AIMC Topic: Genetic Variation
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Forest and Trees: Exploring Bacterial Virulence with Genome-wide Association Studies and Machine Learning.
Trends in microbiology
Jan 14, 2021
The advent of inexpensive and rapid sequencing technologies has allowed bacterial whole-genome sequences to be generated at an unprecedented pace. This wealth of information has revealed an unanticipated degree of strain-to-strain genetic diversity w...
A Revised Model of Anatomically Modern Human Expansions Out of Africa through a Machine Learning Approximate Bayesian Computation Approach.
Genes
Dec 16, 2020
There is a wide consensus in considering Africa as the birthplace of anatomically modern humans (AMH), but the dispersal pattern and the main routes followed by our ancestors to colonize the world are still matters of debate. It is still an open ques...
DeepVariant-on-Spark: Small-Scale Genome Analysis Using a Cloud-Based Computing Framework.
Computational and mathematical methods in medicine
Sep 1, 2020
Although sequencing a human genome has become affordable, identifying genetic variants from whole-genome sequence data is still a hurdle for researchers without adequate computing equipment or bioinformatics support. GATK is a gold standard method fo...
A Linear Regression and Deep Learning Approach for Detecting Reliable Genetic Alterations in Cancer Using DNA Methylation and Gene Expression Data.
Genes
Aug 12, 2020
DNA methylation change has been useful for cancer biomarker discovery, classification, and potential treatment development. So far, existing methods use either differentially methylated CpG sites or combined CpG sites, namely differentially methylate...
Cross-species regulatory sequence activity prediction.
PLoS computational biology
Jul 20, 2020
Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, mod...
Quantitative Trait Loci
Genetic Variation
Gene Expression Regulation
Genome, Human
Species Specificity
Computational Biology
Epigenomics
Models, Genetic
Databases, Genetic
Sequence Analysis, DNA
Models, Statistical
Mutation
Hepatocytes
Algorithms
Animals
Mice
Genomics
Neural Networks, Computer
Humans
Machine Learning
Software
Predicting geographic location from genetic variation with deep neural networks.
eLife
Jun 8, 2020
Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of kn...
Artificial intelligence as the next step towards precision pathology.
Journal of internal medicine
Mar 3, 2020
Pathology is the cornerstone of cancer care. The need for accuracy in histopathologic diagnosis of cancer is increasing as personalized cancer therapy requires accurate biomarker assessment. The appearance of digital image analysis holds promise to i...
Machine-learning based patient classification using Hepatitis B virus full-length genome quasispecies from Asian and European cohorts.
Scientific reports
Dec 11, 2019
Chronic infection with Hepatitis B virus (HBV) is a major risk factor for the development of advanced liver disease including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The relative contribution of virological factors to disease progres...
PharmVar GeneFocus: CYP2D6.
Clinical pharmacology and therapeutics
Dec 9, 2019
The Pharmacogene Variation Consortium (PharmVar) provides nomenclature for the highly polymorphic human CYP2D6 gene locus. CYP2D6 genetic variation impacts the metabolism of numerous drugs and, thus, can impact drug efficacy and safety. This GeneFocu...
Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing.
Cells
Nov 26, 2019
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects ha...
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