{"id":"https://openalex.org/W7225324820","doi":"https://doi.org/10.1038/s41588-026-02781-x","title":"An information-theoretic framework for inferring T cell dynamics from single-cell RNA and T cell receptor sequencing","display_name":"An information-theoretic framework for inferring T cell dynamics from single-cell RNA and T cell receptor sequencing","publication_year":2026,"publication_date":"2026-11-05","ids":{"openalex":"https://openalex.org/W7225324820","doi":"https://doi.org/10.1038/s41588-026-02781-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/42988899"},"language":"en","primary_location":{"id":"doi:10.1038/s41588-026-02781-x","doi":"https://doi.org/10.1038/s41588-026-02781-x","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41588-026-02781-x","pdf_url":"https://www.nature.com/articles/s41588-026-02781-x.pdf","source":{"id":"https://openalex.org/S137905309","display_name":"Nature Genetics","issn_l":"1061-4036","issn":["1061-4036","1546-1718"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Genetics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s41588-026-02781-x.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041842371","display_name":"Nicholas Ceglia","orcid":"https://orcid.org/0000-0001-9387-103X","observed_orcids":["https://orcid.org/0000-0001-9387-103X"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Ceglia","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109457856","display_name":"Sohrab Salehi","orcid":"https://orcid.org/0009-0008-8276-1765","observed_orcids":["https://orcid.org/0009-0008-8276-1765"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sohrab Salehi","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA","institution_ids":["https://openalex.org/I78577930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084804922","display_name":"Zachary M. Sethna","orcid":"https://orcid.org/0000-0001-8859-1084","observed_orcids":["https://orcid.org/0000-0001-8859-1084"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary M. Sethna","raw_affiliation_strings":["Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA","Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA","Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","The Olayan Center for Cancer Vaccines, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"The Olayan Center for Cancer Vaccines, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013528712","display_name":"Yuval Elhanati","orcid":"https://orcid.org/0000-0002-4354-8864","observed_orcids":["https://orcid.org/0000-0002-4354-8864"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuval Elhanati","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-4354-8864","affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062509177","display_name":"Samuel S. Freeman","orcid":"https://orcid.org/0000-0001-8285-0057","observed_orcids":["https://orcid.org/0000-0001-8285-0057"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samuel S. Freeman","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0001-8285-0057","affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051478375","display_name":"Olga Lyudovyk","orcid":"https://orcid.org/0000-0001-8793-8920","observed_orcids":["https://orcid.org/0000-0001-8793-8920"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Olga Lyudovyk","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003273432","display_name":"Bharat Burman","orcid":"https://orcid.org/0000-0002-0824-1357","observed_orcids":["https://orcid.org/0000-0002-0824-1357"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bharat Burman","raw_affiliation_strings":["Department of Medicine, Weill-Cornell School of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Weill-Cornell School of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160837366","display_name":"Andrew Chow","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew Chow","raw_affiliation_strings":["Department of Medicine, Weill-Cornell School of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Medicine, Weill-Cornell School of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026953370","display_name":"Dmitriy Zamarin","orcid":"https://orcid.org/0000-0002-0094-0161","observed_orcids":["https://orcid.org/0000-0002-0094-0161"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dmitriy Zamarin","raw_affiliation_strings":["Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA","Department of Medicine, Weill-Cornell School of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-0094-0161","affiliations":[{"raw_affiliation_string":"Department of Medicine, Gynecologic Medical Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Department of Medicine, Weill-Cornell School of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032156716","display_name":"Susan DeWolf","orcid":"https://orcid.org/0000-0002-2754-3537","observed_orcids":["https://orcid.org/0000-0002-2754-3537"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Susan