Journal Article
. 2013 Nov; 9(10):e1003266.
doi: 10.1371/journal.pcbi.1003266.

Properties of MHC class I presented peptides that enhance immunogenicity

Jorg J A Calis 1 Matt Maybeno  Jason A Greenbaum  Daniela Weiskopf  Aruna D De Silva  Alessandro Sette  Can Keşmir  Bjoern Peters  
Affiliations
  • PMID: 24204222
  •     75 References
  •     238 citations

Abstract

T-cells have to recognize peptides presented on MHC molecules to be activated and elicit their effector functions. Several studies demonstrate that some peptides are more immunogenic than others and therefore more likely to be T-cell epitopes. We set out to determine which properties cause such differences in immunogenicity. To this end, we collected and analyzed a large set of data describing the immunogenicity of peptides presented on various MHC-I molecules. Two main conclusions could be drawn from this analysis: First, in line with previous observations, we showed that positions P4-6 of a presented peptide are more important for immunogenicity. Second, some amino acids, especially those with large and aromatic side chains, are associated with immunogenicity. This information was combined into a simple model that was used to demonstrate that immunogenicity is, to a certain extent, predictable. This model (made available at http://tools.iedb.org/immunogenicity/) was validated with data from two independent epitope discovery studies. Interestingly, with this model we could show that T-cells are equipped to better recognize viral than human (self) peptides. After the past successful elucidation of different steps in the MHC-I presentation pathway, the identification of variables that influence immunogenicity will be an important next step in the investigation of T-cell epitopes and our understanding of cellular immune responses.

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Viruses, 2017 May 17; 9(5). PMID: 28509875    Free PMC article.
HLA-A24 ligandome analysis of colon and lung cancer cells identifies a novel cancer-testis antigen and a neoantigen that elicits specific and strong CTL responses.
Vitaly Kochin, Takayuki Kanaseki, +11 authors, Toshihiko Torigoe.
Oncoimmunology, 2017 May 24; 6(4). PMID: 28533942    Free PMC article.
In silico and cell-based analyses reveal strong divergence between prediction and observation of T-cell-recognized tumor antigen T-cell epitopes.
Julien Schmidt, Philippe Guillaume, +3 authors, Immanuel Luescher.
J Biol Chem, 2017 May 26; 292(28). PMID: 28536262    Free PMC article.
T-cell epitopes predicted from the Nucleocapsid protein of Sin Nombre virus restricted to 30 HLA alleles common to the North American population.
Sathish Sankar, Mageshbabu Ramamurthy, Balaji Nandagopal, Gopalan Sridharan.
Bioinformation, 2017 Jun 07; 13(3). PMID: 28584450    Free PMC article.
Identification of putative unique immunogenic ZIKV and DENV1-4 peptides for diagnostic cellular based tests.
Aaron L Oom, Davey Smith, Kevan Akrami.
Sci Rep, 2017 Jul 26; 7(1). PMID: 28740150    Free PMC article.
The Role of Multiscale Protein Dynamics in Antigen Presentation and T Lymphocyte Recognition.
R Charlotte Eccleston, Shunzhou Wan, Neil Dalchau, Peter V Coveney.
Front Immunol, 2017 Jul 26; 8. PMID: 28740497    Free PMC article.
On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition.
Nicolas De Neuter, Wout Bittremieux, +8 authors, Pieter Meysman.
Immunogenetics, 2017 Aug 06; 70(3). PMID: 28779185
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient.
Alejandro Jiménez-Sánchez, Danish Memon, +16 authors, Martin L Miller.
Cell, 2017 Aug 26; 170(5). PMID: 28841418    Free PMC article.
Highly Cited.
Soluble HLA-associated peptide from PSF1 has a cancer vaccine potency.
Mari Yoshida, Yukichi Ishioka, +10 authors, Nobuyuki Takakura.
Sci Rep, 2017 Sep 13; 7(1). PMID: 28894200    Free PMC article.
Neoantigen prediction and the need for validation.
Antonella Vitiello, Maurizio Zanetti.
Nat Biotechnol, 2017 Sep 13; 35(9). PMID: 28898209
Development of Peptide Vaccines in Dengue.
Kavita Reginald, Yanqi Chan, Magdalena Plebanski, Chit Laa Poh.
Curr Pharm Des, 2017 Sep 16; 24(11). PMID: 28914200    Free PMC article.
Review.
Emerging Concepts in TCR Specificity: Rationalizing and (Maybe) Predicting Outcomes.
Nishant K Singh, Timothy P Riley, +3 authors, Brian M Baker.
J Immunol, 2017 Sep 20; 199(7). PMID: 28923982    Free PMC article.
Review.
A novel in silico framework to improve MHC-I epitopes and break the tolerance to melanoma.
Cristian Capasso, Aniket Magarkar, +9 authors, Vincenzo Cerullo.
Oncoimmunology, 2017 Sep 22; 6(9). PMID: 28932628    Free PMC article.
Short peptide epitope design from hantaviruses causing HFRS.
Sathish Sankar, Mageshbabu Ramamurthy, Balaji Nandagopal, Gopalan Sridharan.
Bioinformation, 2017 Sep 26; 13(7). PMID: 28943728    Free PMC article.
'Hotspots' of Antigen Presentation Revealed by Human Leukocyte Antigen Ligandomics for Neoantigen Prioritization.
Markus Müller, David Gfeller, George Coukos, Michal Bassani-Sternberg.
Front Immunol, 2017 Nov 07; 8. PMID: 29104575    Free PMC article.
Increased herpes zoster risk associated with poor HLA-A immediate early 62 protein (IE62) affinity.
Pieter Meysman, Nicolas De Neuter, +19 authors, Benson Ogunjimi.
Immunogenetics, 2017 Dec 03; 70(6). PMID: 29196796
MHC class I loaded ligands from breast cancer cell lines: A potential HLA-I-typed antigen collection.
Dmitri V Rozanov, Nikita D Rozanov, +26 authors, Paul T Spellman.
J Proteomics, 2018 Jan 15; 176. PMID: 29331515    Free PMC article.
Novel Immunoinformatics Approaches to Design Multi-epitope Subunit Vaccine for Malaria by Investigating Anopheles Salivary Protein.
Rajan Kumar Pandey, Tarun Kumar Bhatt, Vijay Kumar Prajapati.
Sci Rep, 2018 Jan 20; 8(1). PMID: 29348555    Free PMC article.
Exceptional Response to Pembrolizumab in a Metastatic, Chemotherapy/Radiation-Resistant Ovarian Cancer Patient Harboring a PD-L1-Genetic Rearrangement.
Stefania Bellone, Natalia Buza, +8 authors, Alessandro D Santin.
Clin Cancer Res, 2018 Jan 21; 24(14). PMID: 29351920    Free PMC article.
Computer aided epitope design as a peptide vaccine component against Lassa virus.
Ar-Rafi Md Faisal, Syed Hassan Imtiaz, +2 authors, Hossain Uddin Shekhar.
Bioinformation, 2018 Jan 31; 13(12). PMID: 29379262    Free PMC article.
Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation.
Markus W Löffler, Daniel J Kowalewski, +15 authors, Sebastian P Haen.
Cancer Res, 2018 May 24; 78(16). PMID: 29789417    Free PMC article.
Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii.
Vandana Solanki, Vishvanath Tiwari.
Sci Rep, 2018 Jun 15; 8(1). PMID: 29899345    Free PMC article.
Gemcitabine alters the proteasome composition and immunopeptidome of tumour cells.
A M Gravett, N Trautwein, +2 authors, J Copier.
