Edison Ong
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View article: Design and preclinical assessment of mRNA-1345 prefusion F glycoprotein-encoding mRNA vaccine for respiratory syncytial virus
Design and preclinical assessment of mRNA-1345 prefusion F glycoprotein-encoding mRNA vaccine for respiratory syncytial virus Open
Respiratory syncytial virus (RSV) is a significant cause of lower respiratory tract disease in young children and older adults. We designed a codon-optimized mRNA vaccine, mRNA-1345, encoding the RSV F-glycoprotein stabilized in the prefus…
View article: VO: The Vaccine Ontology
VO: The Vaccine Ontology Open
With the widespread use of vaccines in research and clinical settings, there is an urgent need to standardize vaccine representation, integrate information across diverse vaccine types, and support computer-assisted reasoning. Accordingly,…
View article: An assessment of Croissant ML metadata descriptors for AI-ready datasets
An assessment of Croissant ML metadata descriptors for AI-ready datasets Open
To advance the use of machine learning to address humanity’s grand challenges such as the understanding of disease conditions and biodiversity loss in the anthropocene, it is important to promote FAIR AI-ready datasets, since data scientis…
View article: Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors
Spatial transcriptomics identifies novel Pseudomonas aeruginosa virulence factors Open
To examine host-pathogen interactions, we leveraged a dual spatial transcriptomics approach that simultaneously captures the expression of Pseudomonas aeruginosa genes alongside the entire host transcriptome using a murine model of ocular …
View article: Design and preclinical assessment of mRNA-1345 prefusion F glycoprotein-encoding mRNA vaccine for respiratory syncytial virus
Design and preclinical assessment of mRNA-1345 prefusion F glycoprotein-encoding mRNA vaccine for respiratory syncytial virus Open
Respiratory syncytial virus (RSV) is a significant cause of lower respiratory tract disease in young children and older adults. We designed a codon optimized mRNA vaccine, mRNA-1345, that encodes the RSV F-glycoprotein stabilized in the pr…
View article: Spatial transcriptomics identifies novel<i>Pseudomonas aeruginosa</i>virulence factors
Spatial transcriptomics identifies novel<i>Pseudomonas aeruginosa</i>virulence factors Open
To holistically unravel the complexity of pathogen-host interactions within infected tissues we leverage a dual spatial transcriptomic approach that, for the first time, simultaneously captures the expression of Pseudomonas aeruginosa gene…
View article: CanVaxKB: a web-based cancer vaccine knowledgebase
CanVaxKB: a web-based cancer vaccine knowledgebase Open
Cancer vaccines have been increasingly studied and developed to prevent or treat various types of cancers. To systematically survey and analyze different reported cancer vaccines, we developed CanVaxKB (https://violinet.org/canvaxkb), the …
View article: mtx-COBRA: Subcellular localization prediction for bacterial proteins
mtx-COBRA: Subcellular localization prediction for bacterial proteins Open
Background Bacteria can have beneficial effects on our health and environment; however, many are responsible for serious infectious diseases, warranting the need for vaccines against such pathogens. Bioinformatic and experimental technolog…
View article: Ontology-based representation and analysis of conditional vaccine immune responses using Omics data.
Ontology-based representation and analysis of conditional vaccine immune responses using Omics data. Open
ImmPort, the world's largest repository of immunology data, includes many vaccine immune response datasets. ImmPort maps the metadata of these studies to ontology and database schema. As of February 28, 2023, our ImmPort data analysis iden…
View article: A new framework for host-pathogen interaction research
A new framework for host-pathogen interaction research Open
COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose…
View article: COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning
COVID-19 vaccine design using reverse and structural vaccinology, ontology-based literature mining and machine learning Open
Rational vaccine design, especially vaccine antigen identification and optimization, is critical to successful and efficient vaccine development against various infectious diseases including coronavirus disease 2019 (COVID-19). In general,…
View article: Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology
Additional file 4 of A comprehensive update on CIDO: the community-based coronavirus infectious disease ontology Open
Additional file 4: Supplemental Table 3. Protein Ontology representation of SARS-CoV-2 proteins. Comparative information in RefSeq and UniProtKB is also provided.
