Research graph
References from AI-guided epitope engineering of a SARS-CoV-2 spike antigen for broad sarbecovirus neutralization. Local targets link to admitted publications; unresolved targets remain external evidence.
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
10.1126/science.abp8337 · 2022 · External reference
The origins of SARS-CoV-2: A critical review
10.1016/j.cell.2021.08.017 · 2021 · External reference
Developing safe and effective Covid vaccines — Operation Warp Speed’s strategy and approach
10.1056/nejmp2027405 · 2020 · External reference
Warp Speed” operations in the COVID-19 pandemic
10.1016/j.jacbts.2020.06.001 · 2020 · External reference
mRNA and adenoviral vector vaccine platforms utilized in COVID-19 vaccines: Technologies, ecosystem, and future directions
10.3390/vaccines11121737 · 2023 · External reference
COVID-19 mRNA vaccines: Platforms and current developments
10.1016/j.ymthe.2022.02.016 · 2022 · External reference
Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine
10.1056/nejmoa2034577 · 2020 · External reference
Challenges to the effectiveness and immunogenicity of COVID-19 vaccines: A narrative review with a systematic approach
10.3390/vaccines13080789 · 2025 · External reference
Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population
10.1038/s41591-023-02219-5 · 2023 · External reference
Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies
10.1039/d1cc01747k · 2021 · External reference
SARS-CoV-2 variants, spike mutations and immune escape
10.1038/s41579-021-00573-0 · 2021 · External reference
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
10.1016/j.cell.2020.09.037 · 2020 · External reference
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
10.1038/s41586-021-04385-3 · 2022 · External reference
Comparative analysis of antibody titers against the spike protein of SARS-CoV-2 variants in infected patient cohorts and diverse vaccination regimes
10.3390/ijms232012231 · 2022 · External reference
The Batalogue: An overview of betacoronaviruses with future pandemic potential
10.1093/femsre/fuaf023 · 2025 · External reference
Origin and evolution of pathogenic coronaviruses
10.1038/s41579-018-0118-9 · 2019 · External reference
Beyond the pandemic era: Recent advances and efficacy of SARS-CoV-2 vaccines against emerging variants of concern
10.3390/vaccines13040424 · 2025 · External reference
Effect of antigenic drift on influenza vaccine effectiveness in the United States—2019–2020
10.1093/cid/ciaa1884 · 2021 · External reference
Influenza vaccine strain selection with an AI-based evolutionary and antigenicity model
10.1038/s41591-025-03917-y · 2025 · External reference
Original SARS-CoV-2 monovalent and Omicron BA.4/BA.5 bivalent COVID-19 mRNA vaccines: Phase 2/3 trial interim results
10.1038/s41591-023-02517-y · 2023 · External reference
Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant in mice
10.1038/s41591-022-02092-8 · 2023 · External reference
Broad-spectrum Delta-BA. 2 tandem-fused heterodimer mRNA vaccine delivered by lipopolyplex
10.1371/journal.ppat.1012116 · 2024 · External reference
Toward a pan-SARS-CoV-2 vaccine targeting conserved epitopes on spike and non-spike proteins for potent, broad and durable immune responses
10.1371/journal.ppat.1010870 · 2023 · External reference
Broad-spectrum coronavirus vaccines: Integrated strategies to combat viral diversity
10.1080/14760584.2025.2538561 · 2025 · External reference
SARS-CoV-2 pandemic: Not the first, not the last
10.3390/microorganisms9020433 · 2021 · External reference
Emerging pandemic diseases: How we got to COVID-19
10.1016/j.cell.2020.08.021 · 2020 · External reference
Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting
10.1016/j.celrep.2022.110561 · 2022 · External reference
Pan-variant SARS-CoV-2 vaccines induce protective immunity by targeting conserved epitopes
10.1002/advs.202409919 · 2025 · External reference
Deep learning of antibody epitopes using positional permutation vectors
10.1016/j.csbj.2024.06.005 · 2024 · External reference
Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models
10.1126/science.abq0839 · 2022 · External reference
Designed mosaic nanoparticles enhance cross-reactive immune responses in mice
10.1016/j.cell.2024.12.015 · 2025 · External reference
Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals
10.1016/j.cell.2024.07.052 · 2024 · External reference
A spike virosome vaccine induces pan-sarbecovirus antibody responses in mice
10.1016/j.isci.2024.109719 · 2024 · External reference
Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses
10.1038/s41565-024-01655-9 · 2024 · External reference
Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice
10.1126/science.abi4506 · 2021 · External reference
Broad-spectrum vaccines against various and evolving viruses: From antigen design to nanoparticle delivery
10.1128/jvi.00997-25 · 2025 · External reference
Chimeric hemagglutinin split vaccines elicit broadly cross-reactive antibodies and protection against group 2 influenza viruses in mice
10.1126/sciadv.adi4753 · 2023 · External reference
Rational design of an influenza-COVID-19 chimeric protective vaccine with HA-stalk and S-RBD
10.1080/22221751.2023.2231573 · 2023 · External reference
Multivalent mRNA vaccine elicits broad protection against SARS-CoV-2 variants of concern
10.3390/vaccines12070714 · 2024 · External reference
Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses
10.1016/j.celrep.2020.108666 · 2024 · External reference
The immunodominant and neutralization linear epitopes for SARS-CoV-2
10.1101/2020.08.27.267716 · 2021 · External reference
Computationally designed Spike antigens induce neutralising responses against the breadth of SARS-CoV-2 variants
10.1038/s41541-024-00950-9 · 2024 · External reference
De novo protein design enables the precise induction of RSV-neutralizing antibodies
10.1126/science.aay5051 · 2020 · External reference
Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein
10.1016/j.cell.2020.02.058 · 2020 · External reference
Controlling the SARS-CoV-2 spike glycoprotein conformation
10.1038/s41594-020-0479-4 · 2020 · External reference
Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike
10.7554/elife.75433 · 2022 · External reference
Understanding the implications of delaying seasonal influenza vaccine recommendations: An industry perspective
10.3390/vaccines13090891 · 2025 · External reference
SARS-CoV-2 XBB.1.5 mRNA booster vaccination elicits limited mucosal immunity
10.1126/scitranslmed.adp8920 · 2026 · External reference
Insufficient anti-spike RBD IgA responses after triple vaccination with intramuscular mRNA BNT162b2 vaccine against SARS-CoV-2
10.1016/j.heliyon.2023.e23595 · 2024 · External reference
Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection
10.1038/s41591-021-01377-8 · 2021 · External reference
Evidence for antibody as a protective correlate for COVID-19 vaccines
10.1016/j.vaccine.2021.05.063 · 2021 · External reference
Unadjuvanted intranasal spike vaccine elicits protective mucosal immunity against sarbecoviruses
10.1126/science.abo2523 · 2026 · External reference
Protein Data Bank: the single global archive for 3D macromolecular structure data
10.1093/nar/gky949 · 2019 · External reference
Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein
10.1038/s41594-023-01023-6 · 2023 · External reference
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
10.1038/nmeth0809-551 · 2009 · External reference
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency
10.1093/bib/bbad486 · 2024 · External reference
The Rosetta all-atom energy function for macromolecular modeling and design
10.1021/acs.jctc.7b00125 · 2017 · External reference
Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules
10.1021/acs.jctc.6b00819 · 2016 · External reference
A Pareto-optimal refinement method for protein design scaffolds
10.1371/journal.pone.0059004 · 2013 · External reference
Relaxation of backbone bond geometry improves protein energy landscape modeling
10.1002/pro.2389 · 2014 · External reference
Potent cross-reactive antibodies following Omicron breakthrough in vaccinees
10.1016/j.cell.2022.05.014 · 2022 · External reference
PROPKA3: consistent treatment of internal and surface residues in empirical p K a predictions
10.1021/ct100578z · 2011 · External reference
Vulnerabilities in coronavirus glycan shields despite extensive glycosylation
10.1038/s41467-020-16567-0 · 2020 · External reference
GROMACS: Fast, flexible, and free
10.1002/jcc.20291 · 2005 · External reference
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB
10.1021/acs.jctc.5b00255 · 2015 · External reference
GLYCAM06: A generalizable biomolecular force field. Carbohydrates
