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For: Saethang T, Hirose O, Kimkong I, Tran VA, Dang XT, Nguyen LAT, Le TKT, Kubo M, Yamada Y, Satou K. PAAQD: Predicting immunogenicity of MHC class I binding peptides using amino acid pairwise contact potentials and quantum topological molecular similarity descriptors. J Immunol Methods 2012;387:293-302. [PMID: 23058674 DOI: 10.1016/j.jim.2012.09.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 09/17/2012] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
1
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
2
Wu J, Qi M, Zhang F, Zheng Y. TPBTE: A model based on convolutional Transformer for predicting the binding of TCR to epitope. Mol Immunol 2023;157:30-41. [PMID: 36966551 DOI: 10.1016/j.molimm.2023.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/12/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
3
Cai Y, Chen R, Gao S, Li W, Liu Y, Su G, Song M, Jiang M, Jiang C, Zhang X. Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy. Front Oncol 2023;12:1054231. [PMID: 36698417 PMCID: PMC9868469 DOI: 10.3389/fonc.2022.1054231] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023]  Open
4
Liu Y, Sun B, Wang J, Sun H, Lu Z, Chen L, Lan M, Xu J, Pan J, Shi J, Sun Y, Zhang X, Wang J, Jiang D, Yang K. In silico analyses and experimental validation of the MHC class-I restricted epitopes of Ebolavirus GP. Int Immunol 2022;34:313-325. [PMID: 35192720 DOI: 10.1093/intimm/dxac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022]  Open
5
Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Brief Bioinform 2021;22:bbab160. [PMID: 34009266 PMCID: PMC8135853 DOI: 10.1093/bib/bbab160] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023]  Open
6
Schaap-Johansen AL, Vujović M, Borch A, Hadrup SR, Marcatili P. T Cell Epitope Prediction and Its Application to Immunotherapy. Front Immunol 2021;12:712488. [PMID: 34603286 PMCID: PMC8479193 DOI: 10.3389/fimmu.2021.712488] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/12/2021] [Indexed: 12/13/2022]  Open
7
Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.12.24.424262. [PMID: 33398286 PMCID: PMC7781330 DOI: 10.1101/2020.12.24.424262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
8
Haji Abdolvahab M, Venselaar H, Fazeli A, Arab SS, Behmanesh M. Point Mutation Approach to Reduce Antigenicity of Interferon Beta. Int J Pept Res Ther 2020. [DOI: 10.1007/s10989-019-09938-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
9
Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process. Cancers (Basel) 2020;12:cancers12061660. [PMID: 32585818 PMCID: PMC7352969 DOI: 10.3390/cancers12061660] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/11/2020] [Accepted: 06/20/2020] [Indexed: 12/14/2022]  Open
10
Mei S, Li F, Leier A, Marquez-Lago TT, Giam K, Croft NP, Akutsu T, Smith AI, Li J, Rossjohn J, Purcell AW, Song J. A comprehensive review and performance evaluation of bioinformatics tools for HLA class I peptide-binding prediction. Brief Bioinform 2020;21:1119-1135. [PMID: 31204427 DOI: 10.1093/bib/bbz051] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022]  Open
11
Kim S, Kim H, Kim E, Lee M, Shin EC, Paik S, Kim S. Neopepsee: accurate genome-level prediction of neoantigens by harnessing sequence and amino acid immunogenicity information. Ann Oncol 2018;29:1030-1036. [DOI: 10.1093/annonc/mdy022] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
12
Antunes DA, Abella JR, Devaurs D, Rigo MM, Kavraki LE. Structure-based Methods for Binding Mode and Binding Affinity Prediction for Peptide-MHC Complexes. Curr Top Med Chem 2018;18:2239-2255. [PMID: 30582480 PMCID: PMC6361695 DOI: 10.2174/1568026619666181224101744] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 11/29/2018] [Accepted: 12/08/2018] [Indexed: 12/26/2022]
13
Liu XS, Mardis ER. Applications of Immunogenomics to Cancer. Cell 2017;168:600-612. [PMID: 28187283 DOI: 10.1016/j.cell.2017.01.014] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/10/2017] [Accepted: 01/10/2017] [Indexed: 01/05/2023]
14
Saethang T, Payne DM, Avihingsanon Y, Pisitkun T. A machine learning strategy for predicting localization of post-translational modification sites in protein-protein interacting regions. BMC Bioinformatics 2016;17:307. [PMID: 27534850 PMCID: PMC4989344 DOI: 10.1186/s12859-016-1165-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 08/05/2016] [Indexed: 02/02/2023]  Open
15
Gfeller D, Bassani-Sternberg M, Schmidt J, Luescher IF. Current tools for predicting cancer-specific T cell immunity. Oncoimmunology 2016;5:e1177691. [PMID: 27622028 DOI: 10.1080/2162402x.2016.1177691] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 04/06/2016] [Accepted: 04/06/2016] [Indexed: 12/20/2022]  Open
16
Zhang W, Niu Y, Zou H, Luo L, Liu Q, Wu W. Accurate prediction of immunogenic T-cell epitopes from epitope sequences using the genetic algorithm-based ensemble learning. PLoS One 2015;10:e0128194. [PMID: 26020952 PMCID: PMC4447411 DOI: 10.1371/journal.pone.0128194] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/24/2015] [Indexed: 11/19/2022]  Open
17
Olsen LR, Campos B, Barnkob MS, Winther O, Brusic V, Andersen MH. Bioinformatics for cancer immunotherapy target discovery. Cancer Immunol Immunother 2014;63:1235-49. [PMID: 25344903 PMCID: PMC11029190 DOI: 10.1007/s00262-014-1627-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 10/08/2014] [Indexed: 12/13/2022]
18
Varicella-zoster virus-derived major histocompatibility complex class I-restricted peptide affinity is a determining factor in the HLA risk profile for the development of postherpetic neuralgia. J Virol 2014;89:962-9. [PMID: 25355886 DOI: 10.1128/jvi.02500-14] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
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