AIMC Topic: Genetic Variation

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GermVersity: A free and user-friendly interface to enhance the visualization and analysis of genebank data.

PloS one
Genebanks are crucial for food security and industrial applications. However, their heterogeneous nature hinders effective utilization. To address this, the GermVersity platform was developed to integrate conventional, artificial intelligence, and da...

Heterogeneity of genetic sequence within quasi-species of influenza virus revealed by single-molecule sequencing.

eLife
Influenza viruses exhibit high mutation rates and extensive genetic diversity, which hinder effective vaccine development and facilitate immune evasion (Taubenberger and Morens, 2006; Barr et al., 2010). These mutations arise from the error-prone vir...

BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations.

Genome research
Gene-level rare variant association tests (RVATs) are essential for uncovering disease mechanisms and identifying therapeutic targets. Advances in sequence-based machine learning have generated diverse variant pathogenicity scores, creating opportuni...

Rubisco is slow across the tree of life.

Proceedings of the National Academy of Sciences of the United States of America
Rubisco is the main gateway through which inorganic carbon enters the biosphere, catalyzing the vast majority of carbon fixation on Earth. This pivotal enzyme has long been observed to be kinetically constrained. Yet, this impression is based on kine...

ClairS-TO: a deep-learning method for long-read tumor-only somatic small variant calling.

Nature communications
Accurate detection of somatic variants in tumors is of critical importance and remains challenging. Current methods typically require matched normal samples for reliable detection, which are often unavailable in real-world research and clinical scena...

Common genetic variation influencing the human lung imaging phenotypes.

Nature communications
Lung structures are critical for gas exchange and contribute to the pathogenesis of respiratory diseases, exhibiting notable lobe-specific heterogeneity. To investigate their genetic basis, we apply a deep-learning AI system and Pyradiomics to define...

Next-generation molecular breeding tools to harness higher genetic gains in sugarcane.

Planta
Next-generation molecular tools with AI integration can accelerate genetic gain in sugarcane by enhancing variation, accuracy, and efficiency, enabling rapid development of high-yielding, high-quality, and climate-resilient varieties. Enhancing genet...

Multi-class machine learning-based classification of SCID-related genetic variants.

Immunologic research
BACKGROUND: Variants of uncertain significance (VUS) represent a major diagnostic challenge in the interpretation of genetic testing results, particularly in the context of inborn errors of immunity such as severe combined immunodeficiency (SCID). Th...

Machine learning-based penetrance of genetic variants.

Science (New York, N.Y.)
Accurate variant penetrance estimation is crucial for precision medicine. We constructed machine learning (ML) models for 10 diseases using 1,347,298 participants with electronic health records, then applied them to an independent cohort with linked ...

Investigating genetic, antigenic, and structural diversity in the outer membrane protein, PorB: implications for vaccine design.

mBio
UNLABELLED: Vaccines targeting are needed to reduce disease burden and help address the problem of antimicrobial resistance, with an understanding of relationships between gonococcal genetics and molecules influencing diversity, infection, and the i...