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For: Jokinen E, Huuhtanen J, Mustjoki S, Heinonen M, Lähdesmäki H. Predicting recognition between T cell receptors and epitopes with TCRGP. PLoS Comput Biol 2021;17:e1008814. [PMID: 33764977 PMCID: PMC8023491 DOI: 10.1371/journal.pcbi.1008814] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 04/06/2021] [Accepted: 02/17/2021] [Indexed: 12/31/2022]  Open
Number Cited by Other Article(s)
1
Yadav S, Vora DS, Sundar D, Dhanjal JK. TCR-ESM: Employing protein language embeddings to predict TCR-peptide-MHC binding. Comput Struct Biotechnol J 2024;23:165-173. [PMID: 38146434 PMCID: PMC10749252 DOI: 10.1016/j.csbj.2023.11.037] [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: 09/10/2023] [Revised: 11/19/2023] [Accepted: 11/20/2023] [Indexed: 12/27/2023]  Open
2
Pham MDN, Su CTT, Nguyen TN, Nguyen HN, Nguyen DDA, Giang H, Nguyen DT, Phan MD, Nguyen V. epiTCR-KDA: knowledge distillation model on dihedral angles for TCR-peptide prediction. BIOINFORMATICS ADVANCES 2024;4:vbae190. [PMID: 39678207 PMCID: PMC11646569 DOI: 10.1093/bioadv/vbae190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 11/03/2024] [Accepted: 11/27/2024] [Indexed: 12/17/2024]
3
Postovskaya A, Vercauteren K, Meysman P, Laukens K. tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs. Brief Bioinform 2024;26:bbae602. [PMID: 39576224 PMCID: PMC11583439 DOI: 10.1093/bib/bbae602] [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: 05/22/2024] [Revised: 10/07/2024] [Accepted: 11/05/2024] [Indexed: 11/24/2024]  Open
4
Xu L, Yang Q, Dong W, Li X, Wang K, Dong S, Zhang X, Yang T, Luo G, Liao X, Gao X, Wang G. Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy. Brief Bioinform 2024;26:bbae625. [PMID: 39656887 DOI: 10.1093/bib/bbae625] [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: 03/11/2024] [Revised: 09/18/2024] [Accepted: 11/14/2024] [Indexed: 12/17/2024]  Open
5
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]
6
Zhang Y, Leng X, Shenhav A. Make or break: The influence of expected challenges and rewards on the motivation and experience associated with cognitive effort exertion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.05.570154. [PMID: 38106182 PMCID: PMC10723292 DOI: 10.1101/2023.12.05.570154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
7
Ehrlich R, Glynn E, Singh M, Ghersi D. Computational Methods for Predicting Key Interactions in T Cell-Mediated Adaptive Immunity. Annu Rev Biomed Data Sci 2024;7:295-316. [PMID: 38748864 DOI: 10.1146/annurev-biodatasci-102423-122741] [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: 08/25/2024]
8
Meynard-Piganeau B, Feinauer C, Weigt M, Walczak AM, Mora T. TULIP: A transformer-based unsupervised language model for interacting peptides and T cell receptors that generalizes to unseen epitopes. Proc Natl Acad Sci U S A 2024;121:e2316401121. [PMID: 38838016 PMCID: PMC11181096 DOI: 10.1073/pnas.2316401121] [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: 09/20/2023] [Accepted: 04/29/2024] [Indexed: 06/07/2024]  Open
9
Lundgren S, Myllymäki M, Järvinen T, Keränen MAI, Theodoropoulos J, Smolander J, Kim D, Salmenniemi U, Walldin G, Savola P, Kelkka T, Rajala H, Hellström-Lindberg E, Itälä-Remes M, Kankainen M, Mustjoki S. Somatic mutations associate with clonal expansion of CD8+ T cells. SCIENCE ADVANCES 2024;10:eadj0787. [PMID: 38848368 PMCID: PMC11160466 DOI: 10.1126/sciadv.adj0787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
