{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,8]],"date-time":"2026-09-08T10:40:55Z","timestamp":1788864055054,"version":"build-2803163510"},"reference-count":122,"publisher":"Elsevier BV","issue":"7","license":[{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T00:00:00Z","timestamp":1782864000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T00:00:00Z","timestamp":1779148800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018955","name":"Leeds Biomedical Research Centre","doi-asserted-by":"publisher","award":["NIHR203331"],"award-info":[{"award-number":["NIHR203331"]}],"id":[{"id":"10.13039\/501100018955","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000781","name":"European Research Council","doi-asserted-by":"publisher","award":["101088594"],"award-info":[{"award-number":["101088594"]}],"id":[{"id":"10.13039\/501100000781","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003495","name":"Hessian Ministry of Science and Research Arts and Culture","doi-asserted-by":"publisher","award":["LOEWE\/2\/17\/519\/03\/10.001(0004)\/111"],"award-info":[{"award-number":["LOEWE\/2\/17\/519\/03\/10.001(0004)\/111"]}],"id":[{"id":"10.13039\/501100003495","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["496906589"],"award-info":[{"award-number":["496906589"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["EN 1338\/1-1"],"award-info":[{"award-number":["EN 1338\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["455784452"],"award-info":[{"award-number":["455784452"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB1530"],"award-info":[{"award-number":["SFB1530"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100005972","name":"German Cancer Aid","doi-asserted-by":"publisher","award":["70116591"],"award-info":[{"award-number":["70116591"]}],"id":[{"id":"10.13039\/501100005972","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000272","name":"National Institute for Health and Care Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000272","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000780","name":"European Commission","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000016","name":"U.S. Department of Health and Human Services","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000016","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100013342","name":"NIHR Imperial Biomedical Research Centre","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100013342","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["203151\/Z\/16\/Z"],"award-info":[{"award-number":["203151\/Z\/16\/Z"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000289","name":"Cancer Research UK","doi-asserted-by":"publisher","award":["100072"],"award-info":[{"award-number":["100072"]}],"id":[{"id":"10.13039\/501100000289","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003185","name":"Fraunhofer Society for the Advancement of Applied Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003185","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018956","name":"NIHR Cambridge Biomedical Research Centre","doi-asserted-by":"publisher","award":["7027-23"],"award-info":[{"award-number":["7027-23"]}],"id":[{"id":"10.13039\/501100018956","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100018956","name":"NIHR Cambridge Biomedical Research Centre","doi-asserted-by":"publisher","award":["BRC-1215-20014"],"award-info":[{"award-number":["BRC-1215-20014"]}],"id":[{"id":"10.13039\/501100018956","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005189","name":"Leukemia & Lymphoma Society","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100005189","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100022011","name":"Cancer Research UK Cambridge Research Institute","doi-asserted-by":"publisher","award":["C49940\/A25117"],"award-info":[{"award-number":["C49940\/A25117"]}],"id":[{"id":"10.13039\/501100022011","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cancer Cell"],"published-print":{"date-parts":[[2026,7]]},"DOI":"10.1016\/j.ccell.2026.05.008","type":"journal-article","created":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T15:23:49Z","timestamp":1780586629000},"page":"1437-1457.e14","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":2,"title":["Pathogenesis of diffuse large B cell lymphoma proteogenotypes"],"prefix":"10.1016","volume":"44","author":[{"given":"Julius C.","family":"Enssle","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bj\u00f6rn","family":"H\u00e4upl","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arber","family":"Qoku","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Boya","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"George W.","family":"Wright","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon","family":"Barrans","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yulai","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew A.","family":"Care","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cathy","family":"Burton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caitlin","family":"Gribbin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jennifer","family":"Ziello","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason","family":"Weirather","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yibo","family":"Dai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Atish","family":"Kizhakeyil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xubin","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James