Oncoimmunology, 2018 Jun 23; 7(6). PMID: 29930882    Free PMC article.
Predicting HLA CD4 Immunogenicity in Human Populations.
Sandeep Kumar Dhanda, Edita Karosiene, +8 authors, Alessandro Sette.
Front Immunol, 2018 Jul 03; 9. PMID: 29963059    Free PMC article.
Predicting Antigen Presentation-What Could We Learn From a Million Peptides?
David Gfeller, Michal Bassani-Sternberg.
Front Immunol, 2018 Aug 10; 9. PMID: 30090105    Free PMC article.
Highly Cited. Review.
A dormant TIL phenotype defines non-small cell lung carcinomas sensitive to immune checkpoint blockers.
S N Gettinger, J Choi, +19 authors, K A Schalper.
Nat Commun, 2018 Aug 12; 9(1). PMID: 30097571    Free PMC article.
Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands.
Sinu Paul, Edita Karosiene, +5 authors, Bjoern Peters.
Front Immunol, 2018 Aug 22; 9. PMID: 30127785    Free PMC article.
Exploring the pre-immune landscape of antigen-specific T cells.
Mikhail V Pogorelyy, Alla D Fedorova, +9 authors, Mikhail Shugay.
Genome Med, 2018 Aug 27; 10(1). PMID: 30144804    Free PMC article.
Identifying neoantigens for use in immunotherapy.
Sharon Hutchison, Antonia L Pritchard.
Mamm Genome, 2018 Sep 01; 29(11-12). PMID: 30167844    Free PMC article.
Review.
The potential HLA Class I-restricted epitopes derived from LeIF and TSA of Leishmania donovani evoke anti-leishmania CD8+ T lymphocyte response.
Manas Ranjan Dikhit, Sushmita Das, +11 authors, Pradeep Das.
Sci Rep, 2018 Sep 23; 8(1). PMID: 30242172    Free PMC article.
Designing of CD8+ and CD8+-overlapped CD4+ epitope vaccine by targeting late and early proteins of human papillomavirus.
Satyavani Kaliamurthi, Gurudeeban Selvaraj, +2 authors, Dong-Qing Wei.
Biologics, 2018 Oct 17; 12. PMID: 30323556    Free PMC article.
A comprehensive in silico analysis for identification of therapeutic epitopes in HPV16, 18, 31 and 45 oncoproteins.
Heidar Ali Panahi, Azam Bolhassani, Gholamreza Javadi, Zahra Noormohammadi.
PLoS One, 2018 Oct 26; 13(10). PMID: 30356257    Free PMC article.
Predicting T cell recognition of MHC class I restricted neoepitopes.
Zeynep Koşaloğlu-Yalçın, Manasa Lanka, +8 authors, Bjoern Peters.
Oncoimmunology, 2018 Nov 01; 7(11). PMID: 30377561    Free PMC article.
Immunoinformatics Approach for Epitope-Based Peptide Vaccine Design and Active Site Prediction against Polyprotein of Emerging Oropouche Virus.
Utpal Kumar Adhikari, Mourad Tayebi, M Mizanur Rahman.
J Immunol Res, 2018 Nov 08; 2018. PMID: 30402510    Free PMC article.
Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes.
Weilong Zhao, Xinwei Sher.
PLoS Comput Biol, 2018 Nov 09; 14(11). PMID: 30408041    Free PMC article.
Rejection of immunogenic tumor clones is limited by clonal fraction.
Ron S Gejman, Aaron Y Chang, +4 authors, David A Scheinberg.
Elife, 2018 Dec 01; 7. PMID: 30499773    Free PMC article.
Structural basis of development of multi-epitope vaccine against Middle East respiratory syndrome using in silico approach.
Sukrit Srivastava, Mohit Kamthania, +2 authors, Nishi Sharma.
Infect Drug Resist, 2018 Dec 13; 11. PMID: 30538505    Free PMC article.
Immunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae.
Hamza Arshad Dar, Tahreem Zaheer, +5 authors, Amjad Ali.
Vaccines (Basel), 2019 Aug 15; 7(3). PMID: 31409021    Free PMC article.
A comprehensive analysis of amino-peptidase N1 protein (APN) from Anopheles culicifacies for epitope design using Immuno-informatics models.
Renu Jakhar, Pawan Kumar, Neelam Sehrawat, Surendra Kumar Gakhar.
Bioinformation, 2019 Nov 14; 15(8). PMID: 31719771    Free PMC article.
Machine Learning for Cancer Immunotherapies Based on Epitope Recognition by T Cell Receptors.
Anja Mösch, Silke Raffegerst, +2 authors, Dmitrij Frishman.
Front Genet, 2019 Dec 05; 10. PMID: 31798635    Free PMC article.
Review.
In silico Design of an Epitope-Based Vaccine Ensemble for Chagas Disease.
Lucas Michel-Todó, Pedro Antonio Reche, +3 authors, Julio Alonso-Padilla.
Front Immunol, 2019 Dec 12; 10. PMID: 31824493    Free PMC article.
Identification of Plasmodium falciparum proteoforms from liver stage models.
Benjamin Winer, Kimberly A Edgel, +9 authors, Vincent R Gerbasi.
Malar J, 2020 Jan 09; 19(1). PMID: 31910830    Free PMC article.
pMHC Structural Comparisons as a Pivotal Element to Detect and Validate T-Cell Targets for Vaccine Development and Immunotherapy-A New Methodological Proposal.
Priscila Vianna, Marcus F A Mendes, +4 authors, Gustavo F Vieira.
Cells, 2019 Nov 27; 8(12). PMID: 31766602    Free PMC article.
An overview of immunoinformatics approaches and databases linking T cell receptor repertoires to their antigen specificity.
Ivan V Zvyagin, Vasily O Tsvetkov, Dmitry M Chudakov, Mikhail Shugay.
Immunogenetics, 2019 Nov 20; 72(1-2). PMID: 31741011
Review.
The Immune Epitope Database and Analysis Resource Program 2003-2018: reflections and outlook.
Sheridan Martini, Morten Nielsen, Bjoern Peters, Alessandro Sette.
Immunogenetics, 2019 Nov 26; 72(1-2). PMID: 31761977    Free PMC article.
Review.
Prioritization of potential vaccine targets using comparative proteomics and designing of the chimeric multi-epitope vaccine against Pseudomonas aeruginosa.
Vandana Solanki, Monalisa Tiwari, Vishvanath Tiwari.
Sci Rep, 2019 Mar 29; 9(1). PMID: 30918289    Free PMC article.
Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma.
Aaron S Mansfield, Tobias Peikert, +23 authors, George Vasmatzis.
J Thorac Oncol, 2018 Oct 14; 14(2). PMID: 30316012    Free PMC article.
High-Throughput Stability Screening of Neoantigen/HLA Complexes Improves Immunogenicity Predictions.
Dylan T Blaha, Scott D Anderson, +4 authors, David M Kranz.
Cancer Immunol Res, 2018 Nov 15; 7(1). PMID: 30425106    Free PMC article.
Weighted lambda superstrings applied to vaccine design.
Luis Martínez, Martin Milanič, +3 authors, Ildefonso M de la Fuente.
PLoS One, 2019 Feb 09; 14(2). PMID: 30735507    Free PMC article.
Amino acid signatures of HLA Class-I and II molecules are strongly associated with SLE susceptibility and autoantibody production in Eastern Asians.
Julio E Molineros, Loren L Looger, +30 authors, Swapan K Nath.
PLoS Genet, 2019 Apr 26; 15(4). PMID: 31022184    Free PMC article.
