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For: Hudson D, Fernandes RA, Basham M, Ogg G, Koohy H. Can we predict T cell specificity with digital biology and machine learning? Nat Rev Immunol 2023;23:511-521. [PMID: 36755161 PMCID: PMC9908307 DOI: 10.1038/s41577-023-00835-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 02/10/2023]
Number Cited by Other Article(s)
1
Wang S, Zhou Y, Ding K, Ding ZQ, Zhang W, Liu Y. High-throughput and multimodal profiling of antigen-specific T cells with a droplet-based cell-cell interaction screening platform. Biosens Bioelectron 2025;267:116815. [PMID: 39348735 DOI: 10.1016/j.bios.2024.116815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 09/04/2024] [Accepted: 09/24/2024] [Indexed: 10/02/2024]
2
Hanna SJ, Bonami RH, Corrie B, Westley M, Posgai AL, Luning Prak ET, Breden F, Michels AW, Brusko TM. The Type 1 Diabetes T Cell Receptor and B Cell Receptor Repository in the AIRR Data Commons: a practical guide for access, use and contributions through the Type 1 Diabetes AIRR Consortium. Diabetologia 2025;68:186-202. [PMID: 39467874 DOI: 10.1007/s00125-024-06298-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Accepted: 08/19/2024] [Indexed: 10/30/2024]
3
Shapiro MR, Tallon EM, Brown ME, Posgai AL, Clements MA, Brusko TM. Leveraging artificial intelligence and machine learning to accelerate discovery of disease-modifying therapies in type 1 diabetes. Diabetologia 2024:10.1007/s00125-024-06339-6. [PMID: 39694914 DOI: 10.1007/s00125-024-06339-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 10/28/2024] [Indexed: 12/20/2024]
4
O'Donnell TJ, Kanduri C, Isacchini G, Limenitakis JP, Brachman RA, Alvarez RA, Haff IH, Sandve GK, Greiff V. Reading the repertoire: Progress in adaptive immune receptor analysis using machine learning. Cell Syst 2024;15:1168-1189. [PMID: 39701034 DOI: 10.1016/j.cels.2024.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 08/16/2024] [Accepted: 11/14/2024] [Indexed: 12/21/2024]
5
Liu J, Zhou S, Zang M, Liu C, Liu T, Wang Q. Multiple instance learning method based on convolutional neural network and self-attention for early cancer detection. Comput Methods Biomech Biomed Engin 2024:1-16. [PMID: 39644499 DOI: 10.1080/10255842.2024.2436909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Revised: 10/07/2024] [Accepted: 11/27/2024] [Indexed: 12/09/2024]
6
McMaster B, Thorpe CJ, Rossjohn J, Deane CM, Koohy H. Quantifying conformational changes in the TCR:pMHC-I binding interface. Front Immunol 2024;15:1491656. [PMID: 39687625 PMCID: PMC11646856 DOI: 10.3389/fimmu.2024.1491656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 10/24/2024] [Indexed: 12/18/2024]  Open
7
Asediya VS, Anjaria PA, Mathakiya RA, Koringa PG, Nayak JB, Bisht D, Fulmali D, Patel VA, Desai DN. Vaccine development using artificial intelligence and machine learning: A review. Int J Biol Macromol 2024;282:136643. [PMID: 39426778 DOI: 10.1016/j.ijbiomac.2024.136643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 09/30/2024] [Accepted: 10/15/2024] [Indexed: 10/21/2024]
8
Human CD8+ T cell map with single-cell transcriptome and TCR information. Nat Methods 2024:10.1038/s41592-024-02529-7. [PMID: 39614112 DOI: 10.1038/s41592-024-02529-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2024]
9
Fritsch N, Aparicio-Soto M, Curato C, Riedel F, Thierse HJ, Luch A, Siewert K. Chemical-Specific T Cell Tests Aim to Bridge a Gap in Skin Sensitization Evaluation. TOXICS 2024;12:802. [PMID: 39590982 PMCID: PMC11598016 DOI: 10.3390/toxics12110802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 10/30/2024] [Accepted: 11/02/2024] [Indexed: 11/28/2024]
