AIMC Topic: Evolution, Molecular
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Whole‑exome evolutionary profiling of osteosarcoma uncovers metastasis‑related driver mutations and generates an independently validated predictive classifier.
Journal of translational medicine
Jul 7, 2025
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...
Tracing the evolutionary pathway of SARS-CoV-2 through RNA sequencing analysis.
Scientific reports
Jul 4, 2025
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...
Lineage-specific regulatory evolution: insights from massively parallel reporter assays.
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...
Genome-wide annotation and comparative analysis of miniature inverted-repeat transposable elements (MITEs) in six pear species.
Planta
Jun 16, 2025
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...
What does evolution make? Learning in living lineages and machines.
Trends in genetics : TIG
Jun 10, 2025
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 ...
AMPGen: an evolutionary information-reserved and diffusion-driven generative model for de novo design of antimicrobial peptides.
Communications biology
May 30, 2025
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...
Evolutionary Dynamics and Functional Differences in Clinically Relevant Pen β-Lactamases from spp.
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-...
Exploring species taxonomic kingdom using information entropy and nucleotide compositional features of coding sequences based on machine learning methods.
Methods (San Diego, Calif.)
Apr 23, 2025
The flow of genetic information from DNA to protein is governed by the central dogma of molecular biology. Genetic drift and mutations usually lead to changes in DNA composition, thereby affecting the coding sequences (CDS) that encode functional pro...
Genome evolution of Kaposi sarcoma-associated herpesvirus (KSHV).
Journal of virology
Apr 16, 2025
UNLABELLED: Kaposi sarcoma (KS) is the most common cancer in people living with HIV (PLWH), particularly in sub-Saharan Africa (SSA), where Kaposi sarcoma herpesvirus (KSHV or human herpesvirus 8 [HHV-8]) is endemic. In KSHV endemic areas, the overal...
Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis.
Journal of chemical theory and computation
Mar 13, 2025
Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these fa...
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