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For: Tian Y, da Silva Antunes R, Sidney J, Lindestam Arlehamn CS, Grifoni A, Dhanda SK, Paul S, Peters B, Weiskopf D, Sette A. A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis. Front Immunol 2018;9:2778. [PMID: 30555469 PMCID: PMC6281829 DOI: 10.3389/fimmu.2018.02778] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023]  Open
Number Cited by Other Article(s)
1
da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023;3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [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: 11/16/2023]
2
da Silva Antunes R, Garrigan E, Quiambao LG, Dhanda SK, Marrama D, Westernberg L, Wang E, Abawi A, Sutherland A, Armstrong SK, Brickman TJ, Sidney J, Frazier A, Merkel TJ, Peters B, Sette A. T cell reactivity to Bordetella pertussis is highly diverse regardless of childhood vaccination. Cell Host Microbe 2023;31:1404-1416.e4. [PMID: 37490913 PMCID: PMC10528758 DOI: 10.1016/j.chom.2023.06.015] [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: 03/27/2023] [Revised: 05/17/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
3
da Silva Antunes R, Garrigan E, Quiambao LG, Dhanda SK, Marrama D, Westernberg L, Wang E, Sutherland A, Armstrong SK, Brickman TJ, Sidney J, Frazier A, Merkel T, Peters B, Sette A. Genome-wide characterization of T cell responses to Bordetella pertussis reveals broad reactivity and similar polarization irrespective of childhood vaccination profiles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.24.534182. [PMID: 36993748 PMCID: PMC10055406 DOI: 10.1101/2023.03.24.534182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
4
Loh JT, Lam KP. Fungal infections: Immune defense, immunotherapies and vaccines. Adv Drug Deliv Rev 2023;196:114775. [PMID: 36924530 DOI: 10.1016/j.addr.2023.114775] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/05/2023] [Accepted: 03/07/2023] [Indexed: 03/17/2023]
5
Larsen SE, Erasmus JH, Reese VA, Pecor T, Archer J, Kandahar A, Hsu FC, Nicholes K, Reed SG, Baldwin SL, Coler RN. An RNA-Based Vaccine Platform for Use against Mycobacterium tuberculosis. Vaccines (Basel) 2023;11:vaccines11010130. [PMID: 36679975 PMCID: PMC9862644 DOI: 10.3390/vaccines11010130] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 01/07/2023]  Open
6
Moezzi MS, Derakhshandeh A, Hemmatzadeh F. Immunoinformatics analysis of candidate proteins for controlling bovine paratuberculosis. PLoS One 2022;17:e0277751. [PMID: 36409703 PMCID: PMC9678287 DOI: 10.1371/journal.pone.0277751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/02/2022] [Indexed: 11/22/2022]  Open
7
Bi J, Zheng Y, Wang C, Ding Y. An Attention Based Bidirectional LSTM Method to Predict the Binding of TCR and Epitope. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022;19:3272-3280. [PMID: 34559661 DOI: 10.1109/tcbb.2021.3115353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
8
Soto LF, Romaní AC, Jiménez-Avalos G, Silva Y, Ordinola-Ramirez CM, Lopez Lapa RM, Requena D. Immunoinformatic analysis of the whole proteome for vaccine design: An application to Clostridium perfringens. Front Immunol 2022;13:942907. [PMID: 36110855 PMCID: PMC9469472 DOI: 10.3389/fimmu.2022.942907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/02/2022] [Indexed: 11/21/2022]  Open
9
Roy P, Sidney J, Lindestam Arlehamn CS, Phillips E, Mallal S, Suthahar SSA, Billitti M, Rubiro P, Marrama D, Drago F, Vallejo J, Suryawanshi V, Orecchioni M, Makings J, Kim PJ, McNamara CA, Peters B, Sette A, Ley K. Immunodominant MHC-II (Major Histocompatibility Complex II) Restricted Epitopes in Human Apolipoprotein B. Circ Res 2022;131:258-276. [PMID: 35766025 PMCID: PMC9536649 DOI: 10.1161/circresaha.122.321116] [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] [Indexed: 11/16/2022]
10
Coppola M, Lai RPJ, Wilkinson RJ, Ottenhoff THM. The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung. Front Immunol 2022;12:763364. [PMID: 35003075 PMCID: PMC8727759 DOI: 10.3389/fimmu.2021.763364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/17/2021] [Indexed: 11/30/2022]  Open
11
da Silva Antunes R, Sutherland A, Frazier A, Schulten V, Pomés A, Glesner J, Calatroni A, Altman MC, Wood RA, O'Connor GT, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill M, Liu AH, Zoratti E, Kattan M, Busse PJ, Bacharier LB, Teach SJ, Wheatley LM, Togias A, Busse WW, Jackson DJ, Sette A. Heterogeneity of magnitude, allergen immunodominance, and cytokine polarization of cockroach allergen-specific T cell responses in allergic sensitized children. Clin Transl Allergy 2021;11:e12073. [PMID: 34691392 PMCID: PMC8514843 DOI: 10.1002/clt2.12073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/13/2021] [Accepted: 10/03/2021] [Indexed: 02/02/2023]  Open
12
A T-Cell Epitope-Based Multi-Epitope Vaccine Designed Using Human HLA Specific T Cell Epitopes Induces a Near-Sterile Immunity against Experimental Visceral Leishmaniasis in Hamsters. Vaccines (Basel) 2021;9:vaccines9101058. [PMID: 34696166 PMCID: PMC8537199 DOI: 10.3390/vaccines9101058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/08/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022]  Open