DeWolf","raw_affiliation_strings":["Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-2754-3537","affiliations":[{"raw_affiliation_string":"Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080214475","display_name":"Sanam Shahid","orcid":"https://orcid.org/0000-0003-4281-4910","observed_orcids":["https://orcid.org/0000-0003-4281-4910"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sanam Shahid","raw_affiliation_strings":["Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0003-4281-4910","affiliations":[{"raw_affiliation_string":"Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082886062","display_name":"Viktoria Bojilova","orcid":"https://orcid.org/0009-0009-4902-7216","observed_orcids":["https://orcid.org/0009-0009-4902-7216"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Viktoria Bojilova","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047614639","display_name":"Nicole Rusk","orcid":"https://orcid.org/0000-0003-2663-6288","observed_orcids":["https://orcid.org/0000-0003-2663-6288"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicole Rusk","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0003-2663-6288","affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060380153","display_name":"Vinod P. Balachandran","orcid":"https://orcid.org/0000-0002-2956-223X","observed_orcids":["https://orcid.org/0000-0002-2956-223X"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vinod P. Balachandran","raw_affiliation_strings":["Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA","Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA","The Olayan Center for Cancer Vaccines, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-2956-223X","affiliations":[{"raw_affiliation_string":"Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"The Olayan Center for Cancer Vaccines, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050657151","display_name":"Andrew McPherson","orcid":"https://orcid.org/0000-0002-5654-5101","observed_orcids":["https://orcid.org/0000-0002-5654-5101"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrew McPherson","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-5654-5101","affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA","institution_ids":["https://openalex.org/I1334819555"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033441782","display_name":"Sohrab P. Shah","orcid":"https://orcid.org/0000-0001-6402-523X","observed_orcids":["https://orcid.org/0000-0001-6402-523X"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I4387153466","display_name":"Weill Cornell Medicine","ror":"https://ror.org/02r109517","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295","https://openalex.org/I4387153466"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sohrab P. Shah","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. shahs3@mskcc.org","Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA. shahs3@mskcc.org"],"raw_orcid":"https://orcid.org/0000-0001-6402-523X","affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. shahs3@mskcc.org","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA. shahs3@mskcc.org","institution_ids":["https://openalex.org/I4387153466"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063215100","display_name":"Benjamin D. Greenbaum","orcid":"https://orcid.org/0000-0001-6153-8793","observed_orcids":["https://orcid.org/0000-0001-6153-8793"]},"institutions":[{"id":"https://openalex.org/I1334819555","display_name":"Memorial Sloan Kettering Cancer Center","ror":"https://ror.org/02yrq0923","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1334819555"]},{"id":"https://openalex.org/I78577930","display_name":"Columbia University","ror":"https://ror.org/00hj8s172","country_code":"US","type":"education","lineage":["https://openalex.org/I78577930"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Benjamin D. Greenbaum","raw_affiliation_strings":["Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. greenbab@mskcc.org","Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA. greenbab@mskcc.org","The Olayan Center for Cancer Vaccines, Memorial Sloan Kettering Cancer Center, New York, NY, USA. greenbab@mskcc.org"],"raw_orcid":"https://orcid.org/0000-0001-6153-8793","affiliations":[{"raw_affiliation_string":"Halvorsen Center for Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA. greenbab@mskcc.org","institution_ids":["https://openalex.org/I1334819555"]},{"raw_affiliation_string":"Irving Institute for Cancer Dynamics, Columbia University, New York, NY, USA. greenbab@mskcc.org","institution_ids":["https://openalex.org/I78577930"]},{"raw_affiliation_string":"The Olayan Center for Cancer Vaccines, Memorial Sloan Kettering Cancer Center, New York, NY, USA. greenbab@mskcc.org","institution_ids":["https://openalex.org/I1334819555"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5033441782","https://openalex.org/A5063215100"],"corresponding_institution_ids":["https://openalex.org/I1334819555","https://openalex.org/I4387153466","https://openalex.org/I78577930"],"apc_list":{"value":12690,"currency":"USD","value_usd":12690},"apc_paid":{"value":12690,"currency":"USD","value_usd":12690},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"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":0.9789999723434448,"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":0.9789999723434448,"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":0.014499999582767487,"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/T10158","display_name":"Cancer