Best practices for bioinformatic characterization of neoantigens for clinical utility.
Megan M Richters, Huiming Xia, +3 authors, Malachi Griffith.
Genome Med, 2019 Aug 30; 11(1). PMID: 31462330    Free PMC article.
Highly Cited. Review.
Structure Based Prediction of Neoantigen Immunogenicity.
Timothy P Riley, Grant L J Keller, +4 authors, Brian M Baker.
Front Immunol, 2019 Sep 27; 10. PMID: 31555277    Free PMC article.
Programmable RNA-Guided RNA Effector Proteins Built from Human Parts.
Simone Rauch, Emily He, +3 authors, Bryan C Dickinson.
Cell, 2019 Jun 25; 178(1). PMID: 31230714    Free PMC article.
Overlapping CD8+ and CD4+ T-cell epitopes identification for the progression of epitope-based peptide vaccine from nucleocapsid and glycoprotein of emerging Rift Valley fever virus using immunoinformatics approach.
Utpal Kumar Adhikari, M Mizanur Rahman.
Infect Genet Evol, 2017 Nov 07; 56. PMID: 29107145    Free PMC article.
Comprehensive Review of Human Plasmodium falciparum-Specific CD8+ T Cell Epitopes.
Janna Heide, Kerrie C Vaughan, +2 authors, Julian Schulze Zur Wiesch.
Front Immunol, 2019 Apr 06; 10. PMID: 30949162    Free PMC article.
Review.
Quantitative Prediction of the Landscape of T Cell Epitope Immunogenicity in Sequence Space.
Masato Ogishi, Hiroshi Yotsuyanagi.
Front Immunol, 2019 May 07; 10. PMID: 31057550    Free PMC article.
Mutation position is an important determinant for predicting cancer neoantigens.
Aude-Hélène Capietto, Suchit Jhunjhunwala, +18 authors, Lélia Delamarre.
J Exp Med, 2020 Jan 16; 217(4). PMID: 31940002    Free PMC article.
A Phase Ib Study of the Combination of Personalized Autologous Dendritic Cell Vaccine, Aspirin, and Standard of Care Adjuvant Chemotherapy Followed by Nivolumab for Resected Pancreatic Adenocarcinoma-A Proof of Antigen Discovery Feasibility in Three Patients.
Michal Bassani-Sternberg, Antonia Digklia, +15 authors, Lana E Kandalaft.
Front Immunol, 2019 Aug 24; 10. PMID: 31440238    Free PMC article.
Level of neo-epitope predecessor and mutation type determine T cell activation of MHC binding peptides.
Hanan Besser, Sharon Yunger, +2 authors, Yoram Louzoun.
J Immunother Cancer, 2019 May 24; 7(1). PMID: 31118084    Free PMC article.
Computational Analysis of HLA-presentation of Non-synonymous Recipient Mismatches Indicates Effect on the Risk of Chronic Graft-vs.-Host Disease After Allogeneic HSCT.
Jarmo Ritari, Kati Hyvärinen, +9 authors, Jukka Partanen.
Front Immunol, 2019 Aug 06; 10. PMID: 31379830    Free PMC article.
Determinants for Neoantigen Identification.
Andrea Garcia-Garijo, Carlos Alberto Fajardo, Alena Gros.
Front Immunol, 2019 Jul 12; 10. PMID: 31293573    Free PMC article.
Review.
IEDB-AR: immune epitope database-analysis resource in 2019.
Sandeep Kumar Dhanda, Swapnil Mahajan, +10 authors, Bjoern Peters.
Nucleic Acids Res, 2019 May 23; 47(W1). PMID: 31114900    Free PMC article.
Highly Cited.
Cancer neoantigens and immunogenicity: mutation position matters.
Aude-Hélène Capietto, Suchit Jhunjhunwala, Lélia Delamarre.
Mol Cell Oncol, 2020 May 12; 7(3). PMID: 32391432    Free PMC article.
Exploring Lassa Virus Proteome to Design a Multi-epitope Vaccine Through Immunoinformatics and Immune Simulation Analyses.
Sifat Bin Sayed, Zulkar Nain, +3 authors, Utpal Kumar Adhikari.
Int J Pept Res Ther, 2020 May 19;. PMID: 32421065    Free PMC article.
Combination Strategies for Immune-Checkpoint Blockade and Response Prediction by Artificial Intelligence.
Florian Huemer, Michael Leisch, +4 authors, Richard Greil.
Int J Mol Sci, 2020 Apr 25; 21(8). PMID: 32325898    Free PMC article.
Review.
Identifying the immune interactions underlying HLA class I disease associations.
Bisrat J Debebe, Lies Boelen, +8 authors, Becca Asquith.
Elife, 2020 Apr 03; 9. PMID: 32238263    Free PMC article.
Mass spectrometry driven exploration reveals nuances of neoepitope-driven tumor rejection.
Hakimeh Ebrahimi-Nik, Justine Michaux, +8 authors, Pramod K Srivastava.
JCI Insight, 2019 Jun 21; 5. PMID: 31219806    Free PMC article.
Predicting the Immunogenicity of T cell epitopes: From HIV to SARS-CoV-2.
Ang Gao, Zhilin Chen, +4 authors, Boris Julg.
bioRxiv, 2020 Jun 09;. PMID: 32511339    Free PMC article.
Expected immune recognition of COVID-19 virus by memory from earlier infections with common coronaviruses in a large part of the world population.
Johannes M Dijkstra, Keiichiro Hashimoto.
F1000Res, 2020 Jul 31; 9. PMID: 32595955    Free PMC article.
Designing a novel mRNA vaccine against SARS-CoV-2: An immunoinformatics approach.
Ishtiaque Ahammad, Samia Sultana Lira.
Int J Biol Macromol, 2020 Jul 01; 162. PMID: 32599237    Free PMC article.
A candidate multi-epitope vaccine against SARS-CoV-2.
Tamalika Kar, Utkarsh Narsaria, +4 authors, Anurag P Srivastava.
Sci Rep, 2020 Jul 04; 10(1). PMID: 32616763    Free PMC article.
INeo-Epp: A Novel T-Cell HLA Class-I Immunogenicity or Neoantigenic Epitope Prediction Method Based on Sequence-Related Amino Acid Features.
Guangzhi Wang, Huihui Wan, +6 authors, Lu Xie.
Biomed Res Int, 2020 Jul 07; 2020. PMID: 32626747    Free PMC article.
Uncovering the Tumor Antigen Landscape: What to Know about the Discovery Process.
Sara Feola, Jacopo Chiaro, Beatriz Martins, Vincenzo Cerullo.
Cancers (Basel), 2020 Jun 27; 12(6). PMID: 32585818    Free PMC article.
Review.
Functional Recognition by CD8+ T Cells of Epitopes with Amino Acid Variations Outside Known MHC Anchor or T Cell Receptor Recognition Residues.
Kirsty L Wilson, Sue D Xiang, Magdalena Plebanski.
Int J Mol Sci, 2020 Jul 08; 21(13). PMID: 32630213    Free PMC article.
Multiepitope-Based Subunit Vaccine Design and Evaluation against Respiratory Syncytial Virus Using Reverse Vaccinology Approach.
Muhammad Tahir Ul Qamar, Zeeshan Shokat, +6 authors, Nazamid Saari.
Vaccines (Basel), 2020 Jun 12; 8(2). PMID: 32521680    Free PMC article.
Structural Basis for Designing Multiepitope Vaccines Against COVID-19 Infection: In Silico Vaccine Design and Validation.
Sukrit Srivastava, Sonia Verma, +6 authors, Kailash C Pandey.
