AIMC Topic: Selection, Genetic

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NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans.

Genome biology
State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study, we curated 737 high-confidence pathogen...

Attribute selection and model evaluation for the maternal and paternal imprinted genes in bovine (Bos Taurus) using supervised machine learning algorithms.

Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
Imprinted genes display biased expression of paternal and maternal alleles in mammals. They are marked through epigenetic process during gametogenesis. Characterization of imprinted genes has expanded our understanding of the regulation and function ...

Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.

Nature communications
Mycobacterium tuberculosis is a serious human pathogen threat exhibiting complex evolution of antimicrobial resistance (AMR). Accordingly, the many publicly available datasets describing its AMR characteristics demand disparate data-type analyses. He...

A deep convolutional neural network approach for predicting phenotypes from genotypes.

Planta
Deep learning is a promising technology to accurately select individuals with high phenotypic values based on genotypic data. Genomic selection (GS) is a promising breeding strategy by which the phenotypes of plant individuals are usually predicted b...

diploS/HIC: An Updated Approach to Classifying Selective Sweeps.

G3 (Bethesda, Md.)
Identifying selective sweeps in populations that have complex demographic histories remains a difficult problem in population genetics. We previously introduced a supervised machine learning approach, S/HIC, for finding both hard and soft selective s...

Supervised Machine Learning for Population Genetics: A New Paradigm.

Trends in genetics : TIG
As population genomic datasets grow in size, researchers are faced with the daunting task of making sense of a flood of information. To keep pace with this explosion of data, computational methodologies for population genetic inference are rapidly be...

Mutant selection window of four quinolone antibiotics against clinical isolates of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis.

Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy
Community-acquired pneumonia and otitis media are caused by several bacterial species, including Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. For the treatment of these diseases, various quinolones are frequently used....

Cotton genotypes selection through artificial neural networks.

Genetics and molecular research : GMR
Breeding programs currently use statistical analysis to assist in the identification of superior genotypes at various stages of a cultivar's development. Differently from these analyses, the computational intelligence approach has been little explore...

How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation.

PLoS computational biology
One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments. Such variability is crucial for evolvability, but poorly understood. In particular, how can nat...