10
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
11
Machaca V, Goyzueta V, Cruz MG, Sejje E, Pilco LM, López J, Túpac Y. Transformers meets neoantigen detection: a systematic literature review. J Integr Bioinform 2024;21:jib-2023-0043. [PMID: 38960869 PMCID: PMC11377031 DOI: 10.1515/jib-2023-0043] [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: 10/24/2023] [Accepted: 03/20/2024] [Indexed: 07/05/2024]  Open
12
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
13
Jiang F, Guo Y, Ma H, Na S, Zhong W, Han Y, Wang T, Huang J. GTE: a graph learning framework for prediction of T-cell receptors and epitopes binding specificity. Brief Bioinform 2024;25:bbae343. [PMID: 39007599 PMCID: PMC11247411 DOI: 10.1093/bib/bbae343] [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: 01/29/2024] [Revised: 05/15/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024]  Open
14
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
15
Marrer-Berger E, Nicastri A, Augustin A, Kramar V, Liao H, Hanisch LJ, Carpy A, Weinzierl T, Durr E, Schaub N, Nudischer R, Ortiz-Franyuti D, Breous-Nystrom E, Stucki J, Hobi N, Raggi G, Cabon L, Lezan E, Umaña P, Woodhouse I, Bujotzek A, Klein C, Ternette N. The physiological interactome of TCR-like antibody therapeutics in human tissues. Nat Commun 2024;15:3271. [PMID: 38627373 PMCID: PMC11021511 DOI: 10.1038/s41467-024-47062-5] [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: 07/05/2022] [Accepted: 03/19/2024] [Indexed: 04/19/2024]  Open
16
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
17
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
18
Xiong P, Liang A, Cai X, Xia T. APTAnet: an atom-level peptide-TCR interaction affinity prediction model. BIOPHYSICS REPORTS 2024;10:1-14. [PMID: 38737473 PMCID: PMC11079603 DOI: 10.52601/bpr.2023.230037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/26/2024] [Indexed: 05/14/2024]  Open
19
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
20
Huuhtanen J, Adnan-Awad S, Theodoropoulos J, Forstén S, Warfvinge R, Dufva O, Bouhlal J, Dhapola P, Duàn H, Laajala E, Kasanen T, Klievink J, Ilander M, Jaatinen T, Olsson-Strömberg U, Hjorth-Hansen H, Burchert A, Karlsson G, Kreutzman A, Lähdesmäki H, Mustjoki S. Single-cell analysis of immune recognition in chronic myeloid leukemia patients following tyrosine kinase inhibitor discontinuation. Leukemia 2024;38:109-125. [PMID: 37919606 PMCID: PMC10776410 DOI: 10.1038/s41375-023-02074-w] [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: 03/31/2023] [Revised: 09/19/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
21
Han Y, Yang Y, Tian Y, Fattah FJ, von Itzstein MS, Hu Y, Zhang M, Kang X, Yang DM, Liu J, Xue Y, Liang C, Raman I, Zhu C, Xiao O, Dowell JE, Homsi J, Rashdan S, Yang S, Gwin ME, Hsiehchen D, Gloria-McCutchen Y, Pan K, Wu F, Gibbons D, Wang X, Yee C, Huang J, Reuben A, Cheng C, Zhang J, Gerber DE, Wang T. pan-MHC and cross-Species Prediction of T Cell Receptor-Antigen Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.01.569599. [PMID: 38105939 PMCID: PMC10723300 DOI: 10.1101/2023.12.01.569599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
22
Zhao M, Xu SX, Yang Y, Yuan M. GGNpTCR: A Generative Graph Structure Neural Network for Predicting Immunogenic Peptides for T-cell Immune Response. J Chem Inf Model 2023;63:7557-7567. [PMID: 37990917 DOI: 10.1021/acs.jcim.3c01293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
23