JMIR Bioinform Biotech, 2020 Aug 11; 1(1). PMID: 32776022    Free PMC article.
A Rational Design of a Multi-Epitope Vaccine Against SARS-CoV-2 Which Accounts for the Glycan Shield of the Spike Glycoprotein.
William R Martin, Feixiong Cheng.
ChemRxiv, 2020 Aug 15;. PMID: 32793875    Free PMC article.
Designing a multi-epitope vaccine against SARS-CoV-2: an immunoinformatics approach.
Abdus Samad, Foysal Ahammad, +4 authors, Md Shahedur Rahman.
J Biomol Struct Dyn, 2020 Jul 18; 40(1). PMID: 32677533    Free PMC article.
Anti-COVID-19 multi-epitope vaccine designs employing global viral genome sequences.
Tahreem Zaheer, Maaz Waseem, +9 authors, Amjad Ali.
PeerJ, 2020 Aug 25; 8. PMID: 32832263    Free PMC article.
ASNEO: Identification of personalized alternative splicing based neoantigens with RNA-seq.
Zhanbing Zhang, Chi Zhou, +6 authors, Jing Yu.
Aging (Albany NY), 2020 Jul 23; 12(14). PMID: 32697765    Free PMC article.
CoronaVR: A Computational Resource and Analysis of Epitopes and Therapeutics for Severe Acute Respiratory Syndrome Coronavirus-2.
Amit Kumar Gupta, Md Shoaib Khan, +13 authors, Manoj Kumar.
Front Microbiol, 2020 Aug 28; 11. PMID: 32849449    Free PMC article.
Progress in Neoantigen Targeted Cancer Immunotherapies.
Xue-Jiao Han, Xue-Lei Ma, +3 authors, Xia-Wei Wei.
Front Cell Dev Biol, 2020 Aug 28; 8. PMID: 32850843    Free PMC article.
Review.
A Novel Epitope Quality-Based Immune Escape Mechanism Reveals Patient's Suitability for Immune Checkpoint Inhibition.
Michael Wessolly, Susann Stephan-Falkenau, +12 authors, Fabian D Mairinger.
Cancer Manag Res, 2020 Sep 15; 12. PMID: 32922086    Free PMC article.
Neoantigen characteristics in the context of the complete predicted MHC class I self-immunopeptidome.
Scott D Brown, Robert A Holt.
Oncoimmunology, 2019 Feb 07; 8(3). PMID: 30723589    Free PMC article.
Peptide-Based Subunit Vaccine Design of T- and B-Cells Multi-Epitopes against Zika Virus Using Immunoinformatics Approaches.
Vivitri Dewi Prasasty, Karel Grazzolie, +3 authors, Ernawati Sinaga.
Microorganisms, 2019 Aug 03; 7(8). PMID: 31370224    Free PMC article.
Solving an MHC allele-specific bias in the reported immunopeptidome.
Martin G Klatt, Kyeara N Mack, +5 authors, David A Scheinberg.
JCI Insight, 2020 Sep 09; 5(19). PMID: 32897882    Free PMC article.
Computational perspectives revealed prospective vaccine candidates from five structural proteins of novel SARS corona virus 2019 (SARS-CoV-2).
Rajesh Anand, Subham Biswal, Renu Bhatt, Bhupendra N Tiwary.
PeerJ, 2020 Oct 17; 8. PMID: 33062414    Free PMC article.
Designing of cytotoxic and helper T cell epitope map provides insights into the highly contagious nature of the pandemic novel coronavirus SARS-CoV-2.
Seema Mishra.
R Soc Open Sci, 2020 Oct 14; 7(9). PMID: 33047062    Free PMC article.
Main Strategies for the Identification of Neoantigens.
Alexander V Gopanenko, Ekaterina N Kosobokova, Vyacheslav S Kosorukov.
Cancers (Basel), 2020 Oct 11; 12(10). PMID: 33036391    Free PMC article.
Review.
POTN: A Human Leukocyte Antigen-A2 Immunogenic Peptides Screening Model and Its Applications in Tumor Antigens Prediction.
Qingqing Meng, Yahong Wu, +8 authors, Yanfeng Gao.
Front Immunol, 2020 Nov 03; 11. PMID: 33133063    Free PMC article.
Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide.
Sukrit Srivastava, Sonia Verma, +10 authors, Kailash C Pandey.
J Biomol Struct Dyn, 2020 Nov 07; 40(5). PMID: 33155524    Free PMC article.
Predicting Cross-Reactivity and Antigen Specificity of T Cell Receptors.
Chloe H Lee, Mariolina Salio, +3 authors, Hashem Koohy.
Front Immunol, 2020 Nov 17; 11. PMID: 33193332    Free PMC article.
Review.
Designing spike protein (S-Protein) based multi-epitope peptide vaccine against SARS COVID-19 by immunoinformatics.
Hitesh Singh, Renu Jakhar, Neelam Sehrawat.
Heliyon, 2020 Nov 24; 6(11). PMID: 33225084    Free PMC article.
The Landscape of Pseudomonas aeruginosa Membrane-Associated Proteins.
Sara Motta, Davide Vecchietti, +5 authors, Dario Di Silvestre.
Cells, 2020 Nov 11; 9(11). PMID: 33167383    Free PMC article.
Immunogenic peptide discovery in cancer genomes.
Alexandra Snyder, Timothy A Chan.
Curr Opin Genet Dev, 2015 Jan 16; 30. PMID: 25588790    Free PMC article.
Review.
Systems Immunology: Learning the Rules of the Immune System.
Alexandra-Chloé Villani, Siranush Sarkizova, Nir Hacohen.
Annu Rev Immunol, 2018 Apr 21; 36. PMID: 29677477    Free PMC article.
Review.
Deep learning using tumor HLA peptide mass spectrometry datasets improves neoantigen identification.
Brendan Bulik-Sullivan, Jennifer Busby, +36 authors, Roman Yelensky.
Nat Biotechnol, 2018 Dec 18;. PMID: 30556813
Highly Cited.
Multiepitope Subunit Vaccine Design against COVID-19 Based on the Spike Protein of SARS-CoV-2: An In Silico Analysis.
Hamza Arshad Dar, Yasir Waheed, +4 authors, Khalid Muhammad.
J Immunol Res, 2020 Dec 05; 2020. PMID: 33274246    Free PMC article.
Immunoinformatics Driven Prediction of Multiepitopic Vaccine Against Klebsiella pneumoniae and Mycobacterium tuberculosis Coinfection and Its Validation via In Silico Expression.
Sidra Rahmat Ullah, Mahnoor Majid, +2 authors, Saadia Andleeb.
Int J Pept Res Ther, 2020 Dec 08; 27(2). PMID: 33281529    Free PMC article.
An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-CoV-2.
Renu Jakhar, S K Gakhar.
Can J Infect Dis Med Microbiol, 2020 Dec 11; 2020. PMID: 33299503    Free PMC article.
Thermostability profiling of MHC-bound peptides: a new dimension in immunopeptidomics and aid for immunotherapy design.
Emma C Jappe, Christian Garde, +7 authors, Anthony W Purcell.
Nat Commun, 2020 Dec 11; 11(1). PMID: 33298915    Free PMC article.
Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants.
Alice Massacci, Eleonora Sperandio, +5 authors, Matteo Pallocca.
J Transl Med, 2021 Jan 01; 18(1). PMID: 33380328    Free PMC article.
Cytokine signature of inflammation mediated by autoreactive Th-cells, in calf muscle of claudicating patients with Fontaine stage II peripheral artery disease.