D.","family":"Phelan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Smriti","family":"Kanangat","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephan","family":"Eckert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Scheich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian","family":"Wolf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Da Wei","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Josefine","family":"Jakob","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sebastian P.","family":"Perner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrea","family":"Di Fonzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martine","family":"Pape","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marion","family":"Bodach","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dominique","family":"Jahn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uwe","family":"Plessmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Annette M.","family":"Staiger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"German","family":"Ott","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philipp","family":"Berning","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Georg","family":"Lenz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel J.","family":"Hodson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernhard","family":"Kuster","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roland","family":"Schmitz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henning","family":"Urlaub","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael R.","family":"Green","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ari M.","family":"Melnick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reuben","family":"Tooze","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Coraline","family":"Mlynarczyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Giorgio","family":"Inghirami","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Florian","family":"Buettner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Louis M.","family":"Staudt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas","family":"Oellerich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.ccell.2026.05.008_bib1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/35000501","article-title":"Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling","volume":"403","author":"Alizadeh","year":"2000","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib2","doi-asserted-by":"crossref","first-page":"1396","DOI":"10.1056\/NEJMoa1801445","article-title":"Genetics and Pathogenesis of Diffuse Large B-Cell Lymphoma","volume":"378","author":"Schmitz","year":"2018","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib3","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1038\/s41591-018-0016-8","article-title":"Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes","volume":"24","author":"Chapuy","year":"2018","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib4","doi-asserted-by":"crossref","first-page":"1759","DOI":"10.1182\/blood.2019003535","article-title":"Targeted sequencing in DLBCL, molecular subtypes, and outcomes: a Haematological Malignancy Research Network report","volume":"135","author":"Lacy","year":"2020","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib5","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1016\/j.ccell.2020.03.015","article-title":"A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications","volume":"37","author":"Wright","year":"2020","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib6","doi-asserted-by":"crossref","first-page":"1643","DOI":"10.1016\/j.ccell.2021.10.006","article-title":"Effect of ibrutinib with R-CHOP chemotherapy in genetic subtypes of DLBCL","volume":"39","author":"Wilson","year":"2021","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib7","doi-asserted-by":"crossref","first-page":"2313","DOI":"10.1056\/NEJMoa0802885","article-title":"Stromal gene signatures in large-B-cell lymphomas","volume":"359","author":"Lenz","year":"2008","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib8","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1038\/nature08638","article-title":"Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma","volume":"463","author":"Davis","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib9","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1038\/s41586-018-0290-0","article-title":"A multiprotein supercomplex controlling oncogenic signalling in lymphoma","volume":"560","author":"Phelan","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib10","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1111\/imr.12792","article-title":"Pathogenic B-cell receptor signaling in lymphoid malignancies: New insights to improve treatment","volume":"291","author":"Young","year":"2019","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.ccell.2026.05.008_bib11","doi-asserted-by":"crossref","first-page":"1705","DOI":"10.1016\/j.ccell.2023.09.004","article-title":"Genetic