Bias in neural network model training datasets has been observed to decrease prediction accuracy for groups underrepresented in training data. Thus, investigating the composition of training datasets used in machine learning models with healthcare ap...
INTRODUCTION: The identification of peptides eluted from HLA complexes by mass spectrometry (MS) can provide critical data for deep learning models of antigen presentation prediction and promote neoantigen vaccine design. A major challenge remains in...
Methods in molecular biology (Clifton, N.J.)
38907891
Human leukocyte antigen (HLA) imputation is an essential step following genome-wide association study, particularly when putative associations in HLA genes are identified, to fully understand the genetic basis of human traits. Different HLA imputatio...
Cell-type-specific regulatory elements, cataloged through extensive experiments and bioinformatics in large-scale consortiums, have enabled enrichment analyses of genetic associations that primarily utilize positional information of the regulatory el...
Rh phenotype matching reduces but does not eliminate alloimmunization in patients with sickle cell disease (SCD) due to RH genetic diversity that is not distinguishable by serological typing. RH genotype matching can potentially mitigate Rh alloimmun...
UNLABELLED: The erythromycin resistance RNA methyltransferase () confers cross-resistance to all therapeutically important macrolides, lincosamides, and streptogramins (MLS phenotype). The expression of is often induced by the macrolide-mediated rib...
Structural variations (SVs) are diverse forms of genetic alterations and drive a wide range of human diseases. Accurately genotyping SVs, particularly occurring at repetitive genomic regions, from short-read sequencing data remains challenging. Here,...
The purpose of this study was to enhance the prediction of solid-organ recipient and donor crossmatch compatibility by applying machine learning (ML). Prediction of crossmatch compatibility is complex and requires an understanding of the recipient an...
BACKGROUND: Major depressive disorder (MDD) is among the leading causes of disability worldwide and treatment efficacy is variable across patients. Polymorphisms in cytochrome P450 2C19 (CYP2C19) play a role in response and side effects to medication...
Understanding how genetic variation impacts transcription factor (TF) binding remains a major challenge, limiting our ability to model disease-associated variants. Here, we used a highly controlled system of F crosses with extensive genetic diversity...