AIMC Topic: Epitopes
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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...
Using the antibody-antigen binding interface to train image-based deep neural networks for antibody-epitope classification.
PLoS computational biology
Mar 29, 2021
High-throughput B-cell sequencing has opened up new avenues for investigating complex mechanisms underlying our adaptive immune response. These technological advances drive data generation and the need to mine and analyze the information contained in...
Domain-Scan: Combinatorial Sero-Diagnosis of Infectious Diseases Using Machine Learning.
Frontiers in immunology
Feb 10, 2021
The presence of pathogen-specific antibodies in an individual's blood-sample is used as an indication of previous exposure and infection to that specific pathogen (e.g., virus or bacterium). Measurement of the diagnostic antibodies is routinely achie...
HIV Antibodies
Communicable Diseases
AIDS Serodiagnosis
HIV Infections
Humans
Antigen-Antibody Reactions
Peptide Library
DNA, Recombinant
Machine Learning
Epitopes
Peptide Fragments
Polymerase Chain Reaction
HIV Envelope Protein gp160
Serologic Tests
Amino Acid Sequence
Hepatitis C Antibodies
Hepatitis C Antigens
High-Throughput Nucleotide Sequencing
Oligonucleotides
DNA Barcoding, Taxonomic
HIV Core Protein p24
Hepatitis C
Base Sequence
Genetic Vectors
Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy.
BMC bioinformatics
Dec 30, 2020
BACKGROUND: Personalized cancer vaccines are emerging as one of the most promising approaches to immunotherapy of advanced cancers. However, only a small proportion of the neoepitopes generated by somatic DNA mutations in cancer cells lead to tumor r...
Machine learning-guided evolution of BMP-2 knuckle Epitope-Derived osteogenic peptides to target BMP receptor II.
Journal of drug targeting
May 1, 2020
Bone morphogenetic protein-2 (BMP-2) is a key regulator of bone formation, growth and regeneration, which contains a conformational wrist epitope and a linear knuckle epitope that are functionally responsible for the protein by mediating its interact...
A novel algorithm to improve specificity in ovarian cancer detection.
Cancer treatment and research communications
Nov 10, 2017
BACKGROUND: Measurement of autoantibodies (AAbs) to tumor associated antigens has been proposed to aid in the early detection of ovarian cancer with high specificity. Here we describe a multiplex approach to evaluate selected peptide epitopes of p53 ...
Ab-initio conformational epitope structure prediction using genetic algorithm and SVM for vaccine design.
Computer methods and programs in biomedicine
Oct 12, 2017
BACKGROUND AND OBJECTIVE: T-cell epitope structure identification is a significant challenging immunoinformatic problem within epitope-based vaccine design. Epitopes or antigenic peptides are a set of amino acids that bind with the Major Histocompati...
Machine learning reveals a non-canonical mode of peptide binding to MHC class II molecules.
Immunology
Jun 19, 2017
MHC class II molecules play a fundamental role in the cellular immune system: they load short peptide fragments derived from extracellular proteins and present them on the cell surface. It is currently thought that the peptide binds lying more or les...
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