10
Giera M, Aisporna A, Uritboonthai W, Hoang L, Derks RJE, Joseph KM, Baker ES, Siuzdak G. XCMS-METLIN: data-driven metabolite, lipid, and chemical analysis. Mol Syst Biol 2024;20:1153-1155. [PMID: 39300326 PMCID: PMC11535300 DOI: 10.1038/s44320-024-00063-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 08/23/2024] [Indexed: 09/22/2024]  Open
11
Pogorelyy MV, Kirk AM, Adhikari S, Minervina AA, Sundararaman B, Vegesana K, Brice DC, Scott ZB, Thomas PG. TIRTL-seq: Deep, quantitative, and affordable paired TCR repertoire sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.16.613345. [PMID: 39345544 PMCID: PMC11430070 DOI: 10.1101/2024.09.16.613345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
12
Henderson J, Nagano Y, Milighetti M, Tiffeau-Mayer A. Limits on inferring T cell specificity from partial information. Proc Natl Acad Sci U S A 2024;121:e2408696121. [PMID: 39374400 PMCID: PMC11494314 DOI: 10.1073/pnas.2408696121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 09/03/2024] [Indexed: 10/09/2024]  Open
13
Lee JW, Chen EY, Hu T, Perret R, Chaffee ME, Martinov T, Mureli S, McCurdy CL, Jones LA, Gafken PR, Chanana P, Su Y, Chapuis AG, Bradley P, Schmitt TM, Greenberg PD. Overcoming immune evasion from post-translational modification of a mutant KRAS epitope to achieve TCR-T cell-mediated antitumor activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.612965. [PMID: 39345486 PMCID: PMC11429761 DOI: 10.1101/2024.09.18.612965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
14
Teimouri H, Ghoreyshi ZS, Kolomeisky AB, George JT. Feature Selection Enhances Peptide Binding Predictions for TCR-Specific Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.11.617901. [PMID: 39416168 PMCID: PMC11482946 DOI: 10.1101/2024.10.11.617901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
15
Perez MAS, Chiffelle J, Bobisse S, Mayol‐Rullan F, Bugnon M, Bragina ME, Arnaud M, Sauvage C, Barras D, Laniti DD, Huber F, Bassani‐Sternberg M, Coukos G, Harari A, Zoete V. Predicting Antigen-Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2405949. [PMID: 39159239 PMCID: PMC11516110 DOI: 10.1002/advs.202405949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/19/2024] [Indexed: 08/21/2024]
16
Deichmann M, Hansson FG, Jensen ED. Yeast-based screening platforms to understand and improve human health. Trends Biotechnol 2024;42:1258-1272. [PMID: 38677901 DOI: 10.1016/j.tibtech.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 04/29/2024]
17
Lin V, Cheung M, Gowthaman R, Eisenberg M, Baker BM, Pierce BG. TCR3d 2.0: expanding the T cell receptor structure database with new structures, tools and interactions. Nucleic Acids Res 2024:gkae840. [PMID: 39329260 DOI: 10.1093/nar/gkae840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 09/07/2024] [Accepted: 09/13/2024] [Indexed: 09/28/2024]  Open
18
Raybould MIJ, Greenshields-Watson A, Agarwal P, Aguilar-Sanjuan B, Olsen TH, Turnbull OM, Quast NP, Deane CM. The Observed T Cell Receptor Space database enables paired-chain repertoire mining, coherence analysis, and language modeling. Cell Rep 2024;43:114704. [PMID: 39216000 DOI: 10.1016/j.celrep.2024.114704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2024] [Revised: 08/05/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]  Open
19
Drost F, Dorigatti E, Straub A, Hilgendorf P, Wagner KI, Heyer K, López Montes M, Bischl B, Busch DH, Schober K, Schubert B. Predicting T cell receptor functionality against mutant epitopes. CELL GENOMICS 2024;4:100634. [PMID: 39151427 PMCID: PMC11480844 DOI: 10.1016/j.xgen.2024.100634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 04/22/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
