Publications by authors named "Emrah Akkoyun"

Article Synopsis
  • Many algorithms predicting variant effects depend on evolutionary conservation but often neglect the context of substitution events in their calculations.
  • The new approach, PHACTboost, enhances the previous method, PHACT, by using gradient boosting, combining scores from multiple sequence alignments, phylogenetic trees, and ancestral reconstructions.
  • PHACTboost has shown to significantly outperform over 40 existing pathogenicity predictors, especially in challenging cases with conflicting results, and it provides predictions for a vast number of amino acid alterations across numerous proteins.
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Vascular diseases, such as abdominal aortic aneurysms, are associated with tissue degeneration of the aortic wall, resulting in variations in mechanical properties, such as tissue ultimate stress and a high slope. Variations in the mechanical properties of tissues may be associated with an increase in the number of collagen cross-links. Understanding the effect of collagen cross-linking on tissue mechanical properties can significantly aid in predicting diseased aortic tissue rupture and improve the clarity of decisions regarding surgical procedures.

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Evolutionary conservation is a fundamental resource for predicting the substitutability of amino acids and the loss of function in proteins. The use of multiple sequence alignment alone-without considering the evolutionary relationships among sequences-results in the redundant counting of evolutionarily related alteration events, as if they were independent. Here, we propose a new method, PHACT, that predicts the pathogenicity of missense mutations directly from the phylogenetic tree of proteins.

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Objective: The maximum diameter measurement of an abdominal aortic aneurysm (AAA), which depends on orthogonal and axial cross-sections or maximally inscribed spheres within the AAA, plays a significant role in the clinical decision making process. This study aims to build a total of 21 morphological parameters from longitudinal CT scans and analyze their correlations. Furthermore, this work explores the existence of a "master curve" of AAA growth, and tests which parameters serve to enhance its predictability for clinical use.

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Objective: For small abdominal aortic aneurysms (AAAs), a regular follow-up examination is recommended every 12 months for AAAs of 30-39 mm and every six months for AAAs of 40-55 mm. Follow-up diameters can determine if a patient follows the common growth model of the population. However, the rapid expansion of an AAA, often associated with higher rupture risk, may be overlooked even though it requires surgical intervention.

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