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For: Trolle T, Nielsen M. NetTepi: an integrated method for the prediction of T cell epitopes. Immunogenetics 2014;66:449-56. [DOI: 10.1007/s00251-014-0779-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/06/2014] [Indexed: 02/07/2023]
Number Cited by Other Article(s)
1
Koutsoumpli G, Stasiukonyte N, Hoogeboom BN, Daemen T. An in vitro CD8 T-cell priming assay enables epitope selection for hepatitis C virus vaccines. Vaccine 2024;42:126032. [PMID: 38964950 DOI: 10.1016/j.vaccine.2024.05.080] [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: 02/22/2024] [Revised: 04/25/2024] [Accepted: 05/31/2024] [Indexed: 07/06/2024]
2
Guasp P, Reiche C, Sethna Z, Balachandran VP. RNA vaccines for cancer: Principles to practice. Cancer Cell 2024;42:1163-1184. [PMID: 38848720 DOI: 10.1016/j.ccell.2024.05.005] [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: 02/06/2024] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 06/09/2024]
3
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
4
Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2024;13:100030. [PMID: 38577265 PMCID: PMC10994007 DOI: 10.1016/j.immuno.2023.100030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
5
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
6
Zhang B, Bassani-Sternberg M. Current perspectives on mass spectrometry-based immunopeptidomics: the computational angle to tumor antigen discovery. J Immunother Cancer 2023;11:e007073. [PMID: 37899131 PMCID: PMC10619091 DOI: 10.1136/jitc-2023-007073] [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] [Accepted: 07/21/2023] [Indexed: 10/31/2023]  Open
7
Lee CH, Huh J, Buckley PR, Jang M, Pinho MP, Fernandes RA, Antanaviciute A, Simmons A, Koohy H. A robust deep learning workflow to predict CD8 + T-cell epitopes. Genome Med 2023;15:70. [PMID: 37705109 PMCID: PMC10498576 DOI: 10.1186/s13073-023-01225-z] [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: 01/30/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]  Open
8
Bravi B, Di Gioacchino A, Fernandez-de-Cossio-Diaz J, Walczak AM, Mora T, Cocco S, Monasson R. A transfer-learning approach to predict antigen immunogenicity and T-cell receptor specificity. eLife 2023;12:e85126. [PMID: 37681658 PMCID: PMC10522340 DOI: 10.7554/elife.85126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 09/07/2023] [Indexed: 09/09/2023]  Open
9
Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023;19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [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: 05/17/2023] [Indexed: 08/03/2023]
10
Amaya-Ramirez D, Martinez-Enriquez LC, Parra-López C. Usefulness of Docking and Molecular Dynamics in Selecting Tumor Neoantigens to Design Personalized Cancer Vaccines: A Proof of Concept. Vaccines (Basel) 2023;11:1174. [PMID: 37514989 PMCID: PMC10386133 DOI: 10.3390/vaccines11071174] [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: 03/17/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 07/30/2023]  Open
11
Tiwari A, Trivedi R, Lin SY. Tumor microenvironment: barrier or opportunity towards effective cancer therapy. J Biomed Sci 2022;29:83. [PMID: 36253762 PMCID: PMC9575280 DOI: 10.1186/s12929-022-00866-3] [Citation(s) in RCA: 120] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022]  Open
12
Huang X, Zhang G, Tang TY, Gao X, Liang TB. Personalized pancreatic cancer therapy: from the perspective of mRNA vaccine. Mil Med Res 2022;9:53. [PMID: 36224645 PMCID: PMC9556149 DOI: 10.1186/s40779-022-00416-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/14/2022] [Indexed: 11/25/2022]  Open
13
Buckley PR, Lee CH, Ma R, Woodhouse I, Woo J, Tsvetkov VO, Shcherbinin DS, Antanaviciute A, Shughay M, Rei M, Simmons A, Koohy H. Evaluating performance of existing computational models in predicting CD8+ T cell pathogenic epitopes and cancer neoantigens. Brief Bioinform 2022;23:6573960. [PMID: 35471658 PMCID: PMC9116217 DOI: 10.1093/bib/bbac141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/09/2022] [Accepted: 03/26/2022] [Indexed: 12/16/2022]  Open
14
Vijayakumar S. Harnessing Fuzzy Rule Based System for Screening Major Histocompatibility Complex Class I Peptide Epitopes from the Whole Proteome: An Implementation on the Proteome of Leishmania donovani. J Comput Biol 2022;29:1045-1058. [PMID: 35404099 DOI: 10.1089/cmb.2021.0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
15