20
Sim MJW, Hanada KI, Stotz Z, Yu Z, Lu J, Brennan P, Quastel M, Gillespie GM, Long EO, Yang JC, Sun PD. Identification and structural characterization of a mutant KRAS-G12V specific TCR restricted by HLA-A3. Eur J Immunol 2024;54:e2451079. [PMID: 39030753 DOI: 10.1002/eji.202451079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 07/22/2024]
21
T. RR, Demerdash ONA, Smith JC. TCR-H: explainable machine learning prediction of T-cell receptor epitope binding on unseen datasets. Front Immunol 2024;15:1426173. [PMID: 39221256 PMCID: PMC11361934 DOI: 10.3389/fimmu.2024.1426173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]  Open
22
Kim HY, Kim S, Park WY, Kim D. TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data. Bioinformatics 2024;40:btae472. [PMID: 39052940 PMCID: PMC11297499 DOI: 10.1093/bioinformatics/btae472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 06/11/2024] [Accepted: 07/25/2024] [Indexed: 07/27/2024]  Open
23
Alsaafin A, Tizhoosh HR. Harmonizing immune cell sequences for computational analysis with large language models. Biol Methods Protoc 2024;9:bpae055. [PMID: 39290987 PMCID: PMC11407694 DOI: 10.1093/biomethods/bpae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/07/2024] [Accepted: 07/29/2024] [Indexed: 09/19/2024]  Open
24
Pertseva M, Follonier O, Scarcella D, Reddy ST. TCR clustering by contrastive learning on antigen specificity. Brief Bioinform 2024;25:bbae375. [PMID: 39129361 PMCID: PMC11317525 DOI: 10.1093/bib/bbae375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 07/09/2024] [Accepted: 07/25/2024] [Indexed: 08/13/2024]  Open
25
Karnaukhov VK, Shcherbinin DS, Chugunov AO, Chudakov DM, Efremov RG, Zvyagin IV, Shugay M. Structure-based prediction of T cell receptor recognition of unseen epitopes using TCRen. NATURE COMPUTATIONAL SCIENCE 2024;4:510-521. [PMID: 38987378 DOI: 10.1038/s43588-024-00653-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 06/04/2024] [Indexed: 07/12/2024]
26
Huo M, Jiang Y, Li SC. Unlocking T-cell receptor-epitope insights with structural analysis. NATURE COMPUTATIONAL SCIENCE 2024;4:475-476. [PMID: 38987377 DOI: 10.1038/s43588-024-00654-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
27
Yu Z, Jiang M, Lan X. HeteroTCR: A heterogeneous graph neural network-based method for predicting peptide-TCR interaction. Commun Biol 2024;7:684. [PMID: 38834836 PMCID: PMC11150398 DOI: 10.1038/s42003-024-06380-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 05/23/2024] [Indexed: 06/06/2024]  Open
28
Bulashevska A, Nacsa Z, Lang F, Braun M, Machyna M, Diken M, Childs L, König R. Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy. Front Immunol 2024;15:1394003. [PMID: 38868767 PMCID: PMC11167095 DOI: 10.3389/fimmu.2024.1394003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]  Open
29
Jiang M, Yu Z, Lan X. VitTCR: A deep learning method for peptide recognition prediction. iScience 2024;27:109770. [PMID: 38711451 PMCID: PMC11070698 DOI: 10.1016/j.isci.2024.109770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 04/15/2024] [Indexed: 05/08/2024]  Open
30
Gao Y, Dong K, Gao Y, Jin X, Yang J, Yan G, Liu Q. Unified cross-modality integration and analysis of T cell receptors and T cell transcriptomes by low-resource-aware representation learning. CELL GENOMICS 2024;4:100553. [PMID: 38688285 PMCID: PMC11099349 DOI: 10.1016/j.xgen.2024.100553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/09/2024] [Accepted: 04/06/2024] [Indexed: 05/02/2024]
31
