AIMC Topic: HLA Antigens
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HLA-SPREAD: a natural language processing based resource for curating HLA association from PubMed abstracts.
BMC genomics
Jan 7, 2022
Extreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed searc...
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics.
Nature communications
Jun 7, 2021
Characterizing the human leukocyte antigen (HLA) bound ligandome by mass spectrometry (MS) holds great promise for developing vaccines and drugs for immune-oncology. Still, the identification of non-tryptic peptides presents substantial computational...
Improvement of Neoantigen Identification Through Convolution Neural Network.
Frontiers in immunology
May 25, 2021
Accurate prediction of neoantigens and the subsequent elicited protective anti-tumor response are particularly important for the development of cancer vaccine and adoptive T-cell therapy. However, current algorithms for predicting neoantigens are lim...
DeepNetBim: deep learning model for predicting HLA-epitope interactions based on network analysis by harnessing binding and immunogenicity information.
BMC bioinformatics
May 5, 2021
BACKGROUND: Epitope prediction is a useful approach in cancer immunology and immunotherapy. Many computational methods, including machine learning and network analysis, have been developed quickly for such purposes. However, regarding clinical applic...
A deep learning method for HLA imputation and trans-ethnic MHC fine-mapping of type 1 diabetes.
Nature communications
Mar 12, 2021
Conventional human leukocyte antigen (HLA) imputation methods drop their performance for infrequent alleles, which is one of the factors that reduce the reliability of trans-ethnic major histocompatibility complex (MHC) fine-mapping due to inter-ethn...
Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response.
Frontiers in immunology
Feb 18, 2021
Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, div...
Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs.
Scientific reports
Dec 23, 2020
The global population is at present suffering from a pandemic of Coronavirus disease 2019 (COVID-19), caused by the novel coronavirus Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). The goal of this study was to use artificial intellige...
Identification and validation of 174 COVID-19 vaccine candidate epitopes reveals low performance of common epitope prediction tools.
Scientific reports
Nov 24, 2020
The outbreak of SARS-CoV-2 (2019-nCoV) virus has highlighted the need for fast and efficacious vaccine development. Stimulation of a proper immune response that leads to protection is highly dependent on presentation of epitopes to circulating T-cell...
Unbiased Characterization of Peptide-HLA Class II Interactions Based on Large-Scale Peptide Microarrays; Assessment of the Impact on HLA Class II Ligand and Epitope Prediction.
Frontiers in immunology
Aug 5, 2020
Human Leukocyte Antigen class II (HLA-II) molecules present peptides to T lymphocytes and play an important role in adaptive immune responses. Characterizing the binding specificity of single HLA-II molecules has profound impacts for understanding ce...
Patterns of 1,748 Unique Human Alloimmune Responses Seen by Simple Machine Learning Algorithms.
Frontiers in immunology
Jul 28, 2020
Allele specific antibody response against the polymorphic system of HLA is the allogeneic response marker determining the immunological risk for graft acceptance before and after organ transplantation and therefore routinely studied during the patien...
Graft Survival
Treatment Outcome
Cluster Analysis
Immunosuppressive Agents
Female
Adult
Male
Middle Aged
Pattern Recognition, Automated
Isoantibodies
Histocompatibility
Histocompatibility Testing
Isoantigens
Principal Component Analysis
Graft Rejection
Flow Cytometry
HLA Antigens
Humans
Machine Learning
Kidney Transplantation
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