":null,"funder_award_id":"GM131399","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G3661939332","display_name":null,"funder_award_id":"R01 GM131399","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6871231868","display_name":null,"funder_award_id":"U54 AG075931","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G6976381824","display_name":null,"funder_award_id":"R21 HG012482","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320316230","display_name":"Pelotonia","ror":null},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4383757091.pdf","grobid_xml":"https://content.openalex.org/works/W4383757091.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1709815505","https://openalex.org/W1984883254","https://openalex.org/W2053801811","https://openalex.org/W2087216833","https://openalex.org/W2131681506","https://openalex.org/W2295703274","https://openalex.org/W2786672974","https://openalex.org/W2898120081","https://openalex.org/W2901850955","https://openalex.org/W2927507212","https://openalex.org/W2951799803","https://openalex.org/W2997280954","https://openalex.org/W3002623081","https://openalex.org/W3014807564","https://openalex.org/W3035650440","https://openalex.org/W3082739140","https://openalex.org/W3099768174","https://openalex.org/W3102577481","https://openalex.org/W3116751540","https://openalex.org/W3158284947","https://openalex.org/W3164692211","https://openalex.org/W4200112784","https://openalex.org/W4255658650","https://openalex.org/W4307429713","https://openalex.org/W4392218864"],"related_works":["https://openalex.org/W2399513595","https://openalex.org/W4388386498","https://openalex.org/W2028462563","https://openalex.org/W2942994004","https://openalex.org/W2982720988","https://openalex.org/W3150324899","https://openalex.org/W2523545060","https://openalex.org/W4229998356","https://openalex.org/W4379374180","https://openalex.org/W3155641129"],"abstract_inverted_index":{"Single-cell":[0,41],"RNA":[1],"sequencing":[2,45],"(scRNA-seq)":[3],"data":[4,47,66,96,111,164],"has":[5],"been":[6],"widely":[7],"used":[8],"for":[9,88],"cell":[10,39,43,115,144],"trajectory":[11,30,72,101,145,149,262],"inference,":[12,73,146],"with":[13,18,132,173,185],"the":[14,23,28,52,89,106,121,190],"assumption":[15],"that":[16,246],"cells":[17,168,172],"similar":[19],"expression":[20],"profiles":[21],"share":[22],"same":[24],"differentiation":[25,35,100,134,191],"state.":[26],"However,":[27],"inferred":[29],"may":[31],"not":[32],"reveal":[33],"clonal":[34,53,99],"heterogeneity":[36],"among":[37,55],"T":[38,42,167,171],"clones.":[40],"receptor":[44],"(scTCR-seq)":[46],"provides":[48,137,239],"invaluable":[49],"insights":[50],"into":[51],"relationship":[54],"cells,":[56],"yet":[57],"it":[58,229,238],"lacks":[59],"functional":[60],"characteristics.":[61],"Therefore,":[62],"scRNA-seq":[63,95,110,161,200],"and":[64,94,117,125,152,162,169,215,228,244,265],"scTCR-seq":[65,93,163],"complement":[67],"each":[68],"other":[69],"in":[70],"improving":[71],"where":[74],"a":[75,85,138],"reliable":[76],"computational":[77,86],"tool":[78],"is":[79,230],"still":[80],"missing.":[81],"We":[82,156],"developed":[83],"LRT,":[84],"framework":[87,220],"integrative":[90],"analysis":[91,140],"of":[92,165,253,260],"to":[97,112,128,249],"explore":[98,251],"heterogeneity.":[102],"Specifically,":[103],"LRT":[104,136,219],"uses":[105],"transcriptomics":[107],"information":[108,124,127],"from":[109,203],"construct":[113],"overall":[114],"trajectories":[116],"then":[118],"utilizes":[119],"both":[120],"TCR":[122],"sequence":[123],"phenotype":[126],"identify":[129],"clonotype":[130,147,153,183,205,266],"clusters":[131,184,206],"distinct":[133,186],"biasedness.":[135],"comprehensive":[139],"workflow,":[141],"including":[142],"preprocessing,":[143],"clustering,":[148],"biasedness":[150,263],"evaluation,":[151,264],"cluster":[154,267],"characterization.":[155,268],"illustrated":[157],"its":[158],"utility":[159],"using":[160],"CD8+":[166],"CD4+":[170],"acute":[174],"lymphocytic":[175],"choriomeningitis":[176],"virus":[177],"infection.":[178],"These":[179],"analyses":[180],"identified":[181],"several":[182],"skewed":[187],"distribution":[188],"along":[189],"path,":[192],"which":[193],"cannot":[194],"be":[195],"revealed":[196],"solely":[197],"based":[198],"on":[199],"data.":[201],"Clones":[202],"different":[204],"exhibited":[207],"diverse":[208],"expansion":[209],"capability,":[210],"V-J":[211],"gene":[212],"usage":[213],"pattern":[214],"CDR3":[216],"motifs.":[217],"The":[218],"was":[221],"implemented":[222],"as":[223],"an":[224],"R":[225],"package":[226],"'LRT',":[227],"now":[231],"publicly":[232],"accessible":[233],"at":[234],"https://github.com/JuanXie19/LRT.":[235],"In":[236],"addition,":[237],"two":[240],"Shiny":[241],"apps":[242],"'shinyClone'":[243],"'shinyClust'":[245],"allow":[247],"users":[248],"interactively":[250],"distributions":[252],"clonotypes,":[254,261],"conduct":[255],"repertoire":[256],"analysis,":[257],"implement":[258],"clustering":[259]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}