Lang F, Schrörs B, Löwer M, Türeci Ö, Sahin U. Identification of neoantigens for individualized therapeutic cancer vaccines. Nat Rev Drug Discov 2022;21:261-282. [PMID: 35105974 PMCID: PMC7612664 DOI: 10.1038/s41573-021-00387-y] [Citation(s) in RCA: 196] [Impact Index Per Article: 98.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2021] [Indexed: 02/07/2023]
16
Awasthi A, Sharma G, Agrawal P. Computational approaches for vaccine designing. Bioinformatics 2022. [DOI: 10.1016/b978-0-323-89775-4.00011-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
17
Donzelli S, Spinella F, di Domenico EG, Pontone M, Cavallo I, Orlandi G, Iannazzo S, Ricciuto GM, Team ISGVC, Pellini R, Muti P, Strano S, Ciliberto G, Ensoli F, Zapperi S, La Porta CA, Blandino G, Morrone A, Pimpinelli F. Evidence of a SARS-CoV-2 double Spike mutation D614G/S939F potentially affecting immune response of infected subjects. Comput Struct Biotechnol J 2022;20:733-744. [PMID: 35096288 PMCID: PMC8780065 DOI: 10.1016/j.csbj.2022.01.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/16/2022]  Open
18
Dhall A, Jain S, Sharma N, Naorem LD, Kaur D, Patiyal S, Raghava GPS. In silico tools and databases for designing cancer immunotherapy. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021;129:1-50. [PMID: 35305716 DOI: 10.1016/bs.apcsb.2021.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
19
La Porta CAM, Zapperi S. Immune Profile of SARS-CoV-2 Variants of Concern. Front Digit Health 2021;3:704411. [PMID: 34713175 PMCID: PMC8521889 DOI: 10.3389/fdgth.2021.704411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/17/2021] [Indexed: 01/11/2023]  Open
20
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
21
Combinatorial therapy in tumor microenvironment: Where do we stand? Biochim Biophys Acta Rev Cancer 2021;1876:188585. [PMID: 34224836 DOI: 10.1016/j.bbcan.2021.188585] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/28/2021] [Accepted: 06/23/2021] [Indexed: 01/09/2023]
22
Zinsli LV, Stierlin N, Loessner MJ, Schmelcher M. Deimmunization of protein therapeutics - Recent advances in experimental and computational epitope prediction and deletion. Comput Struct Biotechnol J 2020;19:315-329. [PMID: 33425259 PMCID: PMC7779837 DOI: 10.1016/j.csbj.2020.12.024] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]  Open
23
Lee CH, Salio M, Napolitani G, Ogg G, Simmons A, Koohy H. Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors. Front Immunol 2020;11:565096. [PMID: 33193332 PMCID: PMC7642207 DOI: 10.3389/fimmu.2020.565096] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]  Open
24
Gopanenko AV, Kosobokova EN, Kosorukov VS. Main Strategies for the Identification of Neoantigens. Cancers (Basel) 2020;12:E2879. [PMID: 33036391 PMCID: PMC7600129 DOI: 10.3390/cancers12102879] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/01/2020] [Accepted: 10/05/2020] [Indexed: 12/24/2022]  Open
25
La Porta CAM, Zapperi S. Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks. Cell Syst 2020;11:412-417.e2. [PMID: 32916095 PMCID: PMC7488596 DOI: 10.1016/j.cels.2020.08.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/06/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022]
26
Nielsen M, Andreatta M, Peters B, Buus S. Immunoinformatics: Predicting Peptide-MHC Binding. Annu Rev Biomed Data Sci 2020;3:191-215. [PMID: 37427310 PMCID: PMC10328453 DOI: 10.1146/annurev-biodatasci-021920-100259] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2023]
27
Martínez-Rodrigo A, Mas A, Álvarez-Campos D, Orden JA, Domínguez-Bernal G, Carrión J. Epitope Selection for Fighting Visceral Leishmaniosis: Not All Peptides Function the Same Way. Vaccines (Basel) 2020;8:E352. [PMID: 32630347 PMCID: PMC7564088 DOI: 10.3390/vaccines8030352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/23/2020] [Accepted: 06/25/2020] [Indexed: 11/16/2022]  Open
28
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
29
Protecting Tumors by Preventing Human Papilloma Virus Antigen Presentation: Insights from Emerging Bioinformatics Algorithms. Cancers (Basel) 2019;11:cancers11101543. [PMID: 31614809 PMCID: PMC6826432 DOI: 10.3390/cancers11101543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/24/2019] [Accepted: 10/09/2019] [Indexed: 12/11/2022]  Open
30
Liu CC, Steen CB, Newman AM. Computational approaches for characterizing the tumor immune microenvironment. Immunology 2019;158:70-84. [PMID: 31347163 PMCID: PMC6742767 DOI: 10.1111/imm.13101] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Revised: 07/16/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022]  Open
31
Riley TP, Keller GLJ, Smith AR, Davancaze LM, Arbuiso AG, Devlin JR, Baker BM. Structure Based Prediction of Neoantigen Immunogenicity. Front Immunol 2019;10:2047. [PMID: 31555277 PMCID: PMC6724579 DOI: 10.3389/fimmu.2019.02047] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/13/2019] [Indexed: 12/30/2022]  Open