George P Casale, Jonathan R Thompson, +10 authors, Iraklis I Pipinos.
Transl Res, 2020 Aug 25; 228. PMID: 32835907    Free PMC article.
Design of a multi-epitope subunit vaccine for immune-protection against Leishmania parasite.
Sunita Yadav, Jay Prakash, +3 authors, Vikash Kumar Dubey.
Pathog Glob Health, 2020 Nov 10; 114(8). PMID: 33161887    Free PMC article.
TCR Recognition of Peptide-MHC-I: Rule Makers and Breakers.
Christopher Szeto, Christian A Lobos, Andrea T Nguyen, Stephanie Gras.
Int J Mol Sci, 2020 Dec 31; 22(1). PMID: 33374673    Free PMC article.
Review.
DeepImmuno: Deep learning-empowered prediction and generation of immunogenic peptides for T cell immunity.
Guangyuan Li, Balaji Iyer, +2 authors, Nathan Salomonis.
bioRxiv, 2021 Jan 06;. PMID: 33398286    Free PMC article.
Deimmunization of protein therapeutics - Recent advances in experimental and computational epitope prediction and deletion.
Léa V Zinsli, Noël Stierlin, Martin J Loessner, Mathias Schmelcher.
Comput Struct Biotechnol J, 2021 Jan 12; 19. PMID: 33425259    Free PMC article.
Review.
Exploring rotavirus proteome to identify potential B- and T-cell epitope using computational immunoinformatics.
Yengkhom Damayanti Devi, Arpita Devi, +10 authors, Nima D Namsa.
Heliyon, 2021 Jan 12; 6(12). PMID: 33426322    Free PMC article.
Structural dissimilarity from self drives neoepitope escape from immune tolerance.
Jason R Devlin, Jesus A Alonso, +7 authors, Brian M Baker.
Nat Chem Biol, 2020 Aug 19; 16(11). PMID: 32807968    Free PMC article.
Differences in TCR repertoire and T cell activation underlie the divergent outcomes of antitumor immune responses in tumor-eradicating versus tumor-progressing hosts.
Rachel A Woolaver, Xiaoguang Wang, +9 authors, Jing Hong Wang.
J Immunother Cancer, 2021 Jan 09; 9(1). PMID: 33414263    Free PMC article.
Identification of Promiscuous African Swine Fever Virus T-Cell Determinants Using a Multiple Technical Approach.
Laia Bosch-Camós, Elisabet López, +10 authors, Fernando Rodríguez.
Vaccines (Basel), 2021 Jan 13; 9(1). PMID: 33430316    Free PMC article.
Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach.
Aftab Alam, Arbaaz Khan, +4 authors, Romana Ishrat.
Brief Bioinform, 2020 Dec 08; 22(2). PMID: 33285567    Free PMC article.
In silico T cell epitope identification for SARS-CoV-2: Progress and perspectives.
Muhammad Saqib Sohail, Syed Faraz Ahmed, Ahmed Abdul Quadeer, Matthew R McKay.
Adv Drug Deliv Rev, 2021 Jan 20; 171. PMID: 33465451    Free PMC article.
Review.
Immunoinformatics prediction of overlapping CD8+ T-cell, IFN-γ and IL-4 inducer CD4+ T-cell and linear B-cell epitopes based vaccines against COVID-19 (SARS-CoV-2).
Abiodun J Fatoba, Leah Maharaj, +3 authors, Matthew A Adeleke.
Vaccine, 2021 Jan 23; 39(7). PMID: 33478794    Free PMC article.
Identification of SARS-CoV-2 CTL epitopes for development of a multivalent subunit vaccine for COVID-19.
Clayton Fernando Rencilin, Joseph Christina Rosy, +2 authors, Krishnan Sundar.
Infect Genet Evol, 2021 Jan 11; 89. PMID: 33422682    Free PMC article.
SARS-CoV-2 and other human coronaviruses: Mapping of protease recognition sites, antigenic variation of spike protein and their grouping through molecular phylogenetics.
Chiranjib Chakraborty, Ashish Ranjan Sharma, +7 authors, Sang-Soo Lee.
Infect Genet Evol, 2021 Jan 27; 89. PMID: 33497837    Free PMC article.
Alterations in the HLA-B*57:01 Immunopeptidome by Flucloxacillin and Immunogenicity of Drug-Haptenated Peptides.
Montserrat Puig, Suryatheja Ananthula, +16 authors, Michael A Norcross.
Front Immunol, 2021 Feb 27; 11. PMID: 33633747    Free PMC article.
Immunoinformatic based identification of cytotoxic T lymphocyte epitopes from the Indian isolate of SARS-CoV-2.
Viswajit Mulpuru, Nidhi Mishra.
Sci Rep, 2021 Feb 27; 11(1). PMID: 33633155    Free PMC article.
Isoginkgetin derivative IP2 enhances the adaptive immune response against tumor antigens.
Romain Darrigrand, Alison Pierson, +9 authors, Sébastien Apcher.
Commun Biol, 2021 Mar 03; 4(1). PMID: 33649389    Free PMC article.
Exploring novel and potent cell penetrating peptides in the proteome of SARS-COV-2 using bioinformatics approaches.
Kimia Kardani, Azam Bolhassani.
PLoS One, 2021 Feb 20; 16(2). PMID: 33606823    Free PMC article.
Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting.
Julien Schmidt, Angela R Smith, +14 authors, David Gfeller.
Cell Rep Med, 2021 Mar 06; 2(2). PMID: 33665637    Free PMC article.
Immunoinformatics Design of Multi-Epitope Peptide-Based Vaccine Against Schistosoma mansoni Using Transmembrane Proteins as a Target.
Rodrigo C O Sanches, Sandeep Tiwari, +8 authors, Debora O Lopes.
Front Immunol, 2021 Mar 20; 12. PMID: 33737928    Free PMC article.
Bayesian multiple instance regression for modeling immunogenic neoantigens.
Seongoh Park, Xinlei Wang, +3 authors, Tao Wang.
Stat Methods Med Res, 2020 May 14; 29(10). PMID: 32401701    Free PMC article.
Learning from HIV-1 to predict the immunogenicity of T cell epitopes in SARS-CoV-2.
Ang Gao, Zhilin Chen, +9 authors, Boris Julg.
iScience, 2021 Mar 23; 24(4). PMID: 33748696    Free PMC article.
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides.
Tyler Borrman, Brian G Pierce, +2 authors, Zhiping Weng.
Bioinformatics, 2020 Dec 24;. PMID: 33355667    Free PMC article.
Immunoinformatic approach to design a multiepitope vaccine targeting non-mutational hotspot regions of structural and non-structural proteins of the SARS CoV2.
Vandana Solanki, Monalisa Tiwari, Vishvanath Tiwari.
PeerJ, 2021 Apr 09; 9. PMID: 33828922    Free PMC article.
AI Aided Design of Epitope-Based Vaccine for the Induction of Cellular Immune Responses Against SARS-CoV-2.
Giovanni Mazzocco, Iga Niemiec, +9 authors, Piotr Stȩpniak.
Front Genet, 2021 Apr 13; 12. PMID: 33841493    Free PMC article.
Epitope-based universal vaccine for Human T-lymphotropic virus-1 (HTLV-1).
Md Thosif Raza, Shagufta Mizan, +2 authors, Shah Md Shahik.
PLoS One, 2021 Apr 03; 16(4). PMID: 33798232    Free PMC article.
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy.
Ana Marcu, Leon Bichmann, +26 authors, Marian Christoph Neidert.
J Immunother Cancer, 2021 Apr 17; 9(4). PMID: 33858848    Free PMC article.