subtype-guided immunochemotherapy in diffuse large B cell lymphoma: The randomized GUIDANCE-01 trial","volume":"41","author":"Zhang","year":"2023","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib12","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1016\/j.ccell.2021.08.011","article-title":"The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma","volume":"39","author":"Steen","year":"2021","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib13","doi-asserted-by":"crossref","first-page":"1468","DOI":"10.1158\/2159-8290.CD-20-0839","article-title":"Clinical and Biological Subtypes of B-cell Lymphoma Revealed by Microenvironmental Signatures","volume":"11","author":"Kotlov","year":"2021","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ccell.2026.05.008_bib14","doi-asserted-by":"crossref","first-page":"202","DOI":"10.1200\/JCO.18.01314","article-title":"Molecular high-grade B-cell lymphoma: Defining a poor-risk group that requires different approaches to therapy","volume":"37","author":"Sha","year":"2019","journal-title":"J. Clin. Oncol."},{"key":"10.1016\/j.ccell.2026.05.008_bib15","first-page":"2493","article-title":"Molecular determinants of clinical outcomes in a real-world diffuse large B-cell lymphoma population","volume":"141","author":"Alduaij","year":"2023","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib16","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.ccell.2022.02.006","article-title":"The proteogenomic subtypes of acute myeloid leukemia","volume":"40","author":"Jayavelu","year":"2022","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib17","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature18003","article-title":"Proteogenomics connects somatic mutations to signalling in breast cancer","volume":"534","author":"Mertins","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib18","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1016\/j.cell.2019.03.030","article-title":"Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities","volume":"177","author":"Vasaikar","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib19","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1038\/nature13438","article-title":"Proteogenomic characterization of human colon and rectal cancer","volume":"513","author":"Zhang","year":"2014","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib20","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1016\/j.cell.2020.06.012","article-title":"Proteogenomics of Non-smoking Lung Cancer in East Asia Delineates Molecular Signatures of Pathogenesis and Progression","volume":"182","author":"Chen","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib21","doi-asserted-by":"crossref","first-page":"5031","DOI":"10.1016\/j.cell.2021.08.023","article-title":"Proteogenomic characterization of pancreatic ductal adenocarcinoma","volume":"184","author":"Cao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib22","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1016\/j.cell.2024.01.027","article-title":"Pan-cancer proteogenomics characterization of tumor immunity","volume":"187","author":"Petralia","year":"2024","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib23","doi-asserted-by":"crossref","first-page":"1962","DOI":"10.1016\/j.cell.2020.10.044","article-title":"Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer","volume":"183","author":"Petralia","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib24","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1016\/j.ccell.2023.06.009","article-title":"Proteogenomic data and resources for pan-cancer analysis","volume":"41","author":"Li","year":"2023","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib25","doi-asserted-by":"crossref","first-page":"3945","DOI":"10.1016\/j.cell.2023.07.013","article-title":"Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation","volume":"186","author":"Geffen","year":"2023","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib26","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1056\/NEJMoa011795","article-title":"CHOP Chemotherapy plus Rituximab Compared with CHOP Alone in Elderly Patients with Diffuse Large-B-Cell Lymphoma","volume":"346","author":"Coiffier","year":"2002","journal-title":"N. Engl. J. Med. Overseas. Ed."},{"key":"10.1016\/j.ccell.2026.05.008_bib27","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1111\/bjh.17132","article-title":"Application of the LymphGen classification tool to 928 clinically and genetically-characterised cases of diffuse large B cell lymphoma (DLBCL)","volume":"192","author":"Runge","year":"2021","journal-title":"Br. J. Haematol."