A5088261794- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- vaccines and immunoinformatics approaches
- Semantic Web and Ontologies
- Myasthenia Gravis and Thymoma
- Immunotherapy and Immune Responses
- Computational Drug Discovery Methods
- Monoclonal and Polyclonal Antibodies Research
- HIV Research and Treatment
- Immune Response and Inflammation
- Genomics and Rare Diseases
- HER2/EGFR in Cancer Research
- interferon and immune responses
- Machine Learning in Bioinformatics
- Influenza Virus Research Studies
- Reproductive Health and Contraception
- Immunodeficiency and Autoimmune Disorders
- Glycosylation and Glycoproteins Research
- Hepatitis C virus research
- Cell Image Analysis Techniques
- Virus-based gene therapy research
- Protein Tyrosine Phosphatases
- Chemokine receptors and signaling
The University of Texas MD Anderson Cancer Center
2024-2025
Impact Technology Development (United States)
2024
Duke University
2009-2023
National Institute of Environmental Health Sciences
2022-2023
Fred Hutch Cancer Center
2018
University of Washington
2018
Zhongnan Hospital of Wuhan University
2018
Wuhan University
2018
Duke Medical Center
2009-2016
Georgetown University
2013
The Cell Ontology (CL) is an ontology for the representation of in vivo cell types. As biological ontologies such as CL grow complexity, they become increasingly difficult to use and maintain. By making information computable, we can automated reasoners detect errors assist with classification. Here report on generation computable definitions hematopoietic types CL. Computable over 340 classes have been created using a genus-differentia approach. These define according multiple axes...
Abstract Tumor-associated myeloid cells regulate tumor growth and metastasis, their accumulation is a negative prognostic factor for breast cancer. Here we find calcium/calmodulin-dependent kinase (CaMKK2) to be highly expressed within intratumoral in mouse models of cancer, demonstrate that its inhibition suppresses by increasing effector CD8 + T immune-stimulatory subsets. macrophages (TAMs) isolated from Camkk2 −/− mice higher levels chemokines involved the recruitment compared WT....
The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms interrelations. represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence modification metaclasses, there is a separate metaclass for complexes. All metaclasses also have organism-specific derivatives. complements established databases such as UniProtKB, interoperates with other biomedical...
Abstract The Human BioMolecular Atlas Program (HuBMAP) aims to construct a 3D Reference (HRA) of the healthy adult body. Experts from 20+ consortia collaborate develop Common Coordinate Framework (CCF), knowledge graphs and tools that describe multiscale structure human body (from organs tissues down cells, genes biomarkers) use HRA characterize changes occur with aging, disease other perturbations. v.2.0 covers 4,499 unique anatomical structures, 1,195 cell types 2,089 biomarkers (such as...
Immune parameters were analyzed in peripheral blood mononuclear cells (PBMC) and cervical mucosa biopsy specimens of human immunodeficiency virus (HIV)—seronegative women sexually exposed to HIV (exposed seronegative [ESN]), HIV-infected women, healthy without exposure. was not detected PBMC or ESN women. However, interleukin (IL)—6, IL-10, IL-12, interferon (IFN)—γ, tumor necrosis factor (TNF)—α —β mRNA elevated women; CCR5 CXCR4 augmented specimens, but PBMC, HIV-speciflc IFN-γ—secreting...
Biobanking necessitates extensive integration of data to allow analysis and specimen sharing. Ontologies have been demonstrated be a promising approach in fostering better semantic biobank-related data. Hitherto no ontology provided the coverage needed capture broad spectrum biobank user scenarios.Based principles laid out by Open Biological Biomedical Foundry two biobanking ontologies developed. These were merged using modular consistent with initial development principles. The merging was...
Abstract Background The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 2012 have resulted in a series major global public health crises. We argue that interest developing effective safe vaccines drugs to better understand coronaviruses associated disease mechenisms it is necessary integrate large exponentially growing body heterogeneous coronavirus data. Ontologies play an important role standard-based knowledge data representation, integration, sharing, analysis....
Abstract The ability of the envelope glycoprotein gp120 [human immunodeficiency virus (HIV) env] to induce intracellular signals is thought contribute HIV-1 pathogenesis. In present study, we found that exposure CD4+ CD45RA+ naive T cells HIVenv results in a long-lasting hyporesponsiveness antigen stimulation. This phenomenon not dependent on CD4-mediated and also can be generated by cell soluble CD4-HIVenv complexes. analysis proximal signaling reveals does activate Lck as well...