A Mouse Model of PPRV Infection for Elucidating Protective and Pathological Roles of Immune Cells.
Yashu Sharma, Roman Sarkar, +7 authors, Sharvan Sehrawat.
Front Immunol, 2021 Apr 30; 12. PMID: 33912160    Free PMC article.
Antitumour dendritic cell vaccination in a priming and boosting approach.
Alexandre Harari, Michele Graciotti, Michal Bassani-Sternberg, Lana E Kandalaft.
Nat Rev Drug Discov, 2020 Aug 09; 19(9). PMID: 32764681
Review.
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity.
Guangyuan Li, Balaji Iyer, +2 authors, Nathan Salomonis.
Brief Bioinform, 2021 May 20; 22(6). PMID: 34009266    Free PMC article.
SARS-CoV-2 genome-wide T cell epitope mapping reveals immunodominance and substantial CD8+ T cell activation in COVID-19 patients.
Sunil Kumar Saini, Ditte Stampe Hersby, +5 authors, Sine Reker Hadrup.
Sci Immunol, 2021 Apr 16; 6(58). PMID: 33853928    Free PMC article.
Designing a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology.
Hamza Arshad Dar, Saba Ismail, +5 authors, Khalid Muhammad.
Sci Rep, 2021 May 29; 11(1). PMID: 34045649    Free PMC article.
Challenges of Neoantigen Targeting in Lynch Syndrome and Constitutional Mismatch Repair Deficiency Syndrome.
Asima Abidi, Mark A J Gorris, +7 authors, I Jolanda M de Vries.
Cancers (Basel), 2021 Jun 03; 13(10). PMID: 34067951    Free PMC article.
Review.
Multi-epitope-Based Vaccine Designed by Targeting Cytoadherence Proteins of Mycoplasma gallisepticum.
Susithra Priyadarshni Mugunthan, Mani Chandra Harish.
ACS Omega, 2021 Jun 08; 6(21). PMID: 34095666    Free PMC article.
Low-dose CDK4/6 inhibitors induce presentation of pathway specific MHC ligands as potential targets for cancer immunotherapy.
Angel Charles, Christopher M Bourne, +5 authors, David A Scheinberg.
Oncoimmunology, 2021 Jun 10; 10(1). PMID: 34104540    Free PMC article.
Improvement of Neoantigen Identification Through Convolution Neural Network.
Qing Hao, Ping Wei, +3 authors, Jun-Ning Zhao.
Front Immunol, 2021 Jun 12; 12. PMID: 34113354    Free PMC article.
Landscape and selection of vaccine epitopes in SARS-CoV-2.
Christof C Smith, Kelly S Olsen, +25 authors, Alex Rubinsteyn.
Genome Med, 2021 Jun 16; 13(1). PMID: 34127050    Free PMC article.
Identification of novel hepatitis B virus therapeutic vaccine candidates derived from polymerase protein.
Juzeng Zheng, Ziqiang Xia, +5 authors, Jinming Wu.
Aging (Albany NY), 2021 May 22; 13(10). PMID: 34016795    Free PMC article.
Immunoinformatics and molecular dynamics approaches: Next generation vaccine design against West Nile virus.
Md Tahsin Khan, Rahatul Islam, +6 authors, Shakhinur Islam Mondal.
PLoS One, 2021 Jun 18; 16(6). PMID: 34138958    Free PMC article.
An Immunoinformatics Approach for SARS-CoV-2 in Latam Populations and Multi-Epitope Vaccine Candidate Directed towards the World's Population.
Andrés Felipe Cuspoca, Laura Lorena Díaz, +4 authors, Juvenal Yosa Reyes.
Vaccines (Basel), 2021 Jul 03; 9(6). PMID: 34205992    Free PMC article.
Detecting the Dominant T and B Epitopes of Klebsiella pneumoniae Ferric Enterobactin Protein (FepA) and Introducing a Single Epitopic Peptide as Vaccine Candidate.
Fatemeh Nemati Zargaran, Alisha Akya, +2 authors, Mosayeb Rostamian.
Int J Pept Res Ther, 2021 Jul 07; 27(4). PMID: 34226823    Free PMC article.
In silico investigation of the viroporin E as a vaccine target against SARS-CoV-2.
Erasmia Rouka, Konstantinos I Gourgoulianis, Sotirios G Zarogiannis.
Am J Physiol Lung Cell Mol Physiol, 2021 Apr 07; 320(6). PMID: 33822639    Free PMC article.
In silico designing of vaccine candidate against Clostridium difficile.
Srijita Basak, Debashrito Deb, +5 authors, Anurag P Srivastava.
Sci Rep, 2021 Jul 11; 11(1). PMID: 34244557    Free PMC article.
Immunoinformatics approach for multi-epitope vaccine design against structural proteins and ORF1a polyprotein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).
Khalid Mohamed Adam.
Trop Dis Travel Med Vaccines, 2021 Jul 10; 7(1). PMID: 34238372    Free PMC article.
In Silico Design and Immunological Studies of Two Novel Multiepitope DNA-Based Vaccine Candidates Against High-Risk Human Papillomaviruses.
Matin Kayyal, Azam Bolhassani, Zahra Noormohammadi, Majid Sadeghizadeh.
Mol Biotechnol, 2021 Jul 27; 63(12). PMID: 34308516
In silico identification and experimental validation of cellular uptake by a new cell penetrating peptide P1 derived from MARCKS.
Linlin Chen, Xiangli Guo, +7 authors, Hu Wang.
Drug Deliv, 2021 Aug 03; 28(1). PMID: 34338123    Free PMC article.
Immunoinformatics prediction of potential B-cell and T-cell epitopes as effective vaccine candidates for eliciting immunogenic responses against Epstein-Barr virus.
Fisayo A Olotu, Mahmoud E S Soliman.
Biomed J, 2021 Jun 23; 44(3). PMID: 34154948    Free PMC article.
Identification and Targeting of Mutant Peptide Neoantigens in Cancer Immunotherapy.
Daniel J Verdon, Misty R Jenkins.
Cancers (Basel), 2021 Aug 28; 13(16). PMID: 34439399    Free PMC article.
Review.
In silico identification and experimental validation of cellular uptake and intracellular labeling by a new cell penetrating peptide derived from CDN1.
Xiangli Guo, Linlin Chen, +6 authors, Hu Wang.
Drug Deliv, 2021 Sep 01; 28(1). PMID: 34463179    Free PMC article.
Identification of vaccine targets in pathogens and design of a vaccine using computational approaches.
Kamal Rawal, Robin Sinha, +18 authors, Maria Elena Bottazzi.
Sci Rep, 2021 Sep 04; 11(1). PMID: 34475453    Free PMC article.
Design of a Multi-epitope Vaccine Against Acinetobacter baumannii Using Immunoinformatics Approach.
Maryam Touhidinia, Fatemeh Sefid, Mozhgan Bidakhavidi.
Int J Pept Res Ther, 2021 Sep 07; 27(4). PMID: 34483787    Free PMC article.
Leveraging Immunopeptidomics To Study and Combat Infectious Disease.
Owen K Leddy, Forest M White, Bryan D Bryson.
mSystems, 2021 Aug 04; 6(4). PMID: 34342538    Free PMC article.
Revelation of Potent Epitopes Present in Unannotated ORF Antigens of SARS-CoV-2 for Epitope-Based Polyvalent Vaccine Design Using Immunoinformatics Approach.
Patil Pranita Uttamrao, Chakkarai Sathyaseelan, L Ponoop Prasad Patro, Thenmalarchelvi Rathinavelan.