McMaster B, Thorpe C, Ogg G, Deane CM, Koohy H. Can AlphaFold's breakthrough in protein structure help decode the fundamental principles of adaptive cellular immunity? Nat Methods 2024;21:766-776. [PMID: 38654083 DOI: 10.1038/s41592-024-02240-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 03/08/2024] [Indexed: 04/25/2024]
32
Chi H, Pepper M, Thomas PG. Principles and therapeutic applications of adaptive immunity. Cell 2024;187:2052-2078. [PMID: 38670065 PMCID: PMC11177542 DOI: 10.1016/j.cell.2024.03.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/01/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
33
Croce G, Bobisse S, Moreno DL, Schmidt J, Guillame P, Harari A, Gfeller D. Deep learning predictions of TCR-epitope interactions reveal epitope-specific chains in dual alpha T cells. Nat Commun 2024;15:3211. [PMID: 38615042 PMCID: PMC11016097 DOI: 10.1038/s41467-024-47461-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 04/03/2024] [Indexed: 04/15/2024]  Open
34
Wang Y, Wang Z, Yang J, Lei X, Liu Y, Frankiw L, Wang J, Li G. Deciphering Membrane-Protein Interactions and High-Throughput Antigen Identification with Cell Doublets. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024;11:e2305750. [PMID: 38342599 PMCID: PMC10987144 DOI: 10.1002/advs.202305750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/02/2024] [Indexed: 02/13/2024]
35
Ji H, Wang XX, Zhang Q, Zhang C, Zhang HM. Predicting TCR sequences for unseen antigen epitopes using structural and sequence features. Brief Bioinform 2024;25:bbae210. [PMID: 38711371 PMCID: PMC11074592 DOI: 10.1093/bib/bbae210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 05/08/2024]  Open
36
This S, Costantino S, Melichar HJ. Machine learning predictions of T cell antigen specificity from intracellular calcium dynamics. SCIENCE ADVANCES 2024;10:eadk2298. [PMID: 38446885 PMCID: PMC10917351 DOI: 10.1126/sciadv.adk2298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/29/2024] [Indexed: 03/08/2024]
37
Jensen MF, Nielsen M. Enhancing TCR specificity predictions by combined pan- and peptide-specific training, loss-scaling, and sequence similarity integration. eLife 2024;12:RP93934. [PMID: 38437160 PMCID: PMC10942633 DOI: 10.7554/elife.93934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]  Open
38
Hudson D, Lubbock A, Basham M, Koohy H. A comparison of clustering models for inference of T cell receptor antigen specificity. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024;13:None. [PMID: 38525047 PMCID: PMC10955519 DOI: 10.1016/j.immuno.2024.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 03/26/2024]
39
Schäfer PSL, Dimitrov D, Villablanca EJ, Saez-Rodriguez J. Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system. Nat Immunol 2024;25:405-417. [PMID: 38413722 DOI: 10.1038/s41590-024-01768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 01/16/2024] [Indexed: 02/29/2024]
40
Banerjee A, Pattinson DJ, Wincek CL, Bunk P, Chapin SR, Navlakha S, Meyer HV. BATMAN: Improved T cell receptor cross-reactivity prediction benchmarked on a comprehensive mutational scan database. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.22.576714. [PMID: 38370810 PMCID: PMC10871174 DOI: 10.1101/2024.01.22.576714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
41
Becker M, Dirschl SM, Scherm MG, Serr I, Daniel C. Niche-specific control of tissue function by regulatory T cells-Current challenges and perspectives for targeting metabolic disease. Cell Metab 2024;36:229-239. [PMID: 38218187 DOI: 10.1016/j.cmet.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 01/15/2024]