},{"key":"10.1016\/j.ccell.2026.05.008_bib28","doi-asserted-by":"crossref","first-page":"964","DOI":"10.1016\/j.cell.2019.10.007","article-title":"Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma","volume":"179","author":"Clark","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib29","doi-asserted-by":"crossref","first-page":"1600","DOI":"10.1038\/s41467-019-09018-y","article-title":"Breast cancer quantitative proteome and proteogenomic landscape","volume":"10","author":"Johansson","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.05.008_bib30","doi-asserted-by":"crossref","first-page":"200","DOI":"10.1016\/j.cell.2020.06.013","article-title":"Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma","volume":"182","author":"Gillette","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib31","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1111\/j.0105-2896.2006.00373.x","article-title":"A library of gene expression signatures to illuminate normal and pathological lymphoid biology","volume":"210","author":"Shaffer","year":"2006","journal-title":"Immunol. Rev."},{"key":"10.1016\/j.ccell.2026.05.008_bib32","series-title":"Encoding Domain Knowledge in Multi-View Latent Variable Models: A Bayesian Approach with Structured Sparsity","first-page":"11545","author":"Qoku","year":"2023"},{"key":"10.1016\/j.ccell.2026.05.008_bib33","doi-asserted-by":"crossref","first-page":"1937","DOI":"10.1056\/NEJMoa012914","article-title":"The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma","volume":"346","author":"Rosenwald","year":"2002","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib34","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ccell.2026.05.008_bib35","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1158\/2159-8290.CD-20-0174","article-title":"Toward a new molecular taxonomy of diffuse large b-cell lymphoma","volume":"10","author":"Ennishi","year":"2020","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ccell.2026.05.008_bib36","doi-asserted-by":"crossref","first-page":"546","DOI":"10.1158\/2159-8290.CD-18-1090","article-title":"Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition","volume":"9","author":"Ennishi","year":"2019","journal-title":"Cancer Discov."},{"key":"10.1016\/j.ccell.2026.05.008_bib37","doi-asserted-by":"crossref","first-page":"6156","DOI":"10.1182\/bloodadvances.2023010673","article-title":"Comparison of MHG and DZsig reveals shared biology and a core overlap group with inferior prognosis in DLBCL","volume":"7","author":"Davies","year":"2023","journal-title":"Blood Adv."},{"key":"10.1016\/j.ccell.2026.05.008_bib38","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1200\/JCO.18.01583","article-title":"Double-hit gene expression signature defines a distinct subgroup of germinal center B-cell-like diffuse large B-cell lymphoma","volume":"37","author":"Ennishi","year":"2019","journal-title":"J. Clin. Oncol."},{"key":"10.1016\/j.ccell.2026.05.008_bib39","doi-asserted-by":"crossref","first-page":"6790","DOI":"10.1038\/s41467-024-50830-y","article-title":"Transcriptomic classification of diffuse large B-cell lymphoma identifies a high-risk activated B-cell-like subpopulation with targetable MYC dysregulation","volume":"15","author":"Stokes","year":"2024","journal-title":"Nat. Commun."},{"key":"10.1016\/j.ccell.2026.05.008_bib40","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.1038\/s41590-018-0181-4","article-title":"Human germinal center transcriptional programs are de-synchronized in B cell lymphoma","volume":"19","author":"Milpied","year":"2018","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.ccell.2026.05.008_bib41","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.immuni.2008.05.012","article-title":"A Modular Analysis Framework for Blood Genomics Studies: Application to Systemic Lupus Erythematosus","volume":"29","author":"Chaussabel","year":"2008","journal-title":"Immunity"},{"key":"10.1016\/j.ccell.2026.05.008_bib42","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1182\/blood-2004-03-1206","article-title":"Unique gene expression program of human germinal center T helper cells","volume":"104","author":"Kim","year":"2004","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib43","doi-asserted-by":"crossref","first-page":"68","DOI":"10.4049\/jimmunol.173.1.68","article-title":"T Follicular Helper Cells Express a Distinctive Transcriptional Profile, Reflecting Their Role as Non-Th1\/Th2 Effector Cells That Provide Help for B Cells","volume":"173","author":"Chtanova","year":"2004","journal-title":"J. Immunol."},{"key":"10.1016\/j.ccell.2026.05.008_bib44","doi-asserted-by":"crossref","first-page":"2381","DOI":"10.4049\/jimmunol.169.5.2381","article-title":"FDC-SP, a Novel Secreted Protein Expressed by Follicular Dendritic Cells","volume":"169","author":"Marshall","year":"2002","journal-title":"J. Immunol."},{"key":"10.1016\/j.ccell.2026.05.008_bib45","doi-asserted-by":"crossref","first-page":"5526","DOI":"10.4049\/jimmunol.174.9.5526","article-title":"Lymphotoxin-\u03b2 Receptor-Dependent Genes in Lymph Node and Follicular Dendritic Cell Transcriptomes","volume":"174","author":"Huber","year":"2005","journal-title":"J. Immunol."