AIMC Topic: Computational Biology

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A KAN-based hybrid deep neural networks for accurate identification of transcription factor binding sites.

PloS one
BACKGROUND: Predicting protein-DNA binding sites in vivo is a challenging but urgent task in many fields such as drug design and development. Most promoters contain many transcription factor (TF) binding sites, yet only a few have been identified thr...

Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code?

Biomolecules
Proteins are biomolecules characterized by uncommon chemical and physicochemical complexities coupled with extreme responsiveness to even minor chemical modifications or environmental variations. Since the shape that proteins assume is fundamental fo...

Deep learning-based computational approach for predicting ncRNAs-disease associations in metaplastic breast cancer diagnosis.

BMC cancer
Non-coding RNAs (ncRNAs) play a crucial role in breast cancer progression, necessitating advanced computational approaches for precise disease classification. This study introduces a Deep Reinforcement Learning (DRL)-based framework for predicting nc...

Integrated bioinformatics, machine learning, and molecular docking reveal crosstalk genes and potential drugs between periodontitis and systemic lupus erythematosus.

Scientific reports
Evidence indicates a connection between periodontitis (PD) and systemic lupus erythematosus (SLE), though the underlying co-morbid mechanisms remain unclear. This study sought to identify the genetic factors and potential therapeutic agents involved ...

Multiscale simulations that incorporate patient-specific neural network models of platelet calcium signaling predict diverse thrombotic outcomes under flow.

PLoS computational biology
During thrombosis, platelets rapidly deposit and activate on the vessel wall, driving conditions such as myocardial infarction and stroke. The complexity of thrombus formation in pathological flow geometries, along with patient-specific pharmacologic...

Predicting Drug-miRNA Associations Combining SDNE with BiGRU.

IEEE journal of biomedical and health informatics
It is well recognized that abnormal miRNA expression can result in drug resistance and pose a challenge to miRNA-based treatments. However, the drug-miRNA associations (DMA) are still incompletely understood. Conventional biological experiments have ...

iEnhancer-DS: Attention-based improved densenet for identifying enhancers and their strength.

Computational biology and chemistry
Enhancers are short DNA fragments that enhance gene expression by binding to transcription factors. Accurately identifying enhancers and their strength is crucial for understanding gene regulation mechanisms. However, traditional enhancer sequencing ...

M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

BMC bioinformatics
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...