AIMC Topic: Computational Biology
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RETINA: Reconstruction-based pre-trained enhanced TransUNet for electron microscopy segmentation on the CEM500K dataset.
PLoS computational biology
May 28, 2025
Electron microscopy (EM) has revolutionized our understanding of cellular structures at the nanoscale. Accurate image segmentation is required for analyzing EM images. While manual segmentation is reliable, it is labor-intensive, incentivizing the de...
Identification of mitophagy-related biomarkers in severe acute pancreatitis: integration of WGCNA, machine learning algorithms and scRNA-seq.
Frontiers in immunology
May 28, 2025
BACKGROUND: Mitophagy is a highly conserved cellular process in eukaryotic cells that selectively clears dysfunctional or damaged mitochondria through autophagy mechanisms to maintain mitochondrial homeostasis. However, the role of mitophagy in the p...
Immunogenic cell death biomarkers for sepsis diagnosis and mechanism via integrated bioinformatics.
Scientific reports
May 27, 2025
Immunogenic cell death (ICD) has been implicated in sepsis, a condition with high mortality, through mechanisms involving endoplasmic reticulum stress and other pathophysiological pathways. This study aimed to identify and validate ICD-related biomar...
Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.
eLife
May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
EMOCPD: Efficient Attention-Based Models for Computational Protein Design Using Amino Acid Microenvironment.
Journal of chemical information and modeling
May 26, 2025
Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data...
Novel Computational Approaches in the Discovery and Identification of Bioactive Peptides: A Bioinformatics Perspective.
Journal of agricultural and food chemistry
May 24, 2025
Bioactive peptides are protein molecules known for their specific biological functions, offering promising applications across various fields including medicine, food, and cosmetics. Traditional approaches to the investigation of bioactive peptides t...
Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells.
PLoS computational biology
May 23, 2025
Deep learning-based methods for identifying and tracking cells within microscopy images have revolutionized the speed and throughput of data analysis. These methods for analyzing biological and medical data have capitalized on advances from the broad...
Identification of shared mechanisms between Alzheimer's disease and atherosclerosis by integrated bioinformatics analysis.
European journal of medical research
May 22, 2025
Alzheimer's disease (AD) and atherosclerosis (AS) are two interacting diseases mostly affecting aged adults. AD is characterized by the deposition of neuritic plaques mainly consisting of Aβ, and AS is defined by the formation of atheromatous plaque ...
Applying computational protein design to therapeutic antibody discovery - current state and perspectives.
Frontiers in immunology
May 22, 2025
Machine learning applications in protein sciences have ushered in a new era for designing molecules in silico. Antibodies, which currently form the largest group of biologics in clinical use, stand to benefit greatly from this shift. Despite the prol...
Transcriptomic insights into the mechanism of action of telomere-related biomarkers in rheumatoid arthritis.
Frontiers in immunology
May 22, 2025
BACKGROUND: Rheumatoid arthritis (RA) is an autoimmune inflammatory disease. The mechanism by which telomeres are involved in the development of RA remains unclear. This study aimed to investigate the relationship between RA and telomeres.
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