Infectious disease mRNA vaccines and a review on epitope prediction for vaccine design

SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice

(2021) Jing-Hui Tian et al.   Nature Communications

BNT162b2 mRNA Covid-19 Vaccine in a Nationwide Mass Vaccination Setting

(2021) Noa Dagan et al.   NEW ENGLAND JOURNAL OF MEDICINE

HLA class I restricted epitopes prediction of common tumor antigens in white and East Asian populations: Implication on antigen selection for cancer vaccine design

(2020) Wei Hu et al.   PLoS One

Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation

(2020) Daniel Wrapp et al.   SCIENCE

Rational Vaccine Design in the Time of COVID-19

(2020) Dennis R. Burton et al.   Cell Host & Microbe

NetMHCpan-4.1 and NetMHCIIpan-4.0: improved predictions of MHC antigen presentation by concurrent motif deconvolution and integration of MS MHC eluted ligand data

(2020) Birkir Reynisson et al.   NUCLEIC ACIDS RESEARCH

Development of an inactivated vaccine candidate for SARS-CoV-2

(2020) Qiang Gao et al.   SCIENCE

A Thermostable mRNA Vaccine against COVID-19

(2020) Na-Na Zhang et al.   CELL

A novel receptor-binding domain (RBD)-based mRNA vaccine against SARS-CoV-2

(2020) Wanbo Tai et al.   CELL RESEARCH

SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness

(2020) Kizzmekia S. Corbett et al.   NATURE

Evaluation of the mRNA-1273 Vaccine against SARS-CoV-2 in Nonhuman Primates

(2020) Kizzmekia S. Corbett et al.   NEW ENGLAND JOURNAL OF MEDICINE

MHCflurry 2.0: Improved Pan-Allele Prediction of MHC Class I-Presented Peptides by Incorporating Antigen Processing

(2020) Timothy J. O’Donnell et al.   Cell Systems

Enhancement of conformational B-cell epitope prediction using CluSMOTE

(2020) Binti Solihah et al.   PeerJ Computer Science

A COVID-19 mRNA vaccine encoding SARS-CoV-2 virus-like particles induces a strong antiviral-like immune response in mice

(2020) Jing Lu et al.   CELL RESEARCH

mRNA vaccine–induced neoantigen-specific T cell immunity in patients with gastrointestinal cancer

(2020) Gal Cafri et al.   JOURNAL OF CLINICAL INVESTIGATION

Vaccination strategies to combat novel corona virus SARS-CoV-2

(2020) Satish Chandra Pandey et al.   LIFE SCIENCES

SARS-CoV-2 vaccines in development

(2020) Florian Krammer   NATURE

Safety and Immunogenicity of Two RNA-Based Covid-19 Vaccine Candidates

(2020) Edward E. Walsh et al.   NEW ENGLAND JOURNAL OF MEDICINE

Viral epitope profiling of COVID-19 patients reveals cross-reactivity and correlates of severity

(2020) Ellen Shrock et al.   SCIENCE

mRNA as a Transformative Technology for Vaccine Development to Control Infectious Diseases

(2019) Giulietta Maruggi et al.   MOLECULAR THERAPY

New Vaccine Design and Delivery Technologies

(2019) Masaru Kanekiyo et al.   JOURNAL OF INFECTIOUS DISEASES

mRNA vaccines against H10N8 and H7N9 influenza viruses of pandemic potential are immunogenic and well tolerated in healthy adults in phase 1 randomized clinical trials

(2019) Robert A. Feldman et al.   VACCINE

A Comparison of Plasmid DNA and mRNA as Vaccine Technologies

(2019) Liu   Vaccines

Three decades of messenger RNA vaccine development

(2019) Rein Verbeke et al.   Nano Today

Computational tools for modern vaccine development

(2019) Sunita Verma et al.   Human Vaccines & Immunotherapeutics

Combining immunoprofiling with machine learning to assess the effects of adjuvant formulation on human vaccine-induced immunity