Front Immunol, 2021 Sep 10; 12. PMID: 34497604    Free PMC article.
Comparison of the impact of allelic polymorphisms in PfAMA1 on the induction of T Cell responses in high and low malaria endemic communities in Ghana.
Ebenezer A Ofori, John K A Tetteh, +7 authors, Kwadwo A Kusi.
Malar J, 2021 Sep 12; 20(1). PMID: 34507582    Free PMC article.
Self-mediated positive selection of T cells sets an obstacle to the recognition of nonself.
Balázs Koncz, Gergő M Balogh, +3 authors, Máté Manczinger.
Proc Natl Acad Sci U S A, 2021 Sep 12; 118(37). PMID: 34507984    Free PMC article.
Design of Monovalent and Chimeric Tetravalent Dengue Vaccine Using an Immunoinformatics Approach.
Neeraj Kumar Dixit.
Int J Pept Res Ther, 2021 Oct 05;. PMID: 34602919    Free PMC article.
T Cell Epitope Prediction and Its Application to Immunotherapy.
Anna-Lisa Schaap-Johansen, Milena Vujović, +2 authors, Paolo Marcatili.
Front Immunol, 2021 Oct 05; 12. PMID: 34603286    Free PMC article.
Review.
Development of synthetic antigen vaccines for COVID-19.
Maria da Conceição Viana Invenção, Alanne Rayssa da Silva Melo, +5 authors, Antonio Carlos de Freitas.
Hum Vaccin Immunother, 2021 Oct 07; 17(11). PMID: 34613880    Free PMC article.
Review.
Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors.
Ana Marcu, Andreas Schlosser, +18 authors, Matthias Eyrich.
J Immunother Cancer, 2021 Oct 03; 9(10). PMID: 34599019    Free PMC article.
Designing a Multi-Epitope Vaccine against Chlamydia trachomatis by Employing Integrated Core Proteomics, Immuno-Informatics and In Silico Approaches.
Sidra Aslam, Sajjad Ahmad, +7 authors, Khaled S Allemailem.
Biology (Basel), 2021 Oct 24; 10(10). PMID: 34681096    Free PMC article.
Implications of Antigen Selection on T Cell-Based Immunotherapy.
Faye A Camp, Jill E Slansky.
Pharmaceuticals (Basel), 2021 Oct 24; 14(10). PMID: 34681217    Free PMC article.
Review.
Implementation of Vaccinomics and In-Silico Approaches to Construct Multimeric Based Vaccine Against Ovarian Cancer.
Muhammad Sufyan, Farah Shahid, +3 authors, Usman Ali Ashfaq.
Int J Pept Res Ther, 2021 Oct 26; 27(4). PMID: 34690620    Free PMC article.
Proteome-Wide Mapping and Reverse Vaccinology Approaches to Design a Multi-Epitope Vaccine against Clostridium perfringens.
Fahad M Aldakheel, Amna Abrar, +4 authors, Usman Ali Ashfaq.
Vaccines (Basel), 2021 Oct 27; 9(10). PMID: 34696187    Free PMC article.
Rational design of chimeric Multiepitope Based Vaccine (MEBV) against human T-cell lymphotropic virus type 1: An integrated vaccine informatics and molecular docking based approach.
Muhammad Hamza Tariq, Rashid Bhatti, +4 authors, Mohsin Khurshid.
PLoS One, 2021 Oct 28; 16(10). PMID: 34705829    Free PMC article.
Integrating single cell sequencing with a spatial quantitative systems pharmacology model spQSP for personalized prediction of triple-negative breast cancer immunotherapy response.
Shuming Zhang, Chang Gong, +5 authors, Elana J Fertig.
Immunoinformatics (Amst), 2021 Oct 29; 1-2. PMID: 34708216    Free PMC article.
Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach.
Siaw Shi Boon, Chichao Xia, +7 authors, Zigui Chen.
mBio, 2021 Oct 28; 12(5). PMID: 34700382    Free PMC article.
Identification of SARS-CoV-2 Nucleocapsid and Spike T-Cell Epitopes for Assessing T-Cell Immunity.
Eunok Lee, Kerrie Sandgren, +7 authors, Sarah Palmer.
J Virol, 2021 Jan 15; 95(6). PMID: 33443088    Free PMC article.
A Computational Reverse Vaccinology Approach for the Design and Development of Multi-Epitopic Vaccine Against Avian Pathogen Mycoplasma gallisepticum.
Susithra Priyadarshni Mugunthan, Harish Mani Chandra.
Front Vet Sci, 2021 Nov 13; 8. PMID: 34765664    Free PMC article.
Designing of a Chimeric Vaccine Using EIS (Rv2416c) Protein Against Mycobacterium tuberculosis H37Rv: an Immunoinformatics Approach.
R Logesh, V Lavanya, Shazia Jamal, Neesar Ahmed.
Appl Biochem Biotechnol, 2021 Nov 25; 194(1). PMID: 34817805
Designing of a Multi-epitope Vaccine against the Structural Proteins of Marburg Virus Exploiting the Immunoinformatics Approach.
Saad Ahmed Sami, Kay Kay Shain Marma, +11 authors, Talha Bin Emran.
ACS Omega, 2021 Dec 07; 6(47). PMID: 34870027    Free PMC article.
The Impact of HBV Quasispecies Features on Immune Status in HBsAg+/HBsAb+ Patients With HBV Genotype C Using Next-Generation Sequencing.
Ying Wang, Xiao Xiao, +10 authors, Chunfang Gao.
Front Immunol, 2021 Dec 14; 12. PMID: 34899733    Free PMC article.
Vaccines Targeting Numerous Coronavirus Antigens, Ensuring Broader Global Population Coverage: Multi-epitope and Multi-patch Vaccines.
Sukrit Srivastava, Spyros D Chatziefthymiou, Michael Kolbe.
Methods Mol Biol, 2021 Dec 17; 2410. PMID: 34914046
EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes.
Cristina S Ferreira, Yasmmin C Martins, Rangel Celso Souza, Ana Tereza R Vasconcelos.
PeerJ, 2021 Dec 16; 9. PMID: 34909278    Free PMC article.
A machine learning model for ranking candidate HLA class I neoantigens based on known neoepitopes from multiple human tumor types.
Jared J Gartner, Maria R Parkhurst, +15 authors, Paul F Robbins.
Nat Cancer, 2021 Dec 21; 2(5). PMID: 34927080    Free PMC article.
Immunoinformatics Analysis of SARS-CoV-2 ORF1ab Polyproteins to Identify Promiscuous and Highly Conserved T-Cell Epitopes to Formulate Vaccine for Indonesia and the World Population.
Marsia Gustiananda, Bobby Prabowo Sulistyo, David Agustriawan, Sita Andarini.
Vaccines (Basel), 2021 Dec 29; 9(12). PMID: 34960205    Free PMC article.
In silico construction of a multiepitope Zika virus vaccine using immunoinformatics tools.
Ana Clara Barbosa Antonelli, Vinnycius Pereira Almeida, +8 authors, Simone Gonçalves Fonseca.
Sci Rep, 2022 Jan 09; 12(1). PMID: 34997041    Free PMC article.
Identification of vaccine and drug targets in Shigella dysenteriae sd197 using reverse vaccinology approach.
Khurshid Jalal, Tareq Abu-Izneid, +4 authors, Reaz Uddin.
Sci Rep, 2022 Jan 09; 12(1). PMID: 34997046    Free PMC article.
In silico Design and Characterization of Multi-epitopes Vaccine for SARS-CoV2 from Its Spike Protein.
