Anthony Huffman
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SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis Open
With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-suppo…
View article: SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis
SEA CDM: Study-Experiment-Assay Common Data Model and Databases for Cross-Domain Data Integration and Analysis Open
With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-suppo…
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: Immune Biomarkers, Profiles, and Responses: A Vaccine Ontology Perspective
Immune Biomarkers, Profiles, and Responses: A Vaccine Ontology Perspective Open
Background Vaccines have the ability to induce a range of immune responses under different conditions, for example stimulating the production of neutralizing antibodies to block pathogen entry or activating cytotoxic T-cells to eliminate i…
Systematic collection, annotation, and pattern analysis of viral vaccines in the VIOLIN vaccine knowledgebase Open
Background Viral vaccines have been proven significant in protecting us against viral diseases such as COVID-19. To better understand and design viral vaccines, it is critical to systematically collect, annotate, and analyse various viral …
Dietary cinnamon promotes longevity and extends healthspan via mTORC1 and autophagy signaling Open
Cinnamon, renowned for its aromatic flavor, represents one of the most widely used spices worldwide. Cinnamon is also considered beneficial to human health with therapeutic potential for treating various diseases, ranging from diabetes and…
Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis Open
Background The exploration of cancer vaccines has yielded a multitude of studies, resulting in a diverse collection of information. The heterogeneity of cancer vaccine data significantly impedes effective integration and analysis. While Ca…
Grounding Realizable Entities Open
Ontological representations of qualities, dispositions, and roles have been refined over the past decade, clarifying subtle distinctions in life science research. After articulating a widely-used characterization of these entities within t…
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 …
CanVaxKB: A Web-based Cancer Vaccine Knowledgebase Open
CanVaxKB is a web-based cancer vaccine knowledgebase. CanVaxKB collects, annotates and analyzes various types of cancer vaccines around the world. Currently it contains all cancer vaccines stored in the VIOLIN vaccine database. CanVaxKB al…
CanVaxKB: A Web-based Cancer Vaccine Knowledgebase Open
CanVaxKB is a web-based cancer vaccine knowledgebase. CanVaxKB collects, annotates and analyzes various types of cancer vaccines around the world. Currently it contains all cancer vaccines stored in the VIOLIN vaccine database. CanVaxKB al…
Grounding Realizable Entities in Applied Ontologies Open
Ontological representations of qualities, dispositions, and roles have been refined over the past decade, clarifying subtle distinctions in life science research. There is, however, more refinement to be done, in particular, on characteriz…
Vaxign-DL: A Deep Learning-based Method for Vaccine Design and its Evaluation Open
Reverse vaccinology (RV) provides a systematic approach to identifying potential vaccine candidates based on protein sequences. The integration of machine learning (ML) into this process has greatly enhanced our ability to predict viable v…
View article: VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data Open
Host responses to vaccines are complex but important to investigate. To facilitate the study, we have developed a tool called Vaccine Induced Gene Expression Analysis Tool (VIGET), with the aim to provide an interactive online tool for use…
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: VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data Open
Host responses to vaccines are complex but important to investigate. To facilitate the study, we have developed a tool called Vaccine Induced Gene Expression Analysis Tool (VIGET), with the aim to provide an interactive online tool for use…
VIGET: A web portal for study of vaccine-induced host responses based on Reactome pathways and ImmPort data Open
Host responses to vaccines are complex but important to investigate. To facilitate the study, we have developed a tool called Vaccine Induced Gene Expression Analysis Tool (VIGET), with the aim to provide an interactive online tool for use…
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: 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: 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: Ontology-based systematic classification and analysis of coronaviruses, hosts, and host-coronavirus interactions towards deep understanding of COVID-19
Ontology-based systematic classification and analysis of coronaviruses, hosts, and host-coronavirus interactions towards deep understanding of COVID-19 Open
Given the existing COVID-19 pandemic worldwide, it is critical to systematically study the interactions between hosts and coronaviruses including SARS-Cov, MERS-Cov, and SARS-CoV-2 (cause of COVID-19). We first created four host-pathogen i…