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Analysis and validation of programmed cell death genes associated with spinal cord injury progression based on bioinformatics and machine learning.
International immunopharmacology
Feb 9, 2025
BACKGROUND: Spinal cord injury (SCI) is a severe condition affecting the central nervous system. It is marked by a high disability rate and potential for death. Research has demonstrated that programmed cell death (PCD) plays a significant role in th...
Integration of single-cell and bulk RNA sequencing data using machine learning identifies oxidative stress-related genes LUM and PCOLCE2 as potential biomarkers for heart failure.
International journal of biological macromolecules
Feb 8, 2025
Oxidative stress (OS) is a pivotal mechanism driving the progression of cardiovascular diseases, particularly heart failure (HF). However, the comprehensive characterisation of OS-related genes in HF remains largely unexplored. In the present study, ...
HybProm: An attention-assisted hybrid CNN-BiLSTM model for the interpretable prediction of DNA promoter.
Methods (San Diego, Calif.)
Feb 8, 2025
Promoter prediction is essential for analyzing gene structures, understanding regulatory networks, transcription mechanisms, and precisely controlling gene expression. Recently, computational and deep learning methods for promoter prediction have gai...
Unravelling single-cell DNA replication timing dynamics using machine learning reveals heterogeneity in cancer progression.
Nature communications
Feb 8, 2025
Genomic heterogeneity has largely been overlooked in single-cell replication timing (scRT) studies. Here, we develop MnM, an efficient machine learning-based tool that allows disentangling scRT profiles from heterogenous samples. We use single-cell c...
Machine Learning-Driven Discovery of Structurally Related Natural Products as Activators of the Cardiac Calcium Pump SERCA2a.
ChemMedChem
Feb 6, 2025
A key molecular dysfunction in heart failure is the reduced activity of the cardiac sarcoplasmic reticulum Ca-ATPase (SERCA2a) in cardiac muscle cells. Reactivating SERCA2a improves cardiac function in heart failure models, making it a validated targ...
Discovery of TRPV4-Targeting Small Molecules with Anti-Influenza Effects Through Machine Learning and Experimental Validation.
International journal of molecular sciences
Feb 6, 2025
Transient receptor potential vanilloid 4 (TRPV4) is a calcium-permeable cation channel critical for maintaining intracellular Ca homeostasis and is essential in regulating immune responses, metabolic processes, and signal transduction. Recent studies...
Fast In Vivo Two-Photon Fluorescence Imaging via Lateral and Axial Resolution Restoration With Self-Supervised Learning.
Journal of biophotonics
Feb 5, 2025
Two-photon fluorescence (TPF) imaging opens a new avenue to achieve high resolution at extended penetration depths. However, it is difficult for conventional TPF imaging systems to simultaneously achieve high resolution and speed. In this work, we de...
Artificial intelligence using a latent diffusion model enables the generation of diverse and potent antimicrobial peptides.
Science advances
Feb 5, 2025
Artificial intelligence holds great promise for the design of antimicrobial peptides (AMPs); however, current models face limitations in generating AMPs with sufficient novelty and diversity, and they are rarely applied to the generation of antifunga...
UTR-Insight: integrating deep learning for efficient 5' UTR discovery and design.
BMC genomics
Feb 4, 2025
The 5' UTR is critical for mRNA stability and translation efficiency in therapeutics. We developed UTR-Insight, a model integrating a pretrained language model with a CNN-Transformer architecture, explaining 89.1% of the mean ribosome load (MRL) vari...
A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions.
Nature communications
Feb 3, 2025
Cells are regulated at multiple levels, from regulations of individual genes to interactions across multiple genes. Some recent neural network models can connect molecular changes to cellular phenotypes, but their design lacks modeling of regulatory ...
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