Korpela D, Jokinen E, Dumitrescu A, Huuhtanen J, Mustjoki S, Lähdesmäki H. EPIC-TRACE: predicting TCR binding to unseen epitopes using attention and contextualized embeddings. Bioinformatics 2023;39:btad743. [PMID: 38070156 PMCID: PMC10963061 DOI: 10.1093/bioinformatics/btad743] [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: 06/30/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]  Open
24
Khan AR, Reinders MJT, Khatri I. Determining epitope specificity of T-cell receptors with transformers. Bioinformatics 2023;39:btad632. [PMID: 37847663 PMCID: PMC10636277 DOI: 10.1093/bioinformatics/btad632] [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: 04/09/2023] [Revised: 09/09/2023] [Accepted: 10/16/2023] [Indexed: 10/19/2023]  Open
25
Flumens D, Gielis S, Bartholomeus E, Campillo-Davo D, van der Heijden S, Versteven M, De Reu H, Smits E, Ogunjimi B, Laukens K, Meysman P, Lion E. Training of epitope-TCR prediction models with healthy donor-derived cancer-specific T cells. Methods Cell Biol 2023;183:143-160. [PMID: 38548410 DOI: 10.1016/bs.mcb.2023.08.001] [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] [Indexed: 04/02/2024]
26
Ghoreyshi ZS, George JT. Quantitative approaches for decoding the specificity of the human T cell repertoire. Front Immunol 2023;14:1228873. [PMID: 37781387 PMCID: PMC10539903 DOI: 10.3389/fimmu.2023.1228873] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023]  Open
27
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] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 02/10/2023]
28
Myronov A, Mazzocco G, Król P, Plewczynski D. BERTrand-peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing. Bioinformatics 2023;39:btad468. [PMID: 37535685 PMCID: PMC10444968 DOI: 10.1093/bioinformatics/btad468] [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: 01/04/2023] [Revised: 06/28/2023] [Accepted: 08/01/2023] [Indexed: 08/05/2023]  Open
29
Lee MH, Theodoropoulos J, Huuhtanen J, Bhattacharya D, Järvinen P, Tornberg S, Nísen H, Mirtti T, Uski I, Kumari A, Peltonen K, Draghi A, Donia M, Kreutzman A, Mustjoki S. Immunologic Characterization and T cell Receptor Repertoires of Expanded Tumor-infiltrating Lymphocytes in Patients with Renal Cell Carcinoma. CANCER RESEARCH COMMUNICATIONS 2023;3:1260-1276. [PMID: 37484198 PMCID: PMC10361538 DOI: 10.1158/2767-9764.crc-22-0514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/27/2023] [Accepted: 06/21/2023] [Indexed: 07/25/2023]
30
Shen Y, Voigt A, Leng X, Rodriguez AA, Nguyen CQ. A current and future perspective on T cell receptor repertoire profiling. Front Genet 2023;14:1159109. [PMID: 37408774 PMCID: PMC10319011 DOI: 10.3389/fgene.2023.1159109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 06/12/2023] [Indexed: 07/07/2023]  Open
31
Pham MDN, Nguyen TN, Tran LS, Nguyen QTB, Nguyen TPH, Pham TMQ, Nguyen HN, Giang H, Phan MD, Nguyen V. epiTCR: a highly sensitive predictor for TCR-peptide binding. Bioinformatics 2023;39:btad284. [PMID: 37094220 PMCID: PMC10159657 DOI: 10.1093/bioinformatics/btad284] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 02/28/2023] [Accepted: 04/22/2023] [Indexed: 04/26/2023]  Open
32
Huuhtanen J, Kasanen H, Peltola K, Lönnberg T, Glumoff V, Brück O, Dufva O, Peltonen K, Vikkula J, Jokinen E, Ilander M, Lee MH, Mäkelä S, Nyakas M, Li B, Hernberg M, Bono P, Lähdesmäki H, Kreutzman A, Mustjoki S. Single-cell characterization of anti-LAG-3 and anti-PD-1 combination treatment in patients with melanoma. J Clin Invest 2023;133:164809. [PMID: 36719749 PMCID: PMC10014104 DOI: 10.1172/jci164809] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/25/2023] [Indexed: 02/01/2023]  Open
