Introduction Persistent oral infections with high-risk human papillomavirus (HR-HPV) are a potential cause of most oropharyngeal cancers (OPCs). Oral HR-HPV infection and persistence are significantly higher in people living with HIV (PLWH). Most …
Protein-language models (pLMs) provide a novel means for mapping the protein space. Which of these new maps best advances specific biological analyses, however, is not obvious. To elucidate the principles of model selection, we benchmarked fourteen …
Background Whole metagenome shotgun sequencing (WMS) is widely used to profile microbial function. However, technical variability in sequencing and analysis often obscures true biological patterns. Large-scale studies are particularly susceptible to …
Functional metagenomics enables the study of unexplored bacterial diversity, gene families, and pathways essential to microbial communities. However, discovering biological insights with these data is impeded by the scarcity of quality annotations. …
Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community …
Motivation Protein language models based on the transformer architecture are increasingly improving performance on protein prediction tasks, including secondary structure, subcellular localization, and more. Despite being trained only on protein …
Over the years, many computational methods have been created for the analysis of the impact of single amino acid substitutions resulting from single-nucleotide variants in genome coding regions. Historically, all methods have been supervised and thus …
Determining the repertoire of a microbe's molecular functions is a central question in microbial biology. Modern techniques achieve this goal by comparing microbial genetic material against reference databases of functionally annotated genes/proteins …
AbstractPurpose of ReviewPreparing for pandemics requires a degree of interdisciplinary work that is challenging under the current paradigm. This review summarizes the challenges faced by the field of pandemic science and proposes how to address …