Gunderao H Kathwate.
Int J Pept Res Ther, 2022 Jan 11; 28(1). PMID: 35002585    Free PMC article.
Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage.
Priyank Shukla, Preeti Pandey, +10 authors, Anthony J Bjourson.
Brief Bioinform, 2021 Dec 29; 23(1). PMID: 34962259    Free PMC article.
Phylogeny, Structure, Functions, and Role of AIRE in the Formation of T-Cell Subsets.
Daniil Shevyrev, Valeriy Tereshchenko, Vladimir Kozlov, Sergey Sennikov.
Cells, 2022 Jan 22; 11(2). PMID: 35053310    Free PMC article.
Review.
A New Epitope Selection Method: Application to Design a Multi-Valent Epitope Vaccine Targeting HRAS Oncogene in Squamous Cell Carcinoma.
Kush Savsani, Gabriel Jabbour, Sivanesan Dakshanamurthy.
Vaccines (Basel), 2022 Jan 23; 10(1). PMID: 35062725    Free PMC article.
Identification of neoantigens for individualized therapeutic cancer vaccines.
Franziska Lang, Barbara Schrörs, +2 authors, Ugur Sahin.
Nat Rev Drug Discov, 2022 Feb 03; 21(4). PMID: 35105974    Free PMC article.
Review.
Peptide-Based Vaccines for Tuberculosis.
Wenping Gong, Chao Pan, +3 authors, Xueqiong Wu.
Front Immunol, 2022 Feb 18; 13. PMID: 35173740    Free PMC article.
Review.
Prediction and evaluation of multi epitope based sub-unit vaccine against Salmonella typhimurium.
Samavia Zafar, Huma Ajab, +8 authors, Muhammad Asif Rasheed.
Saudi J Biol Sci, 2022 Feb 25; 29(2). PMID: 35197778    Free PMC article.
Neoantigen Quantity and Quality in Relation to Pancreatic Cancer Survival.
Iris J M Levink, Lodewijk A A Brosens, +7 authors, Marco J Bruno.
Front Med (Lausanne), 2022 Mar 01; 8. PMID: 35223878    Free PMC article.
Immune epitopes identification and designing of a multi-epitope vaccine against bovine leukemia virus: a molecular dynamics and immune simulation approaches.
Abdus Samad, Nigar Sultana Meghla, +2 authors, Md Shahedur Rahman.
Cancer Immunol Immunother, 2022 Mar 17;. PMID: 35294591    Free PMC article.
Structural Prediction of Peptide-MHC Binding Modes.
Marta A S Perez, Michel A Cuendet, +2 authors, Vincent Zoete.
Methods Mol Biol, 2022 Mar 18; 2405. PMID: 35298818
Review.
Proteasomal Processing Immune Escape Mechanisms in Platinum-Treated Advanced Bladder Cancer.
Michael Wessolly, Fabian D Mairinger, +3 authors, Henning Reis.
Genes (Basel), 2022 Mar 26; 13(3). PMID: 35327977    Free PMC article.
Effect of non-repetitive linker on in vitro and in vivo properties of an anti-VEGF scFv.
Merve Arslan, Murat Karadag, +3 authors, Sibel Kalyoncu.
Sci Rep, 2022 Apr 02; 12(1). PMID: 35361822    Free PMC article.
A Systematic Immuno-Informatic Approach to Design a Multiepitope-Based Vaccine Against Emerging Multiple Drug Resistant Serratia marcescens.
Marcelo Silva Folhas Damas, Fernando Gabriel Mazur, +2 authors, Maria-Cristina da Silva Pranchevicius.
Front Immunol, 2022 Apr 05; 13. PMID: 35371033    Free PMC article.
In Silico Prediction of Epitopes in Virulence Proteins of Mycobacterium ulcerans for Vaccine Designing.
Taruna Mohinani, Aditya Saxena, Shoor Vir Singh.
Curr Genomics, 2022 Apr 08; 22(7). PMID: 35386432    Free PMC article.
Functional Profile of CD8+ T-Cells in Response to HLA-A*02:01-Restricted Mutated Epitopes Derived from the Gag Protein of Circulating HIV-1 Strains from Medellín, Colombia.
Alexandra Sánchez-Martínez, Liliana Acevedo-Sáenz, +6 authors, Paula Andrea Velilla.
Front Immunol, 2022 Apr 09; 13. PMID: 35392101    Free PMC article.
Potential Immunogenic Activity of Computationally Designed mRNA- and Peptide-Based Prophylactic Vaccines against MERS, SARS-CoV, and SARS-CoV-2: A Reverse Vaccinology Approach.
Taimoor Khan, Abbas Khan, +4 authors, Yasir Waheed.
Molecules, 2022 Apr 13; 27(7). PMID: 35408772    Free PMC article.
Epitope Identification and Designing a Potent Multi-epitope Vaccine Construct against SARS-CoV-2 Including the Emerging Variants.
Sivasubramanian Srinivasan, Gracy Fathima Selvaraj, +7 authors, Satish Srinivas Kitambi.
J Glob Infect Dis, 2022 Apr 15; 14(1). PMID: 35418729    Free PMC article.
Design of a multi-epitope vaccine against SARS-CoV-2: immunoinformatic and computational methods.
Md Oliullah Rafi, Khattab Al-Khafaji, +3 authors, Md Shahedur Rahman.
RSC Adv, 2022 Apr 16; 12(7). PMID: 35425433    Free PMC article.
Designing a novel mRNA vaccine against Vibrio harveyi infection in fish: an immunoinformatics approach.
Sk Injamamul Islam, Moslema Jahan Mou, +3 authors, Sarower Mahfuj.
Genomics Inform, 2022 Apr 12; 20(1). PMID: 35399010    Free PMC article.
A rational design of a multi-epitope vaccine against SARS-CoV-2 which accounts for the glycan shield of the spike glycoprotein.
William R Martin, Feixiong Cheng.
J Biomol Struct Dyn, 2021 Mar 16;. PMID: 33715598    Free PMC article.
Immunoinformatics-guided design of a multi-epitope vaccine based on the structural proteins of severe acute respiratory syndrome coronavirus 2.
Ahmad J Obaidullah, Mohammed M Alanazi, +6 authors, Talha Bin Emran.
RSC Adv, 2022 Apr 29; 11(29). PMID: 35480208    Free PMC article.
Mining the Proteome of Toxoplasma Parasites Seeking Vaccine and Diagnostic Candidates.
Sajad Rashidi, Javier Sánchez-Montejo, +6 authors, Paul Nguewa.
Animals (Basel), 2022 May 15; 12(9). PMID: 35565525    Free PMC article.
Review.
In Silico Analysis Predicts a Limited Impact of SARS-CoV-2 Variants on CD8 T Cell Recognition.
Olga I Isaeva, Steven L C Ketelaars, Pia Kvistborg.
Front Immunol, 2022 May 17; 13. PMID: 35572563    Free PMC article.
In silico design and analyses of a multi-epitope vaccine against Crimean-Congo hemorrhagic fever virus through reverse vaccinology and immunoinformatics approaches.
Akinyemi Ademola Omoniyi, Samuel Sunday Adebisi, +6 authors, Jens Randel Nyengaard.
Sci Rep, 2022 May 25; 12(1). PMID: 35610299
Designing a novel multi-epitope vaccine to evoke a robust immune response against pathogenic multidrug-resistant Enterococcus faecium bacterium.
Jyotirmayee Dey, Soumya Ranjan Mahapatra, +6 authors, Mrutyunjay Suar.
Gut Pathog, 2022 May 28; 14(1). PMID: 35624464