View article: Identification of Mycobacterium tuberculosis Antigens with Vaccine Potential Using a Machine Learning-Based Reverse Vaccinology Approach
Identification of Mycobacterium tuberculosis Antigens with Vaccine Potential Using a Machine Learning-Based Reverse Vaccinology Approach Open
Tuberculosis (TB) is the leading cause of death of any single infectious agent, having led to 1.4 million deaths in 2019 alone. Moreover, an estimated one-quarter of the global population is latently infected with Mycobacterium tuberculosi…
View article: Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning
Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning Open
Vaccination is one of the most significant inventions in medicine. Reverse vaccinology (RV) is a state-of-the-art technique to predict vaccine candidates from pathogen's genome(s). To promote vaccine development, we updated Vaxign2, the fi…
View article: VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms
VaximmutorDB: A Web-Based Vaccine Immune Factor Database and Its Application for Understanding Vaccine-Induced Immune Mechanisms Open
Vaccines stimulate various immune factors critical to protective immune responses. However, a comprehensive picture of vaccine-induced immune factors and pathways have not been systematically collected and analyzed. To address this issue, …
View article: Reverse Microbiomics: A New Reverse Dysbiosis Analysis Strategy and Its Usage in Prediction of Autoantigens and Virulent Factors in Dysbiotic Gut Microbiomes From Rheumatoid Arthritis Patients
Reverse Microbiomics: A New Reverse Dysbiosis Analysis Strategy and Its Usage in Prediction of Autoantigens and Virulent Factors in Dysbiotic Gut Microbiomes From Rheumatoid Arthritis Patients Open
Alterations in the gut microbiome have been associated with various human diseases. Most existing gut microbiome studies stopped at the stage of identifying microbial alterations between diseased or healthy conditions. As inspired by rever…
View article: Rational Vaccine Design by Reverse & Structural Vaccinology and Ontology
Rational Vaccine Design by Reverse & Structural Vaccinology and Ontology Open
Vaccination is one of the most successful public health interventions in modern medicine. However, it is still challenging to develop effective vaccines against many infectious diseases such as tuberculosis, HIV, and malaria. There are cha…
View article: Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering
Computational design of SARS-CoV-2 spike glycoproteins to increase immunogenicity by T cell epitope engineering Open
The development of effective and safe vaccines is the ultimate way to efficiently stop the ongoing COVID-19 pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Built on the fact that SARS-CoV-2 utiliz…
View article: Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering
Rational Design of SARS-CoV-2 Spike Glycoproteins To Increase Immunogenicity By T Cell Epitope Engineering Open
The current COVID-19 pandemic caused by SARS-CoV-2 has resulted in millions of confirmed cases and thousands of deaths globally. Extensive efforts and progress have been made to develop effective and safe vaccines against COVID-19. A prima…
View article: COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning
COVID-19 Coronavirus Vaccine Design Using Reverse Vaccinology and Machine Learning Open
To ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that t…
View article: Improvement in the Analysis of Vaccine Adverse Event Reporting System Database
Improvement in the Analysis of Vaccine Adverse Event Reporting System Database Open
As a national public health surveillance resource, Vaccine Adverse Event Reporting System (VAERS) is a key component in ensuring the safety of vaccines. Numerous methods have been used to conduct safety studies with the VAERS database. The…
View article: COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning
COVID-19 coronavirus vaccine design using reverse vaccinology and machine learning Open
To ultimately combat the emerging COVID-19 pandemic, it is desired to develop an effective and safe vaccine against this highly contagious disease caused by the SARS-CoV-2 coronavirus. Our literature and clinical trial survey showed that t…
View article: Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens
Vaxign-ML: supervised machine learning reverse vaccinology model for improved prediction of bacterial protective antigens Open
Motivation Reverse vaccinology (RV) is a milestone in rational vaccine design, and machine learning (ML) has been applied to enhance the accuracy of RV prediction. However, ML-based RV still faces challenges in prediction accuracy and prog…
View article: Improvement in the Analysis of Vaccine Adverse Event Reporting System Database
Improvement in the Analysis of Vaccine Adverse Event Reporting System Database Open
As a national public health surveillance resource, Vaccine Adverse Event Reporting System (VAERS) is a key component in ensuring the safety of vaccines. Numerous methods have been used to conduct safety studies with the VAERS database. The…