AIMC Topic: Computational Biology
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A fast (CNN + MCWS-transformer) based architecture for protein function prediction.
Statistical applications in genetics and molecular biology
Jul 1, 2025
The transformer model for sequence mining has brought a paradigmatic shift to many domains, including biological sequence mining. However, transformers suffer from quadratic complexity, i.e., O( ), where is the sequence length, which affects the tra...
GMFOLD: Subgraph matching for high-throughput DNA-aptamer secondary structure classification and machine learning interpretability.
Mathematical biosciences
Jun 27, 2025
Aptamers are oligonucleotide receptors that bind to their targets with high affinity. Here, we consider aptamers comprised of single-stranded DNA that undergo target-binding-induced conformational changes, giving rise to unique secondary and tertiary...
A Innovative Strategy for Identifying Subtypes Through the Analysis of Multi-Omics Data with Adversarial Autoencoders.
Journal of computational biology : a journal of computational molecular cell biology
Jun 26, 2025
Cancer is a disease that is both complex and diverse, and effective diagnosis and treatment require an accurate depiction of tumor subtypes. Traditional methods of cancer identification, which rely on clinical and histopathological criteria, have lim...
rbpTransformer: A novel deep learning model for prediction of piRNA and mRNA bindings.
PloS one
Jun 25, 2025
An important issue in biotechnology is predicting whether a piRNA and an mRNA will or will not bind. Research and treatment of diseases, drug discovery, and the silencing and regulation of genes, transposons, and genomic stability may all benefit fro...
MLWNNR: LncRNA-Disease Association Prediction with Multi-Kernel Learning-Driven Weighted Nuclear Norm Regularization.
Interdisciplinary sciences, computational life sciences
Jun 23, 2025
Emerging evidence highlights long non-coding RNAs (lncRNAs) as pivotal regulators demonstrating significant linkages with diverse human pathologies through expression dynamics and regulatory cascades. This research endeavors to establish an algorithm...
CPPpred-En: Ensemble framework integrating a protein language model and conventional features for highly accurate cell-penetrating peptide prediction.
Computers in biology and medicine
Jun 20, 2025
Cell-penetrating peptides (CPPs) have gained significant attention for biomedical applications, including drug delivery and therapeutic development, due to their ability to penetrate cell membranes. The accurate prediction of CPPs is critical for acc...
DeepRice6mA: A convolutional neural network approach for 6mA site prediction in the rice Genome.
PloS one
Jun 18, 2025
As one of the most critical post-replication modifications, N6-methylation (6mA) at adenine residue plays an important role in a variety of biological functions. Existing computational methods for identifying 6mA sites across large genomic regions te...
Next-generation cancer therapeutics: unveiling the potential of liposome-based nanoparticles through bioinformatics.
Mikrochimica acta
Jun 16, 2025
Cancer remains one of the most deadly diseases in the world, requiring constant growth and improvements in therapeutic strategies. Traditional cancer treatments, such as chemotherapy, radiotherapy, and surgery, have limitations like off-target releas...
MMSol: Predicting Protein Solubility with an Antinoise Multimodal Deep Model.
Journal of chemical information and modeling
Jun 13, 2025
Protein solubility plays a critical role in determining its biological function, such as enabling proper protein delivery and ensuring that proteins remain soluble during cellular processes or therapeutic applications. Accurate prediction of protein ...
AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.
Science advances
Jun 13, 2025
B cell epitope prediction tools are crucial for designing vaccines and disease diagnostics. However, predicting which antigens a specific antibody binds to and their exact binding sites (epitopes) remains challenging. Here, we present AbEpiTope-1.0, ...
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