AIMC Topic: Computational Biology

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M3S-GRPred: a novel ensemble learning approach for the interpretable prediction of glucocorticoid receptor antagonists using a multi-step stacking strategy.

BMC bioinformatics
Accelerating drug discovery for glucocorticoid receptor (GR)-related disorders, including innovative machine learning (ML)-based approaches, holds promise in advancing therapeutic development, optimizing treatment efficacy, and mitigating adverse eff...

A new strategy for Cas protein recognition based on graph neural networks and SMILES encoding.

Scientific reports
The CRISPR-Cas system, an adaptive immune mechanism found in bacteria and archaea, has evolved into a promising genomic editing tool, with various types of Cas proteins playing a crucial role. In this study, we developed a set of strategies for minin...

Identification and validation of programmed cell death related biomarkers for the treatment and prevention COVID-19.

Annals of medicine
PURPOSE: Programmed cell death (PCD) plays a key role in the progression of coronavirus disease 2019 (COVID-19). However, PCD-relevant biomarkers have not been fully discovered. The aim of this study was to explore the PCD-relevant biomarkers for the...

Exploring deep learning in phage discovery and characterization.

Virology
Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The d...

Machine learning: Python tools for studying biomolecules and drug design.

Molecular diversity
The increasing adoption of computational methods and artificial intelligence in scientific research has led to a growing interest in versatile tools like Python. In the fields of medical chemistry, biochemistry, and bioinformatics, Python has emerged...

Identification of M2 macrophage-related genes associated with diffuse large B-cell lymphoma via bioinformatics and machine learning approaches.

Biology direct
M2 macrophages play a crucial role in the initiation and progression of various tumors, including diffuse large B-cell lymphoma (DLBCL). However, the characterization of M2 macrophage-related genes in DLBCL remains incomplete. In this study, we downl...

Multifractal analysis and support vector machine for the classification of coronaviruses and SARS-CoV-2 variants.

Scientific reports
This study presents a novel approach for the classification of coronavirus species and variants of SARS-CoV-2 using Chaos Game Representation (CGR) and 2D Multifractal Detrended Fluctuation Analysis (2D MF-DFA). By extracting fractal parameters from ...

Identification and Validation of Glycosylation‑Related Genes in Ischemic Stroke Based on Bioinformatics and Machine Learning.

Journal of molecular neuroscience : MN
Ischemic stroke (IS) constitutes a severe neurological disorder with restricted treatment alternatives. Recent investigations have disclosed that glycosylation is closely associated with the occurrence and outcome of IS. Nevertheless, data on the tra...

VTrans: A VAE-Based Pre-Trained Transformer Method for Microbiome Data Analysis.

Journal of computational biology : a journal of computational molecular cell biology
Predicting the survival outcomes and assessing the risk of patients play a pivotal role in comprehending the microbial composition across various stages of cancer. With the ongoing advancements in deep learning, it has been substantiated that deep le...

[Nobel Prize in chemistry 2024: David Baker, Demis Hassabis et John M. Jumper. The revolution of artificial intelligence in structural biology].

Medecine sciences : M/S
The 2024 Nobel Prize in chemistry has been awarded to Demis Hassabis and John M. Jumper (Google DeepMind) for the development of artificial intelligence-guided protein structure prediction and to David Baker (University of Washington, Seattle, USA) f...