10.1002/jcc.20820 · 2008 · External reference
Comparison of simple potential functions for simulating liquid water
10.1063/1.445869 · 1983 · External reference
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
10.1063/1.464397 · 1993 · External reference
Crystal structure and pair potentials: A molecular-dynamics study
10.1103/physrevlett.45.1196 · 1980 · External reference
Polymorphic transitions in single crystals: A new molecular dynamics method
10.1063/1.328693 · 1981 · External reference
LINCS: A linear constraint solver for molecular simulations
10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h · 1997 · External reference
ProDy: protein dynamics inferred from theory and experiments
10.1093/bioinformatics/btr168 · 2011 · External reference
Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity
10.1093/molbev/msz102 · 2019 · External reference
Anisotropy of fluctuation dynamics of proteins with an elastic network model
10.1016/s0006-3495(01)76033-x · 2001 · External reference
Anisotropic network model: systematic evaluation and a new web interface
10.1093/bioinformatics/btl448 · 2006 · External reference
ATPase subdomain IA is a mediator of interdomain allostery in hsp70 molecular chaperones
10.1371/journal.pcbi.1003624 · 2014 · External reference
Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein
10.1371/journal.pcbi.1000544 · 2009 · External reference
Improvements to the APBS biomolecular solvation software suite
10.1002/pro.3280 · 2018 · External reference
PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
10.1093/nar/gkh381 · 2004 · External reference
Accurate calculation of hydration free energies using macroscopic solvent models
10.1021/j100058a043 · 1994 · External reference
LINCS: A linear constraint solver for molecular simulations
10.1002/(sici)1096-987x(199709)18:12<1463::aid-jcc4>3.0.co;2-h · ExternalCitation · doi-reference
Pan-variant SARS-CoV-2 vaccines induce protective immunity by targeting conserved epitopes
10.1002/advs.202409919 · ExternalCitation · doi-reference
GROMACS: Fast, flexible, and free
10.1002/jcc.20291 · ExternalCitation · doi-reference
GLYCAM06: A generalizable biomolecular force field. Carbohydrates
10.1002/jcc.20820 · ExternalCitation · doi-reference
Relaxation of backbone bond geometry improves protein energy landscape modeling
10.1002/pro.2389 · ExternalCitation · doi-reference
Improvements to the APBS biomolecular solvation software suite
10.1002/pro.3280 · ExternalCitation · doi-reference
Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein
10.1016/j.cell.2020.02.058 · ExternalCitation · doi-reference
Emerging pandemic diseases: How we got to COVID-19
10.1016/j.cell.2020.08.021 · ExternalCitation · doi-reference
Mapping neutralizing and immunodominant sites on the SARS-CoV-2 spike receptor-binding domain by structure-guided high-resolution serology
10.1016/j.cell.2020.09.037 · ExternalCitation · doi-reference
The origins of SARS-CoV-2: A critical review
10.1016/j.cell.2021.08.017 · ExternalCitation · doi-reference
Potent cross-reactive antibodies following Omicron breakthrough in vaccinees
10.1016/j.cell.2022.05.014 · ExternalCitation · doi-reference
Mosaic sarbecovirus nanoparticles elicit cross-reactive responses in pre-vaccinated animals
10.1016/j.cell.2024.07.052 · ExternalCitation · doi-reference
Designed mosaic nanoparticles enhance cross-reactive immune responses in mice
10.1016/j.cell.2024.12.015 · ExternalCitation · doi-reference
Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses
10.1016/j.celrep.2020.108666 · ExternalCitation · doi-reference
Rationally designed immunogens enable immune focusing following SARS-CoV-2 spike imprinting
10.1016/j.celrep.2022.110561 · ExternalCitation · doi-reference
Deep learning of antibody epitopes using positional permutation vectors
10.1016/j.csbj.2024.06.005 · ExternalCitation · doi-reference
Insufficient anti-spike RBD IgA responses after triple vaccination with intramuscular mRNA BNT162b2 vaccine against SARS-CoV-2
10.1016/j.heliyon.2023.e23595 · ExternalCitation · doi-reference
A spike virosome vaccine induces pan-sarbecovirus antibody responses in mice
10.1016/j.isci.2024.109719 · ExternalCitation · doi-reference
Warp Speed” operations in the COVID-19 pandemic
10.1016/j.jacbts.2020.06.001 · ExternalCitation · doi-reference
Evidence for antibody as a protective correlate for COVID-19 vaccines
