AIMC Topic: Evolution, Molecular
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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-...
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...
Deep mutational learning for the selection of therapeutic antibodies resistant to the evolution of Omicron variants of SARS-CoV-2.
Nature biomedical engineering
Mar 5, 2025
Most antibodies for treating COVID-19 rely on binding the receptor-binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). However, Omicron and its sub-lineages, as well as other heavily mutated variants, have rendered m...
A compendium of human gene functions derived from evolutionary modelling.
Nature
Feb 26, 2025
A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this g...
Pathogen genomic surveillance and the AI revolution.
Journal of virology
Jan 29, 2025
The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence ...
Tailoring industrial enzymes for thermostability and activity evolution by the machine learning-based iCASE strategy.
Nature communications
Jan 11, 2025
The pursuit of obtaining enzymes with high activity and stability remains a grail in enzyme evolution due to the stability-activity trade-off. Here, we develop an isothermal compressibility-assisted dynamic squeezing index perturbation engineering (i...
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