},{"key":"10.1016\/j.ccell.2026.05.008_bib46","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1016\/j.immuni.2017.11.022","article-title":"CCR6 Defines Memory B Cell Precursors in Mouse and Human Germinal Centers, Revealing Light-Zone Location and Predominant Low Antigen Affinity","volume":"47","author":"Suan","year":"2017","journal-title":"Immunity"},{"key":"10.1016\/j.ccell.2026.05.008_bib47","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S1074-7613(02)00335-7","article-title":"Blimp-1 orchestrates plasma cell differentiation by extinguishing the mature B cell gene expression program","volume":"17","author":"Shaffer","year":"2002","journal-title":"Immunity"},{"key":"10.1016\/j.ccell.2026.05.008_bib48","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1182\/blood-2012-03-415380","article-title":"Identification of human germinal center light and dark zone cells and their relationship to human B-cell lymphomas","volume":"120","author":"Victora","year":"2012","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib49","doi-asserted-by":"crossref","first-page":"1226","DOI":"10.1038\/ni.3533","article-title":"Defining antigen-specific plasmablast and memory B cell subsets in human blood after viral infection or vaccination","volume":"17","author":"Ellebedy","year":"2016","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.ccell.2026.05.008_bib50","doi-asserted-by":"crossref","first-page":"2760","DOI":"10.1182\/blood-2016-11-747022","article-title":"Genetic profiling of MYC and BCL2 in diffuse large B-cell lymphoma determines cell-of-origin-specific clinical impact","volume":"129","author":"Ennishi","year":"2017","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib51","doi-asserted-by":"crossref","first-page":"1119","DOI":"10.1182\/blood.2022015926","article-title":"Aberrant expansion of spontaneous splenic germinal centers induced by hallmark genetic lesions of aggressive lymphoma","volume":"140","author":"Pindzola","year":"2022","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib52","doi-asserted-by":"crossref","first-page":"353","DOI":"10.1038\/nature04296","article-title":"Oncogenic pathway signatures in human cancers as a guide to targeted therapies","volume":"439","author":"Bild","year":"2005","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib53","doi-asserted-by":"crossref","first-page":"2375","DOI":"10.1182\/blood-2016-01-643569","article-title":"The 2016 revision of the World Health Organization classification of lymphoid neoplasms","volume":"127","author":"Swerdlow","year":"2016","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib54","doi-asserted-by":"crossref","first-page":"E2039","DOI":"10.1073\/pnas.1600557113","article-title":"Regulation of normal B-cell differentiation and malignant B-cell survival by OCT2","volume":"113","author":"Hodson","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.ccell.2026.05.008_bib55","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.immuni.2004.06.010","article-title":"XBP1, downstream of Blimp-1, expands the secretory apparatus and other organelles, and increases protein synthesis in plasma cell differentiation","volume":"21","author":"Shaffer","year":"2004","journal-title":"Immunity"},{"key":"10.1016\/j.ccell.2026.05.008_bib56","doi-asserted-by":"crossref","first-page":"6062","DOI":"10.1073\/pnas.0400782101","article-title":"A gene atlas of the mouse and human protein-encoding transcriptomes","volume":"101","author":"Su","year":"2004","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.ccell.2026.05.008_bib57","doi-asserted-by":"crossref","first-page":"1276","DOI":"10.1016\/j.celrep.2013.08.014","article-title":"Characterization and Analysis of the Composition and Dynamics of the Mammalian Riboproteome","volume":"4","author":"Reschke","year":"2013","journal-title":"Cell Rep."},{"key":"10.1016\/j.ccell.2026.05.008_bib58","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1038\/nature11378","article-title":"Burkitt lymphoma pathogenesis and therapeutic targets from structural and functional genomics","volume":"490","author":"Schmitz","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib59","doi-asserted-by":"crossref","first-page":"26ra25","DOI":"10.1126\/scitranslmed.3000251","article-title":"Airway PI3K pathway activation is an early and reversible event in lung cancer development","volume":"2","author":"Gustafson","year":"2010","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib60","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1016\/j.cell.2020.05.049","article-title":"TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate","volume":"182","author":"Venturutti","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib61","doi-asserted-by":"crossref","first-page":"eabj7412","DOI":"10.1126\/science.abj7412","article-title":"BTG1 mutation yields supercompetitive B cells primed for malignant transformation","volume":"379","author":"Mlynarczyk","year":"2023","journal-title":"Science"},{"key":"10.1016\/j.ccell.2026.05.008_bib62","doi-asserted-by":"crossref","first-page":"W212","DOI":"10.1093\/nar\/gkz446","article-title":"ChEA3: transcription factor enrichment analysis by orthogonal omics integration","volume":"47","author":"Keenan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib63","doi-asserted-by":"crossref","first-page":"17834","DOI":"10.1073\/pnas.0604129103","article-title":"Global mapping of c-Myc binding sites and target gene networks in human B cells","volume":"103","author":"Zeller","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.ccell.2026.05.008_bib64","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1016\/j.ccell.2025.12.015","article-title":"Axes of biological variation in diffuse large B cell