33
Frank ML, Lu K, Erdogan C, Han Y, Hu J, Wang T, Heymach JV, Zhang J, Reuben A. T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy. Clin Cancer Res 2023;29:994-1008. [PMID: 36413126 PMCID: PMC10011887 DOI: 10.1158/1078-0432.ccr-22-2469] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/07/2022] [Accepted: 11/14/2022] [Indexed: 11/23/2022]
34
Gao Y, Gao Y, Fan Y, Zhu C, Wei Z, Zhou C, Chuai G, Chen Q, Zhang H, Liu Q. Pan-Peptide Meta Learning for T-cell receptor–antigen binding recognition. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00619-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
35
Akerman O, Isakov H, Levi R, Psevkin V, Louzoun Y. Counting is almost all you need. Front Immunol 2023;13:1031011. [PMID: 36741395 PMCID: PMC9896581 DOI: 10.3389/fimmu.2022.1031011] [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: 08/29/2022] [Accepted: 12/27/2022] [Indexed: 01/21/2023]  Open
36
Valkiers S, Gielis S, Van Deuren VML, Laukens K, Meysman P. Clustering and Annotation of T Cell Receptor Repertoires. Methods Mol Biol 2023;2673:33-51. [PMID: 37258905 DOI: 10.1007/978-1-0716-3239-0_3] [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] [Indexed: 06/02/2023]
37
Kanduri C, Scheffer L, Pavlović M, Rand KD, Chernigovskaya M, Pirvandy O, Yaari G, Greiff V, Sandve GK. simAIRR: simulation of adaptive immune repertoires with realistic receptor sequence sharing for benchmarking of immune state prediction methods. Gigascience 2022;12:giad074. [PMID: 37848619 PMCID: PMC10580376 DOI: 10.1093/gigascience/giad074] [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: 02/21/2023] [Revised: 07/20/2023] [Accepted: 08/29/2023] [Indexed: 10/19/2023]  Open
38
Jokinen E, Dumitrescu A, Huuhtanen J, Gligorijević V, Mustjoki S, Bonneau R, Heinonen M, Lähdesmäki H. TCRconv: predicting recognition between T cell receptors and epitopes using contextualized motifs. Bioinformatics 2022;39:6881078. [PMID: 36477794 PMCID: PMC9825763 DOI: 10.1093/bioinformatics/btac788] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/01/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]  Open
39
Fang Y, Liu X, Liu H. Attention-aware contrastive learning for predicting T cell receptor-antigen binding specificity. Brief Bioinform 2022;23:6696141. [PMID: 36094087 DOI: 10.1093/bib/bbac378] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 12/14/2022]  Open
40
Grazioli F, Mösch A, Machart P, Li K, Alqassem I, O’Donnell TJ, Min MR. On TCR binding predictors failing to generalize to unseen peptides. Front Immunol 2022;13:1014256. [PMID: 36341448 PMCID: PMC9634250 DOI: 10.3389/fimmu.2022.1014256] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/05/2022] [Indexed: 11/18/2022]  Open
41
Huuhtanen J, Chen L, Jokinen E, Kasanen H, Lönnberg T, Kreutzman A, Peltola K, Hernberg M, Wang C, Yee C, Lähdesmäki H, Davis MM, Mustjoki S. Evolution and modulation of antigen-specific T cell responses in melanoma patients. Nat Commun 2022;13:5988. [PMID: 36220826 PMCID: PMC9553985 DOI: 10.1038/s41467-022-33720-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/15/2022] [Indexed: 11/15/2022]  Open
42