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Bravi B. Development and use of machine learning algorithms in vaccine target selection. NPJ Vaccines 2024;9:15. [PMID: 38242890 PMCID: PMC10798987 DOI: 10.1038/s41541-023-00795-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/07/2023] [Indexed: 01/21/2024]  Open
43
Foley CR, Swan SL, Swartz MA. Engineering Challenges and Opportunities in Autologous Cellular Cancer Immunotherapy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024;212:188-198. [PMID: 38166251 PMCID: PMC11155266 DOI: 10.4049/jimmunol.2300642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 01/04/2024]
44
Chen J, Zhao B, Lin S, Sun H, Mao X, Wang M, Chu Y, Hong L, Wei D, Li M, Xiong Y. TEPCAM: Prediction of T-cell receptor-epitope binding specificity via interpretable deep learning. Protein Sci 2024;33:e4841. [PMID: 37983648 PMCID: PMC10731497 DOI: 10.1002/pro.4841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/11/2023] [Accepted: 11/16/2023] [Indexed: 11/22/2023]
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Textor J, Buytenhuijs F, Rogers D, Gauthier ÈM, Sultan S, Wortel IMN, Kalies K, Fähnrich A, Pagel R, Melichar HJ, Westermann J, Mandl JN. Machine learning analysis of the T cell receptor repertoire identifies sequence features of self-reactivity. Cell Syst 2023;14:1059-1073.e5. [PMID: 38061355 DOI: 10.1016/j.cels.2023.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 09/01/2023] [Accepted: 11/09/2023] [Indexed: 12/23/2023]
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Sidiropoulos DN, Ho WJ, Jaffee EM, Kagohara LT, Fertig EJ. Systems immunology spanning tumors, lymph nodes, and periphery. CELL REPORTS METHODS 2023;3:100670. [PMID: 38086385 PMCID: PMC10753389 DOI: 10.1016/j.crmeth.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/20/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
47
Shah RK, Cygan E, Kozlik T, Colina A, Zamora AE. Utilizing immunogenomic approaches to prioritize targetable neoantigens for personalized cancer immunotherapy. Front Immunol 2023;14:1301100. [PMID: 38149253 PMCID: PMC10749952 DOI: 10.3389/fimmu.2023.1301100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]  Open
48
Ishikawa T, Horie K, Takakura Y, Ohki H, Maruyama Y, Hayama M, Miyauchi M, Miyao T, Hagiwara N, Kobayashi TJ, Akiyama N, Akiyama T. T-cell receptor repertoire analysis of CD4-positive T cells from blood and an affected organ in an autoimmune mouse model. Genes Cells 2023;28:929-941. [PMID: 37909727 DOI: 10.1111/gtc.13079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/15/2023] [Accepted: 10/22/2023] [Indexed: 11/03/2023]
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Redruello-Romero A, Benitez-Cantos MS, Lopez-Perez D, García-Rubio J, Tamayo F, Pérez-Bartivas D, Moreno-SanJuan S, Ruiz-Palmero I, Puentes-Pardo JD, Vilchez JR, López-Nevot MÁ, García F, Cano C, León J, Carazo Á. Human adipose tissue as a major reservoir of cytomegalovirus-reactive T cells. Front Immunol 2023;14:1303724. [PMID: 38053998 PMCID: PMC10694288 DOI: 10.3389/fimmu.2023.1303724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023]  Open
50
Schmidt F, Fields HF, Purwanti Y, Milojkovic A, Salim S, Wu KX, Simoni Y, Vitiello A, MacLeod DT, Nardin A, Newell EW, Fink K, Wilm A, Fehlings M. In-depth analysis of human virus-specific CD8+ T cells delineates unique phenotypic signatures for T cell specificity prediction. Cell Rep 2023;42:113250. [PMID: 37837618 DOI: 10.1016/j.celrep.2023.113250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/21/2023] [Accepted: 09/26/2023] [Indexed: 10/16/2023]  Open
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