10.1016/j.vaccine.2021.05.063 · ExternalCitation · doi-reference
COVID-19 mRNA vaccines: Platforms and current developments
10.1016/j.ymthe.2022.02.016 · ExternalCitation · doi-reference
Anisotropy of fluctuation dynamics of proteins with an elastic network model
10.1016/s0006-3495(01)76033-x · ExternalCitation · doi-reference
ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB
10.1021/acs.jctc.5b00255 · ExternalCitation · doi-reference
Simultaneous optimization of biomolecular energy functions on features from small molecules and macromolecules
10.1021/acs.jctc.6b00819 · ExternalCitation · doi-reference
The Rosetta all-atom energy function for macromolecular modeling and design
10.1021/acs.jctc.7b00125 · ExternalCitation · doi-reference
PROPKA3: consistent treatment of internal and surface residues in empirical p K a predictions
10.1021/ct100578z · ExternalCitation · doi-reference
Accurate calculation of hydration free energies using macroscopic solvent models
10.1021/j100058a043 · ExternalCitation · doi-reference
Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling
10.1038/nmeth0809-551 · ExternalCitation · doi-reference
Vulnerabilities in coronavirus glycan shields despite extensive glycosylation
10.1038/s41467-020-16567-0 · ExternalCitation · doi-reference
Computationally designed Spike antigens induce neutralising responses against the breadth of SARS-CoV-2 variants
10.1038/s41541-024-00950-9 · ExternalCitation · doi-reference
Proactive vaccination using multiviral Quartet Nanocages to elicit broad anti-coronavirus responses
10.1038/s41565-024-01655-9 · ExternalCitation · doi-reference
Origin and evolution of pathogenic coronaviruses
10.1038/s41579-018-0118-9 · ExternalCitation · doi-reference
SARS-CoV-2 variants, spike mutations and immune escape
10.1038/s41579-021-00573-0 · ExternalCitation · doi-reference
Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies
10.1038/s41586-021-04385-3 · ExternalCitation · doi-reference
Neutralizing antibody levels are highly predictive of immune protection from symptomatic SARS-CoV-2 infection
10.1038/s41591-021-01377-8 · ExternalCitation · doi-reference
Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant in mice
10.1038/s41591-022-02092-8 · ExternalCitation · doi-reference
Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population
10.1038/s41591-023-02219-5 · ExternalCitation · doi-reference
Original SARS-CoV-2 monovalent and Omicron BA.4/BA.5 bivalent COVID-19 mRNA vaccines: Phase 2/3 trial interim results
10.1038/s41591-023-02517-y · ExternalCitation · doi-reference
Influenza vaccine strain selection with an AI-based evolutionary and antigenicity model
10.1038/s41591-025-03917-y · ExternalCitation · doi-reference
Controlling the SARS-CoV-2 spike glycoprotein conformation
10.1038/s41594-020-0479-4 · ExternalCitation · doi-reference
Structural and functional characteristics of the SARS-CoV-2 Omicron subvariant BA.2 spike protein
10.1038/s41594-023-01023-6 · ExternalCitation · doi-reference
Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies
10.1039/d1cc01747k · ExternalCitation · doi-reference
Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine
10.1056/nejmoa2034577 · ExternalCitation · doi-reference
Developing safe and effective Covid vaccines — Operation Warp Speed’s strategy and approach
10.1056/nejmp2027405 · ExternalCitation · doi-reference
Polymorphic transitions in single crystals: A new molecular dynamics method
10.1063/1.328693 · ExternalCitation · doi-reference
Comparison of simple potential functions for simulating liquid water
10.1063/1.445869 · ExternalCitation · doi-reference
Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems
10.1063/1.464397 · ExternalCitation · doi-reference
Broad-spectrum coronavirus vaccines: Integrated strategies to combat viral diversity
10.1080/14760584.2025.2538561 · ExternalCitation · doi-reference
Rational design of an influenza-COVID-19 chimeric protective vaccine with HA-stalk and S-RBD
10.1080/22221751.2023.2231573 · ExternalCitation · doi-reference
Comprehensive assessment of protein loop modeling programs on large-scale datasets: prediction accuracy and efficiency
10.1093/bib/bbad486 · ExternalCitation · doi-reference
Anisotropic network model: systematic evaluation and a new web interface
10.1093/bioinformatics/btl448 · ExternalCitation · doi-reference
ProDy: protein dynamics inferred from theory and experiments
