AIMC Topic: Haplotypes
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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...
Distinguishing between recent balancing selection and incomplete sweep using deep neural networks.
Molecular ecology resources
Apr 5, 2021
Balancing selection is an important adaptive mechanism underpinning a wide range of phenotypes. Despite its relevance, the detection of recent balancing selection from genomic data is challenging as its signatures are qualitatively similar to those l...
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...
Transfer learning enables prediction of CYP2D6 haplotype function.
PLoS computational biology
Nov 2, 2020
Cytochrome P450 2D6 (CYP2D6) is a highly polymorphic gene whose protein product metabolizes more than 20% of clinically used drugs. Genetic variations in CYP2D6 are responsible for interindividual heterogeneity in drug response that can lead to drug ...
A genotype imputation method for de-identified haplotype reference information by using recurrent neural network.
PLoS computational biology
Oct 1, 2020
Genotype imputation estimates the genotypes of unobserved variants using the genotype data of other observed variants based on a collection of haplotypes for thousands of individuals, which is known as a haplotype reference panel. In general, more ac...
Estimating the Binding of Sars-CoV-2 Peptides to HLA Class I in Human Subpopulations Using Artificial Neural Networks.
Cell systems
Sep 10, 2020
Epidemiological studies show that SARS-CoV-2 infection leads to severe symptoms only in a fraction of patients, but the determinants of individual susceptibility to the virus are still unknown. The major histocompatibility complex (MHC) class I expos...
Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters.
Forensic science international. Genetics
Jun 29, 2020
We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high D...
Machine learning-based analyses support the existence of species complexes for and .
Parasitology
Jun 16, 2020
Human strongyloidiasis is a serious disease mostly attributable to Strongyloides stercoralis and to a lesser extent Strongyloides fuelleborni, a parasite mainly of non-human primates. The role of animals as reservoirs of human-infecting Strongyloides...
Humans
Phylogeny
Feces
Genotype
Machine Learning
Genetic Speciation
Animals
RNA, Ribosomal, 18S
Electron Transport Complex IV
Multilocus Sequence Typing
Genes, Helminth
Strongyloides stercoralis
Computational Biology
Disease Reservoirs
Strongyloides
Strongyloidiasis
Primates
Dogs
Dog Diseases
Haplotypes
Serum vitamin D deficiency and vitamin D receptor gene polymorphism are associated with increased risk of cardiovascular disease in a Chinese rural population.
Nutrition research (New York, N.Y.)
Sep 13, 2018
Several studies have reported a conflicting association between vitamin D deficiency, vitamin D receptor (VDR) polymorphism, and the risk of cardiovascular disease (CVD). We hypothesized that serum 25(OH)D concentrations and single nucleotide polymor...
A heuristic method for fast and accurate phasing and imputation of single-nucleotide polymorphism data in bi-parental plant populations.
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Aug 4, 2018
Key message New fast and accurate method for phasing and imputation of SNP chip genotypes within diploid bi-parental plant populations. This paper presents a new heuristic method for phasing and imputation of genomic data in diploid plant species. Ou...
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