(2019) Sidhartha Chaudhury et al.   Human Vaccines & Immunotherapeutics

Nanoparticles versus Dendritic Cells as Vehicles to Deliver mRNA Encoding Multiple Epitopes for Immunotherapy

(2019) Rebuma Firdessa-Fite et al.   Molecular Therapy-Methods & Clinical Development

Predicting Influenza H3N2 Vaccine Efficacy From Evolution of the Dominant Epitope

(2018) Melia E Bonomo et al.   CLINICAL INFECTIOUS DISEASES

mRNA vaccines — a new era in vaccinology

(2018) Norbert Pardi et al.   NATURE REVIEWS DRUG DISCOVERY

mRNA vaccination with charge-altering releasable transporters elicits human T cell responses and cures established tumors in mice

(2018) Ole A. W. Haabeth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An mRNA Vaccine Protects Mice against Multiple Tick-Transmitted Flavivirus Infections

(2018) Laura A. VanBlargan et al.   Cell Reports

Efficient Targeting and Activation of Antigen-Presenting Cells In Vivo after Modified mRNA Vaccine Administration in Rhesus Macaques

(2017) Frank Liang et al.   MOLECULAR THERAPY

Zika virus protection by a single low-dose nucleoside-modified mRNA vaccination

(2017) Norbert Pardi et al.   NATURE

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

(2017) Martin Closter Jespersen et al.   NUCLEIC ACIDS RESEARCH

Machine Learning for Predicting Vaccine Immunogenicity

(2016) Eva K. Lee et al.   INTERFACES

Sequence-engineered mRNA Without Chemical Nucleoside Modifications Enables an Effective Protein Therapy in Large Animals

(2015) Andreas Thess et al.   MOLECULAR THERAPY

PEASE: predicting B-cell epitopes utilizing antibody sequence

(2014) I. Sela-Culang et al.   BIOINFORMATICS

Proof of principle for epitope-focused vaccine design

(2014) Bruno E. Correia et al.   NATURE

Conformational B-Cell Epitope Prediction on Antigen Protein Structures: A Review of Current Algorithms and Comparison with Common Binding Site Prediction Methods

(2013) Bo Yao et al.   PLoS One

Challenges and advances towards the rational design of mRNA vaccines

(2013) Charlotte Pollard et al.   TRENDS IN MOLECULAR MEDICINE

T-cell epitope vaccine design by immunoinformatics

(2013) A. Patronov et al.   Open Biology

Expression of therapeutic proteins after delivery of chemically modified mRNA in mice

(2011) Michael S D Kormann et al.   NATURE BIOTECHNOLOGY

PAComplex: a web server to infer peptide antigen families and binding models from TCR–pMHC complexes

(2011) I-Hsin Liu et al.   NUCLEIC ACIDS RESEARCH

EPSVR and EPMeta: prediction of antigenic epitopes using support vector regression and multiple server results

(2010) Shide Liang et al.   BMC BIOINFORMATICS

An in vitro-transcribed-mRNA polyepitope construct encoding 32 distinct HLA class I-restricted epitopes from CMV, EBV, and Influenza for use as a functional control in human immune monitoring studies

(2010) Julie S. Nielsen et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior

(2009) Yohan Kim et al.   BMC BIOINFORMATICS

Prediction of antigenic epitopes on protein surfaces by consensus scoring

(2009) Shide Liang et al.   BMC BIOINFORMATICS

SEPPA: a computational server for spatial epitope prediction of protein antigens

(2009) Jing Sun et al.   NUCLEIC ACIDS RESEARCH

Epitope-based vaccination against pneumonic tularemia

(2009) Stephen H. Gregory et al.   VACCINE

PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

(2008) Michael J. Sweredoski et al.   BIOINFORMATICS

A machine-learning approach for predicting B-cell epitopes

(2008) Nimrod D. Rubinstein et al.   MOLECULAR IMMUNOLOGY

COBEpro: a novel system for predicting continuous B-cell epitopes

(2008) Michael J. Sweredoski et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Prediction of pertussis vaccine efficacy using a correlates of protection model

(2008) Robert C. Kohberger et al.   VACCINE