lymphoma","volume":"44","author":"Wang","year":"2026","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib65","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib66","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41588-021-00790-6","article-title":"ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis","volume":"53","author":"Granja","year":"2021","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ccell.2026.05.008_bib67","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/s41587-021-01033-z","article-title":"Differential abundance testing on single-cell data using k-nearest neighbor graphs","volume":"40","author":"Dann","year":"2022","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.05.008_bib68","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nature09671","article-title":"Oncogenically active MYD88 mutations in human lymphoma","volume":"470","author":"Ngo","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.ccell.2026.05.008_bib69","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1182\/blood.2021012081","article-title":"SHMT2 inhibition disrupts the TCF3 transcriptional survival program in Burkitt lymphoma","volume":"139","author":"Wilke","year":"2022","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib70","doi-asserted-by":"crossref","DOI":"10.1126\/scitranslmed.aav5599","article-title":"Targetable genetic alterations of TCF4 (E2-2) drive immunoglobulin expression in diffuse large B cell lymphoma","volume":"11","author":"Jain","year":"2019","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib71","doi-asserted-by":"crossref","first-page":"975","DOI":"10.1126\/science.1228309","article-title":"A genomic regulatory element that directs assembly and function of immune-specific AP-1-IRF complexes","volume":"338","author":"Glasmacher","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.ccell.2026.05.008_bib72","doi-asserted-by":"crossref","first-page":"7591","DOI":"10.1093\/nar\/gku451","article-title":"SPIB and BATF provide alternate determinants of IRF4 occupancy in diffuse large B-cell lymphoma linked to disease heterogeneity","volume":"42","author":"Care","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib73","doi-asserted-by":"crossref","first-page":"723","DOI":"10.1016\/j.ccr.2012.05.024","article-title":"Exploiting synthetic lethality for the therapy of ABC diffuse large B cell lymphoma","volume":"21","author":"Yang","year":"2012","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib74","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/s41587-019-0114-2","article-title":"Determining cell type abundance and expression from bulk tissues with digital cytometry","volume":"37","author":"Newman","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.05.008_bib75","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/s41556-024-01358-2","article-title":"Multimodal and spatially resolved profiling identifies distinct patterns of T cell infiltration in nodal B cell lymphoma entities","volume":"26","author":"Roider","year":"2024","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.ccell.2026.05.008_bib76","doi-asserted-by":"crossref","first-page":"2715","DOI":"10.1038\/s41588-025-02353-5","article-title":"Multi-modal spatial characterization of tumor immune microenvironments identifies targetable inflammatory niches in diffuse large B-cell lymphoma","volume":"57","author":"Dai","year":"2025","journal-title":"Nat. Genet."},{"key":"10.1016\/j.ccell.2026.05.008_bib79","doi-asserted-by":"crossref","first-page":"2007","DOI":"10.1182\/blood-2017-11-742577","article-title":"The MYC oncogene is a global regulator of the immune response","volume":"131","author":"Casey","year":"2018","journal-title":"Blood"},{"key":"10.1016\/j.ccell.2026.05.008_bib80","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1101\/gad.2038411","article-title":"Endogenous Myc maintains the tumor microenvironment","volume":"25","author":"Sodir","year":"2011","journal-title":"Genes Dev."},{"key":"10.1016\/j.ccell.2026.05.008_bib81","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1126\/science.aac9935","article-title":"MYC regulates the antitumor immune response through CD47 and PD-L1","volume":"352","author":"Casey","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.ccell.2026.05.008_bib82","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/s41591-023-02754-1","article-title":"Impact of tumor microenvironment on efficacy of anti-CD19 CAR T cell therapy or chemotherapy and transplant in large B cell lymphoma","volume":"30","author":"Locke","year":"2024","journal-title":"Nat. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib83","doi-asserted-by":"crossref","first-page":"1347","DOI":"10.1016\/j.ccell.2025.06.002","article-title":"Large B cell lymphoma microenvironment archetype profiles","volume":"43","author":"Li","year":"2025","journal-title":"Cancer Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib84","doi-asserted-by":"crossref","first-page":"2143","DOI":"10.1056\/NEJMoa2401532","article-title":"Combination Targeted Therapy in Relapsed Diffuse Large B-Cell Lymphoma","volume":"390","author":"Melani","year":"2024","journal-title":"N. Engl. J. Med."