AIMC Topic: Computational Biology

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GADRC: a graph-based approach for drug repositioning with deep residual networks and computational feature-guided undersampling.

Journal of computer-aided molecular design
Drug repositioning (DR) is a highly promising research strategy aimed at discovering new therapeutic indications for existing drugs. Current computational DR methods have become effective tools for uncovering drug-disease associations, yet they suffe...

GlyTrait: A Versatile Bioinformatics Tool for Glycomics Analysis.

Journal of proteome research
We developed GlyTrait, a Python-based framework designed to enhance Glycomics analysis through the innovative calculation and interpretation of derived traits from -glycome data. Glycomics research often grapples with the interpretability and biologi...

Transformative advances in single-cell omics: a comprehensive review of foundation models, multimodal integration and computational ecosystems.

Journal of translational medicine
Recent advances in single-cell multi-omics technologies have revolutionized cellular analysis, enabling comprehensive exploration of cellular heterogeneity, developmental trajectories, and disease mechanisms at unprecedented resolution. Foundation mo...

Identification of coagulation-related biomarkers in osteoarthritis and immune infiltration analysis based on bioinformatics.

Hereditas
BACKGROUND: Osteoarthritis (OA) is a common degenerative disorder characterized primarily by articular cartilage degradation and chronic inflammation. Although direct evidence elucidating the specific mechanisms underlying the coagulation-immune axis...

Identification of key biomarkers associated with necroptosis and immune infiltration in hepatitis B virus-related acute-on-chronic liver failure.

Scientific reports
Hepatitis B virus-related acute-on-chronic liver failure (ACHBLF) is a severe condition associated with short-term mortality without liver transplantation. Substantial evidence indicates that necroptosis and immune infiltration play critical roles in...

A semi-automated algorithm for image analysis of respiratory organoids.

PLoS computational biology
Respiratory organoids have emerged as a powerful in vitro model for studying respiratory diseases and drug discovery. However, the high-throughput analysis of organoid images remains a challenge due to the lack of automated and accurate segmentation ...

Identification of hub necroptosis-related targets and discovery of potential natural inhibitors in ulcerative colitis based on bioinformatics and computer-aided drug design.

Journal of computer-aided molecular design
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex pathogenesis and limited treatment options. Recently, necroptosis has been found to play a significant role in UC. This study aimed to investigate necroptosis-related mech...

PS3N: leveraging protein sequence-structure similarity for novel drug-drug interaction discovery.

Scientific reports
Adverse drug events represent a key challenge in public health, especially concerning drug safety profiling and drug surveillance. Drug-drug interactions represent one of the most popular types of adverse drug events. Most computational approaches to...

Denoising self-supervised learning for disease-gene association prediction.

BMC bioinformatics
Understanding the interplay between diseases and genes is crucial for gaining deeper insights into disease mechanisms and optimizing therapeutic strategies. In recent years, various computational methods have been developed to uncover potential disea...

GraphComm predicts cell cell communication using a graph based deep learning method in single cell RNA sequencing data.

Scientific reports
Interactions between cells coordinate various functions across cell-types in health and disease states. Novel single-cell techniques enable deep investigation of cellular crosstalk at single-cell resolution. Cell-cell communication (CCC) is mediated ...