AIMC Topic: Alleles
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Snowflake: A deep learning-based human leukocyte antigen matching algorithm considering allele-specific surface accessibility.
Frontiers in immunology
Jul 29, 2022
Histocompatibility in solid-organ transplantation has a strong impact on long-term graft survival. Although recent advances in matching of both B-cell epitopes and T-cell epitopes have improved understanding of allorecognition, the immunogenic determ...
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...
Connecting MHC-I-binding motifs with HLA alleles via deep learning.
Communications biology
Oct 18, 2021
The selection of peptides presented by MHC molecules is crucial for antigen discovery. Previously, several predictors have shown impressive performance on binding affinity. However, the decisive MHC residues and their relation to the selection of bin...
NanoCaller for accurate detection of SNPs and indels in difficult-to-map regions from long-read sequencing by haplotype-aware deep neural networks.
Genome biology
Sep 6, 2021
Long-read sequencing enables variant detection in genomic regions that are considered difficult-to-map by short-read sequencing. To fully exploit the benefits of longer reads, here we present a deep learning method NanoCaller, which detects SNPs usin...
Risk prediction for delayed clearance of high-dose methotrexate in pediatric hematological malignancies by machine learning.
International journal of hematology
Jun 25, 2021
This study aimed to establish a predictive model to identify children with hematologic malignancy at high risk for delayed clearance of high-dose methotrexate (HD-MTX) based on machine learning. A total of 205 patients were recruited. Five variables ...
Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models.
Scientific reports
Jun 16, 2021
Group A Streptococcus (GAS) is a globally significant bacterial pathogen. The GAS genotyping gold standard characterises the nucleotide variation of emm, which encodes a surface-exposed protein that is recombinogenic and under immune-based selection ...
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...
Feasibility of predicting allele specific expression from DNA sequencing using machine learning.
Scientific reports
May 19, 2021
Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severity. Howev...
Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning.
Genome research
Apr 8, 2021
Genomic sequence variation within enhancers and promoters can have a significant impact on the cellular state and phenotype. However, sifting through the millions of candidate variants in a personal genome or a cancer genome, to identify those that i...
Deep learning pan-specific model for interpretable MHC-I peptide binding prediction with improved attention mechanism.
Proteins
Mar 18, 2021
Accurate prediction of peptide binding affinity to the major histocompatibility complex (MHC) proteins has the potential to design better therapeutic vaccines. Previous work has shown that pan-specific prediction algorithms can achieve better predict...
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