32
Bonsack M, Hoppe S, Winter J, Tichy D, Zeller C, Küpper MD, Schitter EC, Blatnik R, Riemer AB. Performance Evaluation of MHC Class-I Binding Prediction Tools Based on an Experimentally Validated MHC–Peptide Binding Data Set. Cancer Immunol Res 2019;7:719-736. [DOI: 10.1158/2326-6066.cir-18-0584] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 11/16/2022]
33
Jurtz VI, Olsen LR. Computational Methods for Identification of T Cell Neoepitopes in Tumors. Methods Mol Biol 2019;1878:157-172. [PMID: 30378075 DOI: 10.1007/978-1-4939-8868-6_9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
34
Yi M, Qin S, Zhao W, Yu S, Chu Q, Wu K. The role of neoantigen in immune checkpoint blockade therapy. Exp Hematol Oncol 2018;7:28. [PMID: 30473928 PMCID: PMC6240277 DOI: 10.1186/s40164-018-0120-y] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/09/2018] [Indexed: 02/07/2023]  Open
35
Jappe EC, Kringelum J, Trolle T, Nielsen M. Predicted MHC peptide binding promiscuity explains MHC class I 'hotspots' of antigen presentation defined by mass spectrometry eluted ligand data. Immunology 2018;154:407-417. [PMID: 29446062 DOI: 10.1111/imm.12905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 01/30/2018] [Accepted: 02/07/2018] [Indexed: 01/04/2023]  Open
36
Kar P, Ruiz-Perez L, Arooj M, Mancera RL. Current methods for the prediction of T-cell epitopes. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24046] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
37
Usmani SS, Kumar R, Bhalla S, Kumar V, Raghava GPS. In Silico Tools and Databases for Designing Peptide-Based Vaccine and Drugs. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2018;112:221-263. [PMID: 29680238 DOI: 10.1016/bs.apcsb.2018.01.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
38
Bioinformatics Tools for the Prediction of T-Cell Epitopes. Methods Mol Biol 2018;1785:269-281. [PMID: 29714025 DOI: 10.1007/978-1-4939-7841-0_18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
39
Analyzing the effect of peptide-HLA-binding ability on the immunogenicity of potential CD8+ and CD4+ T cell epitopes in a large dataset. Immunol Res 2017;64:908-18. [PMID: 27094547 DOI: 10.1007/s12026-016-8795-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
40
Dhanda SK, Usmani SS, Agrawal P, Nagpal G, Gautam A, Raghava GPS. Novel in silico tools for designing peptide-based subunit vaccines and immunotherapeutics. Brief Bioinform 2017;18:467-478. [PMID: 27016393 DOI: 10.1093/bib/bbw025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 12/19/2022]  Open
41
Identification of Immunogenic Epitopes by MS/MS. Cancer J 2017;23:102-107. [PMID: 28410297 DOI: 10.1097/ppo.0000000000000252] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
42
Schmidt J, Guillaume P, Dojcinovic D, Karbach J, Coukos G, Luescher I. In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes. J Biol Chem 2017;292:11840-11849. [PMID: 28536262 DOI: 10.1074/jbc.m117.789511] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/11/2017] [Indexed: 11/06/2022]  Open
43
Hackl H, Charoentong P, Finotello F, Trajanoski Z. Computational genomics tools for dissecting tumour–immune cell interactions. Nat Rev Genet 2016;17:441-58. [DOI: 10.1038/nrg.2016.67] [Citation(s) in RCA: 188] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
44
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
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Andreatta M, Nielsen M. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. ACTA ACUST UNITED AC 2015;32:511-7. [PMID: 26515819 DOI: 10.1093/bioinformatics/btv639] [Citation(s) in RCA: 696] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 10/25/2015] [Indexed: 01/18/2023]
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Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW. Ebolavirus comparative genomics. FEMS Microbiol Rev 2015;39:764-78. [PMID: 26175035 PMCID: PMC4551310 DOI: 10.1093/femsre/fuv031] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/17/2022]  Open
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Diken M, Boegel S, Grunwitz C, Kranz LM, Reuter K, van de Roemer N, Vascotto F, Vormehr M, Kreiter S. CIMT 2014: Next waves in cancer immunotherapy - Report on the 12th annual meeting of the Association for Cancer Immunotherapy. Hum Vaccin Immunother 2014;10:3090-100. [PMID: 25483671 PMCID: PMC5443098 DOI: 10.4161/hv.29767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
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