},{"key":"10.1016\/j.ccell.2026.05.008_bib85","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1111\/bjh.15619","article-title":"Cell-of-origin in diffuse large B-cell lymphoma: findings from the UK's population-based Haematological Malignancy Research Network","volume":"185","author":"Painter","year":"2019","journal-title":"Br. J. Haematol."},{"key":"10.1016\/j.ccell.2026.05.008_bib86","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.05.008_bib87","doi-asserted-by":"crossref","first-page":"453","DOI":"10.1038\/nmeth.3337","article-title":"Robust enumeration of cell subsets from tissue expression profiles","volume":"12","author":"Newman","year":"2015","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ccell.2026.05.008_bib88","doi-asserted-by":"crossref","first-page":"7396","DOI":"10.1073\/pnas.0602353103","article-title":"Tracking germinal center B cells expressing germ-line immunoglobulin gamma1 transcripts by conditional gene targeting","volume":"103","author":"Casola","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.ccell.2026.05.008_bib89","doi-asserted-by":"crossref","first-page":"14943","DOI":"10.1073\/pnas.96.26.14943","article-title":"Constitutive Bcl-2 expression throughout the hematopoietic compartment affects multiple lineages and enhances progenitor cell survival","volume":"96","author":"Ogilvy","year":"1999","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.ccell.2026.05.008_bib90","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.05.008_bib91","article-title":"DreamAI: algorithm for the imputation of proteomics data","author":"Ma","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.ccell.2026.05.008_bib92","doi-asserted-by":"crossref","first-page":"5482","DOI":"10.1016\/j.cell.2021.09.014","article-title":"Atlas of clinically distinct cell states and ecosystems across human solid tumors","volume":"184","author":"Luca","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib93","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41587-021-01094-0","article-title":"Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning","volume":"40","author":"Greenwald","year":"2022","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.ccell.2026.05.008_bib94","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1186\/s13059-020-02015-1","article-title":"MOFA+: A statistical framework for comprehensive integration of multi-modal single-cell data","volume":"21","author":"Argelaguet","year":"2020","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.05.008_bib120","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1158\/2643-3230.BCD-20-0076","article-title":"PRPS-ST: A Protocol-Agnostic Self-training Method for Gene Expression\u2013Based Classification of Blood Cancers","volume":"1","author":"Jiang","year":"2020","journal-title":"Blood Cancer Discov."},{"key":"10.1016\/j.ccell.2026.05.008_bib95","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-17204-5","article-title":"QuPath: Open source software for digital pathology image analysis","volume":"7","author":"Bankhead","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.ccell.2026.05.008_bib96","doi-asserted-by":"crossref","first-page":"4742","DOI":"10.21105\/joss.04742","article-title":"basilisk: a Bioconductor package for managing Python environments","volume":"7","author":"Lun","year":"2022","journal-title":"J. Open Source Softw."},{"key":"10.1016\/j.ccell.2026.05.008_bib97","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1038\/nbt.4091","article-title":"Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors","volume":"36","author":"Haghverdi","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.05.008_bib98","doi-asserted-by":"crossref","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","article-title":"ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.05.008_bib99","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"10.1016\/j.ccell.2026.05.008_bib100","doi-asserted-by":"crossref","first-page":"E15","DOI":"10.1093\/nar\/gkaa1146","article-title":"cola: an R\/Bioconductor package for consensus partitioning through a general framework","volume":"49","author":"Gu","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib101","doi-asserted-by":"crossref","first-page":"2847","DOI":"10.1093\/bioinformatics\/btw313","article-title":"Complex heatmaps reveal patterns and correlations in multidimensional genomic data","volume":"32","author":"Gu","year":"2016","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.05.008_bib102","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"10.1016\/j.ccell.2026.05.008_bib103","doi-asserted-by":"crossref","first-page":"gkaf018","DOI":"10.1093\/nar\/gkaf018","article-title":"edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets","volume":"53","author":"Chen","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib104","article-title":"Fast gene set enrichment analysis","author":"Korotkevich","year":"2021","journal-title":"bioRxiv"},{"key":"10.1016\/j.ccell.2026.05.008_bib105","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: Gene set variation analysis for microarray and RNA-Seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinf."