Whole genome sequencing (WGS) potentially represents a rapid approach for antimicrobial resistance genotype-to-phenotype prediction. However, the challenge still exists to predict fully minimum inhibitory concentrations (MICs) and antimicrobial susce...
Phylodynamics is central to understanding infectious disease dynamics through the integration of genomic and epidemiological data. Despite advancements, including the application of deep learning to overcome computational limitations, significant cha...
As population genetic data increase in size, new methods have been developed to store genetic information in efficient ways, such as tree sequences. These data structures are computationally and storage efficient but are not interchangeable with exis...
MOTIVATION: Multiple sequence alignments (MSAs) are extensively used in biology, from phylogenetic reconstruction to structure and function prediction. Here, we suggest an out-of-the-box approach for the inference of MSAs, which relies on algorithms ...
Identifying and differentiating human activities is crucial for effectively preventing the threats posed by environmental pollution to aquatic ecosystems and human health. Machine learning (ML) is a powerful analytical tool for tracking human impacts...
The human microbiome, the community of microorganisms that reside on and inside the human body, is critically important for health and disease. However, it is influenced by various factors and may vary among individuals residing in distinct geographi...
Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter t...
Evidence suggests that bats are important hosts of filoviruses, yet the specific species involved remain largely unidentified. Niemann-Pick C1 (NPC1) is an essential entry receptor, with amino acid variations influencing viral susceptibility and spec...
The complexity and speed of evolution in viruses with RNA genomes makes predictive identification of variants with epidemic or pandemic potential challenging. In recent years, machine learning has become an increasingly capable technology for address...
Amino acid substitution models play an important role in studying the evolutionary relationships among species from protein sequences. The amino acid substitution model consists of a large number of parameters; therefore, it is estimated from hundred...