13
Saso A, Kampmann B, Roetynck S. Vaccine-Induced Cellular Immunity against Bordetella pertussis: Harnessing Lessons from Animal and Human Studies to Improve Design and Testing of Novel Pertussis Vaccines. Vaccines (Basel) 2021;9:877. [PMID: 34452002 PMCID: PMC8402596 DOI: 10.3390/vaccines9080877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022]  Open
14
Khan A, Khan S, Saleem S, Nizam-Uddin N, Mohammad A, Khan T, Ahmad S, Arshad M, Ali SS, Suleman M, Wei DQ. Immunogenomics guided design of immunomodulatory multi-epitope subunit vaccine against the SARS-CoV-2 new variants, and its validation through in silico cloning and immune simulation. Comput Biol Med 2021;133:104420. [PMID: 33930764 PMCID: PMC8064902 DOI: 10.1016/j.compbiomed.2021.104420] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/17/2021] [Accepted: 04/18/2021] [Indexed: 11/17/2022]
15
da Silva Antunes R, Soldevila F, Pomaznoy M, Babor M, Bennett J, Tian Y, Khalil N, Qian Y, Mandava A, Scheuermann RH, Cortese M, Pulendran B, Petro CD, Gilkes AP, Purcell LA, Sette A, Peters B. A system-view of Bordetella pertussis booster vaccine responses in adults primed with whole-cell versus acellular vaccine in infancy. JCI Insight 2021;6:141023. [PMID: 33690224 PMCID: PMC8119213 DOI: 10.1172/jci.insight.141023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 03/03/2021] [Indexed: 01/26/2023]  Open
16
Mapping Gene-by-Gene Single-Nucleotide Variation in 8,535 Mycobacterium tuberculosis Genomes: a Resource To Support Potential Vaccine and Drug Development. mSphere 2021;6:6/2/e01224-20. [PMID: 33692198 PMCID: PMC8546714 DOI: 10.1128/msphere.01224-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
17
Ahmad S, Waheed Y, Ismail S, Abbasi SW, Najmi MH. A computational study to disclose potential drugs and vaccine ensemble for COVID-19 conundrum. J Mol Liq 2021;324:114734. [PMID: 33199930 PMCID: PMC7654302 DOI: 10.1016/j.molliq.2020.114734] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/01/2020] [Accepted: 11/05/2020] [Indexed: 02/07/2023]
18
Khan S, Shaker B, Ahmad S, Abbasi SW, Arshad M, Haleem A, Ismail S, Zaib A, Sajjad W. Towards a novel peptide vaccine for Middle East respiratory syndrome coronavirus and its possible use against pandemic COVID-19. J Mol Liq 2021;324:114706. [PMID: 33173250 PMCID: PMC7644433 DOI: 10.1016/j.molliq.2020.114706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 09/05/2020] [Accepted: 11/02/2020] [Indexed: 12/02/2022]
19
Bellini C, Horváti K. Recent Advances in the Development of Protein- and Peptide-Based Subunit Vaccines against Tuberculosis. Cells 2020;9:cells9122673. [PMID: 33333744 PMCID: PMC7765234 DOI: 10.3390/cells9122673] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]  Open
20
da Silva Antunes R, Quiambao LG, Soldevila F, Sutherland A, Peters B, Sette A. Lack of evidence supporting a role of IFN-β and TGF-β in differential polarization of Bordetella pertussis specific-T cell responses. Cytokine 2020;137:155313. [PMID: 33002739 DOI: 10.1016/j.cyto.2020.155313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 10/23/2022]
21
Davis MM. T cell analysis in vaccination. Curr Opin Immunol 2020;65:70-73. [PMID: 32604000 PMCID: PMC7872128 DOI: 10.1016/j.coi.2020.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 05/14/2020] [Indexed: 11/26/2022]
22
Fullen AR, Yount KS, Dubey P, Deora R. Whoop! There it is: The surprising resurgence of pertussis. PLoS Pathog 2020;16:e1008625. [PMID: 32702023 PMCID: PMC7377359 DOI: 10.1371/journal.ppat.1008625] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
23
Identification of Common CD8+ T Cell Epitopes from Lassa Fever Survivors in Nigeria and Sierra Leone. J Virol 2020;94:JVI.00153-20. [PMID: 32269122 PMCID: PMC7307091 DOI: 10.1128/jvi.00153-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/24/2020] [Indexed: 01/01/2023]  Open
24
Development and Validation of a Bordetella pertussis Whole-Genome Screening Strategy. J Immunol Res 2020;2020:8202067. [PMID: 32322598 PMCID: PMC7154976 DOI: 10.1155/2020/8202067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023]  Open
25
Thakkar N, Bailey-Kellogg C. Balancing sensitivity and specificity in distinguishing TCR groups by CDR sequence similarity. BMC Bioinformatics 2019;20:241. [PMID: 31092185 PMCID: PMC6521430 DOI: 10.1186/s12859-019-2864-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022]  Open
26
Lehmann PV, Suwansaard M, Zhang T, Roen DR, Kirchenbaum GA, Karulin AY, Lehmann A, Reche PA. Comprehensive Evaluation of the Expressed CD8+ T Cell Epitope Space Using High-Throughput Epitope Mapping. Front Immunol 2019;10:655. [PMID: 31105686 PMCID: PMC6499037 DOI: 10.3389/fimmu.2019.00655] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/11/2019] [Indexed: 12/17/2022]  Open
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