Michał Aleksander Ciach

ParaDISM improves read placement and variant calling accuracy in highly homologous genomic regions by reducing misalignment artifacts.

DiscrimAlign learns substitution matrices and gap penalties for sequence alignment to predict microRNA-target interactions, achieving performance comparable to neural networks while being more interpretable.

The paper identifies 829 xenologs in 44 early diverging fungi, revealing patterns of horizontal gene transfer and its impact on fungal metabolism, adaptation, and immunity.

This paper introduces the Clade Displacement Index to detect horizontal gene transfers in unrooted gene trees and assess gene tree topology stability.

The paper introduces a linear deconvolution method using optimal transport to improve accuracy in mass spectrometry by reducing sensitivity to measurement inaccuracies.