10.1093/bioinformatics/btr168 · ExternalCitation · doi-reference
Effect of antigenic drift on influenza vaccine effectiveness in the United States—2019–2020
10.1093/cid/ciaa1884 · ExternalCitation · doi-reference
The Batalogue: An overview of betacoronaviruses with future pandemic potential
10.1093/femsre/fuaf023 · ExternalCitation · doi-reference
Shared signature dynamics tempered by local fluctuations enables fold adaptability and specificity
10.1093/molbev/msz102 · ExternalCitation · doi-reference
PDB2PQR: an automated pipeline for the setup of Poisson–Boltzmann electrostatics calculations
10.1093/nar/gkh381 · ExternalCitation · doi-reference
Protein Data Bank: the single global archive for 3D macromolecular structure data
10.1093/nar/gky949 · ExternalCitation · doi-reference
The immunodominant and neutralization linear epitopes for SARS-CoV-2
10.1101/2020.08.27.267716 · ExternalCitation · doi-reference
Crystal structure and pair potentials: A molecular-dynamics study
10.1103/physrevlett.45.1196 · ExternalCitation · doi-reference
Chimeric hemagglutinin split vaccines elicit broadly cross-reactive antibodies and protection against group 2 influenza viruses in mice
10.1126/sciadv.adi4753 · ExternalCitation · doi-reference
De novo protein design enables the precise induction of RSV-neutralizing antibodies
10.1126/science.aay5051 · ExternalCitation · doi-reference
Chimeric spike mRNA vaccines protect against Sarbecovirus challenge in mice
10.1126/science.abi4506 · ExternalCitation · doi-reference
Unadjuvanted intranasal spike vaccine elicits protective mucosal immunity against sarbecoviruses
10.1126/science.abo2523 · ExternalCitation · doi-reference
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2
10.1126/science.abp8337 · ExternalCitation · doi-reference
Mosaic RBD nanoparticles protect against challenge by diverse sarbecoviruses in animal models
10.1126/science.abq0839 · ExternalCitation · doi-reference
SARS-CoV-2 XBB.1.5 mRNA booster vaccination elicits limited mucosal immunity
10.1126/scitranslmed.adp8920 · ExternalCitation · doi-reference
Broad-spectrum vaccines against various and evolving viruses: From antigen design to nanoparticle delivery
10.1128/jvi.00997-25 · ExternalCitation · doi-reference
Perturbation-response scanning reveals ligand entry-exit mechanisms of ferric binding protein
10.1371/journal.pcbi.1000544 · ExternalCitation · doi-reference
ATPase subdomain IA is a mediator of interdomain allostery in hsp70 molecular chaperones
10.1371/journal.pcbi.1003624 · ExternalCitation · doi-reference
A Pareto-optimal refinement method for protein design scaffolds
10.1371/journal.pone.0059004 · ExternalCitation · doi-reference
Toward a pan-SARS-CoV-2 vaccine targeting conserved epitopes on spike and non-spike proteins for potent, broad and durable immune responses
10.1371/journal.ppat.1010870 · ExternalCitation · doi-reference
Broad-spectrum Delta-BA. 2 tandem-fused heterodimer mRNA vaccine delivered by lipopolyplex
10.1371/journal.ppat.1012116 · ExternalCitation · doi-reference
Comparative analysis of antibody titers against the spike protein of SARS-CoV-2 variants in infected patient cohorts and diverse vaccination regimes
10.3390/ijms232012231 · ExternalCitation · doi-reference
SARS-CoV-2 pandemic: Not the first, not the last
10.3390/microorganisms9020433 · ExternalCitation · doi-reference
mRNA and adenoviral vector vaccine platforms utilized in COVID-19 vaccines: Technologies, ecosystem, and future directions
10.3390/vaccines11121737 · ExternalCitation · doi-reference
Multivalent mRNA vaccine elicits broad protection against SARS-CoV-2 variants of concern
10.3390/vaccines12070714 · ExternalCitation · doi-reference
Beyond the pandemic era: Recent advances and efficacy of SARS-CoV-2 vaccines against emerging variants of concern
10.3390/vaccines13040424 · ExternalCitation · doi-reference
Challenges to the effectiveness and immunogenicity of COVID-19 vaccines: A narrative review with a systematic approach
10.3390/vaccines13080789 · ExternalCitation · doi-reference
Understanding the implications of delaying seasonal influenza vaccine recommendations: An industry perspective
10.3390/vaccines13090891 · ExternalCitation · doi-reference
Conformational dynamics and allosteric modulation of the SARS-CoV-2 spike
10.7554/elife.75433 · ExternalCitation · doi-reference
