Since 2020, a significant increase in the severity of H5N highly pathogenic avian influenza (HPAI) epidemics in poultry and wild birds has been observed in Poland. To further investigate the genetic diversity of HPAI H5N viruses of clade 2.3.4.4b, HP...
Deep machine learning demonstrates a capacity to uncover evolutionary relationships directly from protein sequences, in effect internalising notions inherent to classical phylogenetic tree inference. We connect these two paradigms by assessing the ca...
Understanding the genetic basis of phenotypic variation is fundamental to biology. Here we introduce GAP, a novel machine learning framework for predicting binary phenotypes from gaps in multi-species sequence alignments. GAP employs a neural network...
This study presents a dual investigation of Salmonella enterica subspecies I, focusing on serovar prediction and core genome characteristics. We utilized two large genomic datasets (panX and NCBI Pathogen Detection) to test machine learning methods f...
Methods in molecular biology (Clifton, N.J.)
39900768
A significantly low success rate of human clinical studies has long been attributed to a capability gap, namely, an ineffective translation of the animal data to the human context. To bridge this capability gap, several correcting measures have been ...
A primary goal of microbial genome-wide association studies is identifying genomic variants associated with a particular habitat. Existing tools fail to identify known causal variants if the analyzed trait shaped the phylogeny. Furthermore, due to in...
Gold standard genomic datasets severely under-represent non-European populations, leading to inequities and a limited understanding of human disease. Therapeutics and outcomes remain hidden because we lack insights that could be gained from analyzing...
Cladistics : the international journal of the Willi Hennig Society
40047286
Proteocephalids are a cosmopolitan and diverse group of tapeworms (Cestoda) that have colonized vertebrate hosts in freshwater and terrestrial environments. Despite the ubiquity of the group, key macroevolutionary processes that have driven the group...
Biosynthetic gene clusters (BGCs), key in synthesizing microbial secondary metabolites, are mostly hidden in microbial genomes and metagenomes. To unearth this vast potential, we present BGC-Prophet, a transformer-based language model for BGC predict...
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their us...