AIMC Topic: Evolution, Molecular

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Exploring species taxonomic kingdom using information entropy and nucleotide compositional features of coding sequences based on machine learning methods.

Methods (San Diego, Calif.)
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
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
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
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
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
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
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...

Site-specific prediction of O-GlcNAc modification in proteins using evolutionary scale model.

PloS one
Protein glycosylation, a vital post-translational modification, is pivotal in various biological processes and disease pathogenesis. Computational approaches, including protein language models and machine learning algorithms, have emerged as valuable...

FluPMT: Prediction of Predominant Strains of Influenza A Viruses via Multi-Task Learning.

IEEE/ACM transactions on computational biology and bioinformatics
Seasonal influenza vaccines play a crucial role in saving numerous lives annually. However, the constant evolution of the influenza A virus necessitates frequent vaccine updates to ensure its ongoing effectiveness. The decision to develop a new vacci...

CSEL-BGC: A Bioinformatics Framework Integrating Machine Learning for Defining the Biosynthetic Evolutionary Landscape of Uncharacterized Antibacterial Natural Products.

Interdisciplinary sciences, computational life sciences
The sluggish pace of new antibacterial drug development reflects a vulnerability in the face of the current severe threat posed by bacterial resistance. Microbial natural products (NPs), as a reservoir of immense chemical potential, have emerged as t...