Immunotherapy and Biomarkers","score":0.002300000051036477,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/t-cell-dynamics","display_name":"T cell dynamics","score":0.8029999732971191},{"id":"https://openalex.org/keywords/tcr-repertoire","display_name":"T cell receptor repertoire","score":0.9350000023841858},{"id":"https://openalex.org/keywords/single-cell-transcriptomics","display_name":"single-cell transcriptomics","score":0.7379999756813049},{"id":"https://openalex.org/keywords/bayesian-hierarchical-model","display_name":"Bayesian hierarchical model","score":0.7369999885559082},{"id":"https://openalex.org/keywords/variational-autoencoder","display_name":"variational autoencoder","score":0.9860000014305115},{"id":"https://openalex.org/keywords/mutual-information","display_name":"mutual information","score":0.7229999899864197},{"id":"https://openalex.org/keywords/cd8-t-cells","display_name":"CD8+ T cells","score":0.9509999752044678},{"id":"https://openalex.org/keywords/cancer-immunotherapy-response","display_name":"cancer immunotherapy response","score":0.8769999742507935}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8019999861717224},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.5963000059127808},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.57669997215271},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.5688999891281128},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5579000115394592},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.4575999975204468},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4154999852180481},{"id":"https://openalex.org/C167672396","wikidata":"https://www.wikidata.org/wiki/Q417800","display_name":"CD8","level":3,"score":0.4108999967575073},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.3970000147819519},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3885999917984009},{"id":"https://openalex.org/C174749747","wikidata":"https://www.wikidata.org/wiki/Q15917269","display_name":"Single cell sequencing","level":5,"score":0.3571000099182129},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.33709999918937683},{"id":"https://openalex.org/C152139883","wikidata":"https://www.wikidata.org/wiki/Q252973","display_name":"Mutual information","level":2,"score":0.33239999413490295},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.31049999594688416},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.30880001187324524},{"id":"https://openalex.org/C2992511266","wikidata":"https://www.wikidata.org/wiki/Q1093098","display_name":"Gene rearrangement","level":3,"score":0.2985999882221222},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.28369998931884766},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2606000006198883},{"id":"https://openalex.org/C49937458","wikidata":"https://www.wikidata.org/wiki/Q2599292","display_name":"Probabilistic logic","level":2,"score":0.25929999351501465}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1038/s41588-026-02781-x","doi":"https://doi.org/10.1038/s41588-026-02781-x","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41588-026-02781-x","pdf_url":"https://www.nature.com/articles/s41588-026-02781-x.pdf","source":{"id":"https://openalex.org/S137905309","display_name":"Nature Genetics","issn_l":"1061-4036","issn":["1061-4036","1546-1718"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Genetics","raw_type":"journal-article"},{"id":"pmid:42988899","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42988899","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,"listed_in":[],"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":"Nature genetics","raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1038/s41588-026-02781-x","doi":"https://doi.org/10.1038/s41588-026-02781-x","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41588-026-02781-x","pdf_url":"https://www.nature.com/articles/s41588-026-02781-x.pdf","source":{"id":"https://openalex.org/S137905309","display_name":"Nature Genetics","issn_l":"1061-4036","issn":["1061-4036","1546-1718"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Genetics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4043000042438507}],"study_designs":[],"awards":[{"id":"https://openalex.org/G2695170217","display_name":null,"funder_award_id":"P30 CA008748","funder_id":"https://openalex.org/F4320332898","funder_display_name":"Stand Up To Cancer"},{"id":"https://openalex.org/G4425862374","display_name":null,"funder_award_id":"CA257881-01A1","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7136384868","display_name":null,"funder_award_id":"P30-CA008748","funder_id":"https://openalex.org/F4320334155","funder_display_name":"Marie-Jos\u00e9e and Henry R. Kravis