},{"key":"10.1016\/j.ccell.2026.05.008_bib106","doi-asserted-by":"crossref","first-page":"e47","DOI":"10.1093\/nar\/gkv007","article-title":"Limma powers differential expression analyses for RNA-sequencing and microarray studies","volume":"43","author":"Ritchie","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib107","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v067.i01","article-title":"Fitting Linear Mixed-Effects Models Using lme4","volume":"67","author":"Bates","year":"2015","journal-title":"J. Stat. Software"},{"key":"10.1016\/j.ccell.2026.05.008_bib108","doi-asserted-by":"crossref","DOI":"10.18637\/jss.v082.i13","article-title":"lmerTest Package: Tests in Linear Mixed Effects Models","volume":"82","author":"Kuznetsova","year":"2017","journal-title":"J. Stat. Software"},{"key":"10.1016\/j.ccell.2026.05.008_bib109","doi-asserted-by":"crossref","first-page":"e39","DOI":"10.1158\/0008-5472.CAN-17-0344","article-title":"Software for the integration of multiomics experiments in bioconductor","volume":"77","author":"Ramos","year":"2017","journal-title":"Cancer Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib110","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1093\/bioinformatics\/btm069","article-title":"pcaMethods\u2014a bioconductor package providing PCA methods for incomplete data","volume":"23","author":"Stacklies","year":"2007","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.05.008_bib111","doi-asserted-by":"crossref","first-page":"1179","DOI":"10.1093\/bioinformatics\/btw777","article-title":"Scater: Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R","volume":"33","author":"McCarthy","year":"2017","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.05.008_bib112","article-title":"A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor","volume":"5","author":"Lun","year":"2016","journal-title":"F1000Res."},{"key":"10.1016\/j.ccell.2026.05.008_bib113","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.05.008_bib114","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with Bioconductor","volume":"17","author":"Amezquita","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.ccell.2026.05.008_bib115","doi-asserted-by":"crossref","first-page":"3128","DOI":"10.1093\/bioinformatics\/btac299","article-title":"SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor","volume":"38","author":"Righelli","year":"2022","journal-title":"Bioinformatics"},{"key":"10.1016\/j.ccell.2026.05.008_bib116","series-title":"Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining 13-17-August-2016","first-page":"785","article-title":"XGBoost: A Scalable Tree Boosting System","author":"Chen","year":"2016"},{"key":"10.1016\/j.ccell.2026.05.008_bib117","series-title":"Guide for the Care and Use of Laboratory Animals","year":"2011"},{"key":"10.1016\/j.ccell.2026.05.008_bib118","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1111\/bjh.12045","article-title":"Whole genome expression profiling based on paraffin embedded tissue can be used to classify diffuse large B-cell lymphoma and predict clinical outcome","volume":"159","author":"Barrans","year":"2012","journal-title":"Br. J. Haematol."},{"key":"10.1016\/j.ccell.2026.05.008_bib119","doi-asserted-by":"crossref","first-page":"e55895","DOI":"10.1371\/journal.pone.0055895","article-title":"A Microarray Platform-Independent Classification Tool for Cell of Origin Class Allows Comparative Analysis of Gene Expression in Diffuse Large B-cell Lymphoma","volume":"8","author":"Care","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.ccell.2026.05.008_bib121","article-title":"Uncertainty Estimates of Predictions via a General Bias-Variance Decomposition","author":"Gruber","year":"2022","journal-title":"arXiv"},{"key":"10.1016\/j.ccell.2026.05.008_bib122","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive Integration of Single-Cell Data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.ccell.2026.05.008_bib123","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1038\/s41587-019-0206-z","article-title":"Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion","volume":"37","author":"Satpathy","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.ccell.2026.05.008_bib124","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with Harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat. Methods"}],"container-title":["Cancer Cell"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535610826002539?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1535610826002539?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T15:06:51Z","timestamp":1783955211000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1535610826002539"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7]]},"references-count":122,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2026,7]]}},"alternative-id":["S1535610826002539"],"URL":"https:\/\/doi.org\/10.1016\/j.ccell.2026.05.008","relation":{},"ISSN":["1535-6108"],"issn-type":[{"value":"1535-6108","type":"print"}],"subject":[],"published":{"date-parts":[[2026,7]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Pathogenesis of diffuse large B cell lymphoma proteogenotypes","name":"articletitle","label":"Article Title"},{"value":"Cancer Cell","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.ccell.2026.05.008","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2026 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}