AIMC Topic: Computational Biology
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Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex.
Cell genomics
May 21, 2025
Identifying cell-type-specific enhancers is critical for developing genetic tools to study the mammalian brain. We organized the "Brain Initiative Cell Census Network (BICCN) Challenge: Predicting Functional Cell Type-Specific Enhancers from Cross-Sp...
CoupleMDA: Metapath-Induced Structural-Semantic Coupling Network for miRNA-Disease Association Prediction.
International journal of molecular sciences
May 21, 2025
The prediction of microRNA-disease associations (MDAs) is crucial for understanding disease mechanisms and biomarker discovery. While graph neural networks have emerged as promising tools for MDA prediction, existing methods face critical limitations...
RNAcare: integrating clinical data with transcriptomic evidence using rheumatoid arthritis as a case study.
BMC medical genomics
May 21, 2025
BACKGROUND: Gene expression analysis is a crucial tool for uncovering the biological mechanisms that underlie differences between patient subgroups, offering insights that can inform clinical decisions. However, despite its potential, gene expression...
Cyclic peptide structure prediction and design using AlphaFold2.
Nature communications
May 21, 2025
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...
TCoCPIn reveals topological characteristics of chemical protein interaction networks for novel feature discovery.
Scientific reports
May 18, 2025
Understanding chemical-protein interactions (CPIs) is crucial for drug discovery and biological research, yet their complexity often challenges traditional methods. We propose TCoCPIn, a novel framework integrating graph neural networks (GNN) with th...
The underlying molecular mechanisms and biomarkers of Hip fracture combined with deep vein thrombosis based on self sequencing bioinformatics analysis.
Journal of orthopaedic surgery and research
May 16, 2025
BACKGROUND: Thrombus formation is a severe complication in orthopedic surgery, significantly increasing mortality in patients with fractures. Therefore, identifying feature genes to determine thrombus presence in fracture surgeries is critical.
Multi-criteria decision making and its application to in silico discovery of vaccine candidates for Toxoplasma gondii.
Vaccine
May 15, 2025
Vaccine discovery against eukaryotic parasites is not trivial and few exist. Reverse vaccinology is an in silico vaccine discovery approach, designed to identify vaccine candidates from the thousands of protein sequences encoded by a target genome. P...
Exploring potential diagnostic markers and therapeutic targets for type 2 diabetes mellitus with major depressive disorder through bioinformatics and in vivo experiments.
Scientific reports
May 15, 2025
Type 2 diabetes mellitus (T2DM) and Major depressive disorder (MDD) act as risk factors for each other, and the comorbidity of both significantly increases the all-cause mortality rate. Therefore, studying the diagnosis and treatment of diabetes with...
Exon-intron boundary detection made easy by physicochemical properties of DNA.
Molecular omics
May 15, 2025
Genome architecture in eukaryotes exhibits a high degree of complexity. Amidst the numerous intricacies, the existence of genes as non-continuous stretches composed of exons and introns has garnered significant attention and curiosity among researche...
Learning a deep language model for microbiomes: The power of large scale unlabeled microbiome data.
PLoS computational biology
May 7, 2025
We use open source human gut microbiome data to learn a microbial "language" model by adapting techniques from Natural Language Processing (NLP). Our microbial "language" model is trained in a self-supervised fashion (i.e., without additional externa...
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