Center for Molecular Oncology"},{"id":"https://openalex.org/G8771761010","display_name":null,"funder_award_id":"R01 CA240924","funder_id":"https://openalex.org/F4320332898","funder_display_name":"Stand Up To Cancer"},{"id":"https://openalex.org/G94832637","display_name":null,"funder_award_id":"P30CA008748","funder_id":"https://openalex.org/F4320338273","funder_display_name":"Congressionally Directed Medical Research Programs"}],"funders":[{"id":"https://openalex.org/F4320306078","display_name":"U.S. Department of Defense","ror":"https://ror.org/0447fe631"},{"id":"https://openalex.org/F4320316669","display_name":"Break Through Cancer","ror":"https://ror.org/00a8me616"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332898","display_name":"Stand Up To Cancer","ror":"https://ror.org/01dmpb598"},{"id":"https://openalex.org/F4320334155","display_name":"Marie-Jos\u00e9e and Henry R. Kravis Center for Molecular Oncology","ror":null},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337432","display_name":"Center for Scientific Review","ror":"https://ror.org/04r5s4b52"},{"id":"https://openalex.org/F4320338273","display_name":"Congressionally Directed Medical Research Programs","ror":"https://ror.org/03g2zjp07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7225324820.pdf","grobid_xml":"https://content.openalex.org/works/W7225324820.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1965555277","https://openalex.org/W1995875735","https://openalex.org/W2039123767","https://openalex.org/W2043071551","https://openalex.org/W2097173970","https://openalex.org/W2140323624","https://openalex.org/W2670890989","https://openalex.org/W2752126733","https://openalex.org/W2803872300","https://openalex.org/W2804073610","https://openalex.org/W2899145148","https://openalex.org/W2901677030","https://openalex.org/W2950472298","https://openalex.org/W2950612260","https://openalex.org/W2963752224","https://openalex.org/W2966465234","https://openalex.org/W2998737960","https://openalex.org/W3002420685","https://openalex.org/W3037088183","https://openalex.org/W3040324319","https://openalex.org/W3082739140","https://openalex.org/W3120050808","https://openalex.org/W3183254943","https://openalex.org/W3196175936","https://openalex.org/W4200168331","https://openalex.org/W4200468913","https://openalex.org/W4206941971","https://openalex.org/W4291624945","https://openalex.org/W4312190528","https://openalex.org/W4376133743","https://openalex.org/W4384925646","https://openalex.org/W4391521615","https://openalex.org/W4400266097","https://openalex.org/W4409995180","https://openalex.org/W7204659620"],"related_works":["https://openalex.org/W4301368523","https://openalex.org/W7135084011","https://openalex.org/W4404039229","https://openalex.org/W4206941971","https://openalex.org/W2295703274","https://openalex.org/W7221789146","https://openalex.org/W3120050808","https://openalex.org/W7212724268","https://openalex.org/W3197266753","https://openalex.org/W3208076196"],"abstract_inverted_index":{"Single-cell":[0],"T":[1,21,139],"cell":[2,22],"receptor":[3],"(TCR)":[4],"repertoire":[5],"sequencing":[6,69],"enables":[7],"simultaneous":[8],"profiling":[9],"of":[10,20,35,158],"gene":[11],"expression":[12,85],"and":[13,25,37,60,67,91,106,121,126],"TCR":[14,68],"sequences,":[15],"providing":[16],"a":[17,46,76,80,87,92,155],"coregistered":[18],"measure":[19],"phenotypic":[23,117,119],"diversity":[24],"clonal":[26],"dynamics.":[27],"However,":[28],"principled":[29,101],"probabilistic":[30,77],"frameworks":[31],"for":[32],"joint":[33,54],"modeling":[34],"clonotype":[36,59,125],"phenotype":[38,62,73,98],"have":[39],"remained":[40],"limited.":[41],"Here":[42],"we":[43],"introduce":[44],"TCRi,":[45],"hierarchical":[47,93],"Bayesian":[48,94],"information-theoretic":[49,113],"framework":[50],"that":[51],"infers":[52],"the":[53],"probability":[55],"distribution":[56],"between":[57,124],"genetic":[58],"transcriptional":[61],"from":[63,141],"paired":[64],"single-cell":[65,84],"transcriptomic":[66],"data.":[70],"TCRi":[71,111,129],"treats":[72],"assignment":[74],"as":[75,154],"inference":[78],"problem:":[79],"variational":[81],"autoencoder":[82],"embeds":[83],"into":[86],"structured":[88],"latent":[89],"space,":[90],"model":[95],"learns":[96],"clonotype-specific":[97],"distributions":[99],"through":[100],"information-sharing":[102],"across":[103],"clonotypes,":[104],"patients":[105,142],"covariates.":[107],"From":[108],"these":[109],"distributions,":[110],"computes":[112],"quantities:":[114],"clonotypic":[115],"entropy,":[116,118],"flux":[120],"mutual":[122,151],"information":[123,152],"phenotype.":[127],"When":[128],"was":[130],"applied":[131],"to":[132],"four":[133],"real-world":[134],"datasets":[135],"comprising":[136],"167,118":[137],"CD8":[138],"cells":[140],"with":[143,146],"cancer":[144],"treated":[145],"anti-PD-(L)1":[147],"immune":[148],"checkpoint":[149],"blockade,":[150],"emerged":[153],"robust":[156],"discriminator":[157],"therapeutic":[159],"response.":[160]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-06T00:00:00"}