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Genotyping Techniques

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Giardia duodenalis assemblages in cats from Virginia, USA.

Veterinary parasitology, regional studies and reports
Giardia duodenalis is considered a species complex that is divided into 8 genetically distinct but morphologically identical assemblages (A-H). Assemblages C-H are generally host adapted, while A and B infect both people and animals and are considere...

Predicting proprotein convertase subtilisin kexin type-9 loss of function mutations using plasma PCSK9 concentration.

Journal of clinical lipidology
BACKGROUND: Low plasma proprotein convertase subtilisin kexin type-9 (PCSK9) concentration has been associated with loss of function (LOF) PCSK9 mutations in several studies. However, the current standard for detection of these LOF mutations is throu...

A genotypic method for determining HIV-2 coreceptor usage enables epidemiological studies and clinical decision support.

Retrovirology
BACKGROUND: CCR5-coreceptor antagonists can be used for treating HIV-2 infected individuals. Before initiating treatment with coreceptor antagonists, viral coreceptor usage should be determined to ensure that the virus can use only the CCR5 corecepto...

A Cascaded Deep Convolutional Neural Network for Joint Segmentation and Genotype Prediction of Brainstem Gliomas.

IEEE transactions on bio-medical engineering
GOAL: Automatic segmentation of brainstem gliomas and prediction of genotype (H3 K27M) mutation status based on magnetic resonance (MR) images are crucial but challenging tasks for computer-aided diagnosis in neurosurgery. In this paper, we present a...

Using Machine Learning To Predict Antimicrobial MICs and Associated Genomic Features for Nontyphoidal .

Journal of clinical microbiology
Nontyphoidal species are the leading bacterial cause of foodborne disease in the United States. Whole-genome sequences and paired antimicrobial susceptibility data are available for strains because of surveillance efforts from public health agencie...

A multi-task convolutional deep neural network for variant calling in single molecule sequencing.

Nature communications
The accurate identification of DNA sequence variants is an important, but challenging task in genomics. It is particularly difficult for single molecule sequencing, which has a per-nucleotide error rate of ~5-15%. Meeting this demand, we developed Cl...

EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.

Nucleic acids research
The associations between diseases/traits and copy number variants (CNVs) have not been systematically investigated in genome-wide association studies (GWASs), primarily due to a lack of robust and accurate tools for CNV genotyping. Herein, we propose...

Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.

Scientific reports
Crohn Disease (CD) is a complex genetic disorder for which more than 140 genes have been identified using genome wide association studies (GWAS). However, the genetic architecture of the trait remains largely unknown. The recent development of machin...

Machine Learning Interpretation of Extended Human Papillomavirus Genotyping by Onclarity in an Asian Cervical Cancer Screening Population.

Journal of clinical microbiology
This study aimed (i) to compare the performance of the BD Onclarity human papillomavirus (HPV) assay with the Cobas HPV test in identifying cervical intraepithelial neoplasia 2/3 or above (CIN2/3+) in an Asian screening population and (ii) to explore...