Immature dendritic cells (iDCs) can be instructed to polarize the immune response toward a noninflammatory pathway by mediators that increase intracellular concentration of cAMP. This phenomenon is associated with ability cyclic nucleoside inhibit release pro-inflammatory cytokines without affecting differentiation process (DCs). Here we investigated cAMP modulate endotoxin signaling exposing DCs exogenous 8-bromium-cyclic AMP in presence or absence H89, selective inhibitor protein kinase A,...
Abstract Background Recent increases in the volume and diversity of life science data information an increasing emphasis on sharing interoperability have resulted creation a large number biological ontologies, including Cell Ontology (CL), designed to provide standardized representation cell types for annotation. Ontologies been shown significant benefits computational analyses sets automated reasoning applications, leading organized attempts improve structure formal rigor ontologies better...
The Toll-like receptors represent a largely evolutionarily conserved pathogen recognition machinery responsible for of bacterial, fungal, protozoan, and viral associated microbial patterns initiation inflammatory response. Structurally the are comprised an extracellular leucine rich repeat domain cytoplasmic Toll/Interleukin 1 receptor domain. Recognition takes place in where as triggers complex signal network required to sustain appropriate immune Signal transduction is regulated by...
Statistics play a critical role in biological and clinical research. However, most reports of scientific results the published literature make it difficult for reader to reproduce statistical analyses performed achieving those because they provide inadequate documentation tests algorithms applied. The Ontology Biological Clinical (OBCS) is put forward here as step towards solving this problem. terms OBCS including 'data collection', transformation statistics', visualization', 'statistical...
Background HIV-1 Protease Inhibitors, namely PIs, originally designed to inhibit aspartic protease, can modulate the immune response by mechanisms largely unknown, and independent from their activity on viral replication. Here, we analyzed ability of PIs interfere with differentiation program monocytes toward dendritic cell (DCs) lineage, a key process in inflammatory response. Methodology/Principal Findings Monocytes healthy donors were isolated induced differentiate vitro presence or...
Thymomas are rare tumours that sustain T-lymphopoiesis and trigger a variety of autoimmune diseases immunodeficiencies, including fatal hypogammaglobulinemia, namely Good's Syndrome (GS). Due to its rarity, GS has been poorly investigated immunological features, as well pathogenetic mechanisms underlying this syndrome, unclear. We studied 30 thymoma patients by performing an assessment, immunophenotype analysis T cell repertoire (TCR). Development was characterized progressive decrease in B,...
The exploration of cancer vaccines has yielded a multitude studies, resulting in diverse collection information. heterogeneity vaccine data significantly impedes effective integration and analysis. While CanVaxKB serves as pioneering database for over 670 manually annotated vaccines, it is important to distinguish that database, on its own, does not offer the structured relationships standardized definitions found an ontology. Recognizing this, we expanded Vaccine Ontology (VO) include those...
Small changes in the complex between a peptide and molecule of major histocompatibility generate ligands able to partially activate (partial agonist) or even inhibit (antagonist) T-cell functions. receptor engagement antagonist results partial zeta chain phosphorylation without activation associated ZAP-70 kinase. Herein we show that, despite strong inhibition both inositol phospholipid hydrolysis extracellular increasing concentrations increased activity CD4-Lck Addition anti-CD4 antibody...
Vaccines stimulate various immune factors critical to protective responses. However, a comprehensive picture of vaccine-induced and pathways have not been systematically collected analyzed. To address this issue, we developed VaximmutorDB, web-based database system vaccine (abbreviated as “vaximmutors”) manually curated from peer-reviewed articles. VaximmutorDB currently stores 1,740 13 host species (e.g., human, mouse, pig). These vaximmutors were induced by 154 vaccines for 46 pathogens....
Abstract Seven years after a surgically resected thymoma, female patient affected by myasthenia gravis and Good's syndrome presented with paroxysmal nocturnal hemoglobinuria (PNH). Co‐culture experiments spectratyping analyses indicated that CD8+ lymphocytes were involved in damaging hematopoietic precursors. While PNH clones have been identified various hematological disorders, the sequential association of thymoma has unreported so far. Am. J. Hematol., 2006. © 2006 Wiley‐Liss, Inc.
Abstract Background With COVID-19 still in its pandemic stage, extensive research has generated increasing amounts of data and knowledge. As many studies are published within a short span time, we often lose an integrative comprehensive picture host-coronavirus interaction (HCI) mechanisms. early April 2021, the ImmPort database stored 7 (with 6 having details) that cover topics including molecular immune signatures, epitopes, sex differences terms mortality patients. The Coronavirus...
Abstract Background Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and associated with several diseases. Extensive HMI studies have generated large amounts data. We propose that logical representation knowledge derived from these data standardized experimental variables can foster integration reproducibility experiments thereby further discovery. Methods Through a multi-institutional collaboration, community-based Ontology Host-Microbiome...