Mateyka LM, Strobl PM, Jarosch S, Scheu SJC, Busch DH, D'Ippolito E. Gene Signatures of T-Cell Activation Can Serve as Predictors of Functionality for SARS-CoV-2-Specific T-Cell Receptors. Vaccines (Basel) 2022;10:vaccines10101617. [PMID: 36298482 PMCID: PMC9611811 DOI: 10.3390/vaccines10101617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/15/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]  Open
43
Huuhtanen J, Ilander M, Yadav B, Dufva OM, Lähteenmäki H, Kasanen T, Klievink J, Olsson-Strömberg U, Stentoft J, Richter J, Koskenvesa P, Höglund M, Söderlund S, Dreimane A, Porkka K, Gedde-Dahl T, Gjertsen BT, Stenke L, Myhr-Eriksson K, Markevärn B, Lübking A, Dimitrijevic A, Udby L, Bjerrum OW, Hjorth-Hansen H, Mustjoki S. IFN-α with dasatinib broadens the immune repertoire in patients with chronic-phase chronic myeloid leukemia. J Clin Invest 2022;132:152585. [PMID: 36047494 PMCID: PMC9433106 DOI: 10.1172/jci152585] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/07/2022] [Indexed: 11/24/2022]  Open
44
Bucktrout SL, Banovich NE, Butterfield LH, Cimen-Bozkus C, Giles JR, Good Z, Goodman D, Jonsson VD, Lareau C, Marson A, Maurer DM, Munson PV, Stubbington M, Taylor S, Cutchin A. Advancing T cell-based cancer therapy with single-cell technologies. Nat Med 2022;28:1761-1764. [PMID: 36127419 DOI: 10.1038/s41591-022-01986-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
45
Cai M, Bang S, Zhang P, Lee H. ATM-TCR: TCR-Epitope Binding Affinity Prediction Using a Multi-Head Self-Attention Model. Front Immunol 2022;13:893247. [PMID: 35874725 PMCID: PMC9299376 DOI: 10.3389/fimmu.2022.893247] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/27/2022] [Indexed: 11/29/2022]  Open
46
Papadopoulou I, Nguyen AP, Weber A, Martínez MR. DECODE: a computational pipeline to discover T cell receptor binding rules. Bioinformatics 2022;38:i246-i254. [PMID: 35758821 PMCID: PMC9235487 DOI: 10.1093/bioinformatics/btac257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
47
Glazer N, Akerman O, Louzoun Y. Naive and memory T cells TCR-HLA-binding prediction. OXFORD OPEN IMMUNOLOGY 2022;3:iqac001. [PMID: 36846560 PMCID: PMC9914496 DOI: 10.1093/oxfimm/iqac001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 05/01/2022] [Accepted: 05/17/2022] [Indexed: 11/12/2022]  Open
48
Yu J, Wang L, Kong X, Cao Y, Zhang M, Sun Z, Liu Y, Wang J, Shen B, Bo X, Feng J. CAD v1.0: Cancer Antigens Database Platform for Cancer Antigen Algorithm Development and Information Exploration. Front Bioeng Biotechnol 2022;10:819583. [PMID: 35646870 PMCID: PMC9133807 DOI: 10.3389/fbioe.2022.819583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 12/02/2022]  Open
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Abondio P, De Intinis C, da Silva Gonçalves Vianez Júnior JL, Pace L. SINGLE CELL MULTIOMIC APPROACHES TO DISENTANGLE T CELL HETEROGENEITY. Immunol Lett 2022;246:37-51. [DOI: 10.1016/j.imlet.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/16/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
50
Huuhtanen J, Bhattacharya D, Lönnberg T, Kankainen M, Kerr C, Theodoropoulos J, Rajala H, Gurnari C, Kasanen T, Braun T, Teramo A, Zambello R, Herling M, Ishida F, Kawakami T, Salmi M, Loughran T, Maciejewski JP, Lähdesmäki H, Kelkka T, Mustjoki S. Single-cell characterization of leukemic and non-leukemic immune repertoires in CD8+ T-cell large granular lymphocytic leukemia. Nat Commun 2022;13:1981. [PMID: 35411050 PMCID: PMC9001660 DOI: 10.1038/s41467-022-29173-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022]  Open
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