AIMC Topic: Computational Biology

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Identification of biomarkers related to neutrophil extracellular traps and potential therapeutic drugs for rheumatoid arthritis using computational analysis.

European journal of medical research
BACKGROUND: Neutrophil extracellular traps (NETs) derived from neutrophils are implicated in the pathogenesis of rheumatoid arthritis (RA) pathogenicity, though the underlying mechanisms remain unclear.

Computational pathology approach for assessment of prognosis and immunotherapy response in pan-gastrointestinal cancer.

Journal of translational medicine
BACKGROUND: Current cancer staging methods cannot accurately predict survival outcomes and therapeutic benefits in cancer patients. Digital pathomics, a rapidly evolving field, holds significant potential to revolutionize disease evaluation.

Bioinformatics identification of key genes correlating NOD1 and Endoplasmic Reticulum stress in Hepatitis B virus-induced acute liver failure.

Scientific reports
Endoplasmic reticulum stress (ERS) has been implicated in a range of biological processes, yet its specific involvement in Hepatitis B virus-associated acute liver failure (HBV-ALF) remains poorly understood. This study aimed to identify key ERS-rela...

A comprehensive benchmark of single-cell Hi-C embedding tools.

Nature communications
Embedding is the key step in single-cell Hi-C (scHi-C) analysis which relies on capturing biological meaningful heterogeneity at various levels of genome architecture. To understand the strength and limitations of existing tools in various applicatio...

Empathi: embedding-based phage protein annotation tool by hierarchical assignment.

Nature communications
Bacteriophages, viruses infecting bacteria, are estimated to outnumber their cellular hosts by 10-fold, acting as key players in all microbial ecosystems. Under evolutionary pressure by their host, they evolve rapidly and encode a large diversity of ...

A prognostic model for gastric cancer constructed by multiple machine learning algorithms.

Journal of molecular histology
Gastric cancer (GC) is a highly heterogeneous disease that requires highly accurate prognostic models. Machine learning is a powerful tool for identifying predictive biomarkers and developing prognostic models. Here, we aim to integrate bioinformatic...

Deep learning detection of dynamic exocytosis events in fluorescence TIRF microscopy.

PLoS computational biology
Segmentation and detection of biological objects in fluorescence microscopy is of paramount importance in cell imaging. Deep learning approaches have recently shown promise to advance, automatize and accelerate analysis. However, most of the interest...

Single-cell RNA sequencing and Mendelian randomization, revealing molecular mechanisms and causal correlation of immune-related genes in periodontitis.

Scientific reports
The immune system has been linked to periodontitis risk in oral inflammation and systemic consequences. Specifically, this study investigated whether hub genes were associated with immune cells via integrating single-cell RNA sequencing (scRNA-seq) a...

ProFlex as a linguistic bridge for decoding protein dynamics in normal mode analysis.

Nature communications
Artificial intelligence is revolutionizing structural bioinformatics, with AlphaFold arguably being the most impactful development to date. The structural atlases generated by these methods present significant opportunities for unraveling biological ...

A generative framework for enhancing drug target interaction prediction in drug discovery.

Scientific reports
In silico drug-target interaction (DTI) prediction plays a key role in accelerating drug discovery and understanding molecular mechanisms. Traditional methods often struggle with the complexity and scale of biochemical data, thus limiting prediction ...