Temperate phages and prophages are well-known carriers of antibiotic resistance genes (ARGs) facilitating their transmission. In contrast, lytic phages rarely harbor functional ARGs. However, by a lenient threshold search strategy combined with a mac...
Proceedings of the National Academy of Sciences of the United States of America
Sep 23, 2025
Convergent evolution, or convergence, refers to repeated, independent emergences of the same trait in two or more lineages of species during evolution, often indicating functional adaptation to specific environmental factors. Many computational metho...
The increasing zoonotic potential of highly pathogenic avian influenza (HPAI) H5N1 poses a growing threat to global public health. This review examines the molecular and evolutionary mechanisms facilitating H5N1 adaptation in mammalian hosts, focusin...
BACKGROUND: Osteosarcoma is the most common primary malignant bone tumor, with high invasiveness and metastatic potential and a poor prognosis in patients with metastatic cancer. Despite the rapid advancements in genomics in recent years that provide...
The COVID-19 pandemic, driven by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), has underscored the need to understand the virus's evolution due to its global health impact. This study employed RNA sequencing (RNA-Seq) to analyze g...
Current opinion in genetics & development
Jun 20, 2025
Lineage-specific genetic variants play a key role in evolutionary divergence, particularly through changes in cis-regulatory elements that fine-tune gene expression. Massively parallel reporter assays (MPRAs) provide a powerful approach to characteri...
Through multi-faceted comparative analysis of MITEs across six pear genomes, we revealed their distribution patterns, functional impacts and their significant role as genomic origins for miRNAs, with copy number being the most critical factor for MIT...
How does genomic information unfold, to give rise to self-constructing living organisms with problem-solving capacities at all levels of organization? We review recent progress that unifies work in developmental genetics and machine learning (ML) to ...
The rapid advancement of artificial intelligence (AI) has enabled de novo design of functional proteins, circumventing the reliance on natural templates or sequencing databases. However, current protein design models are ineffective in generating pro...
Journal of chemical information and modeling
May 2, 2025
Antimicrobial resistance (AMR) is a global threat, with species contributing significantly to difficult-to-treat infections. The Pen family of β-lactamases are produced by all spp., and their mutation or overproduction leads to the resistance of β-...
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