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Computational Biology

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Identifying the NEAT1/miR-26b-5p/S100A2 axis as a regulator in Parkinson's disease based on the ferroptosis-related genes.

PloS one
OBJECTIVES: Parkinson's disease (PD) is a complex neurodegenerative disease with unclear pathogenesis. Some recent studies have shown that there is a close relationship between PD and ferroptosis. We aimed to identify the ferroptosis-related genes (F...

Site-specific prediction of O-GlcNAc modification in proteins using evolutionary scale model.

PloS one
Protein glycosylation, a vital post-translational modification, is pivotal in various biological processes and disease pathogenesis. Computational approaches, including protein language models and machine learning algorithms, have emerged as valuable...

Trans-m5C: A transformer-based model for predicting 5-methylcytosine (m5C) sites.

Methods (San Diego, Calif.)
5-Methylcytosine (m5C) plays a pivotal role in various RNA metabolic processes, including RNA localization, stability, and translation. Current high-throughput sequencing technologies for m5C site identification are resource-intensive in terms of cos...

Identification of sepsis-associated encephalopathy biomarkers through machine learning and bioinformatics approaches.

Scientific reports
Sepsis-associated encephalopathy (SAE) is common in septic patients, characterized by acute and long-term cognitive impairment, and is associated with higher mortality. This study aimed to identify SAE-related biomarkers and evaluate their diagnostic...

Analysis of diagnostic genes and molecular mechanisms of Crohn's disease and colon cancer based on machine learning algorithms.

Scientific reports
Crohn's disease (CD) is a chronic inflammatory bowel condition, and colon adenocarcinoma (COAD), as one of the most prevalent malignant tumors of the digestive tract, has been indicated by research to have a close association with CD. This study empl...

DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.

Scientific reports
Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Tradi...

Systematic benchmarking of deep-learning methods for tertiary RNA structure prediction.

PLoS computational biology
The 3D structure of RNA critically influences its functionality, and understanding this structure is vital for deciphering RNA biology. Experimental methods for determining RNA structures are labour-intensive, expensive, and time-consuming. Computati...

Using genomic data and machine learning to predict antibiotic resistance: A tutorial paper.

PLoS computational biology
Antibiotic resistance is a global public health concern. Bacteria have evolved resistance to most antibiotics, which means that for any given bacterial infection, the bacteria may be resistant to one or several antibiotics. It has been suggested that...

Novel anoikis-related diagnostic biomarkers for aortic dissection based on machine learning.

Scientific reports
Aortic dissection (AD) is one of the most dangerous diseases of the cardiovascular system, which is characterized by acute onset and poor prognosis, while the pathogenesis of AD is still unclear and may affect or even delay the diagnosis of AD. Ancho...

Predicting lncRNA-protein interactions using a hybrid deep learning model with dinucleotide-codon fusion feature encoding.

BMC genomics
Long non-coding RNAs (lncRNAs) play crucial roles in numerous biological processes and are involved in complex human diseases through interactions with proteins. Accurate identification of lncRNA-protein interactions (LPI) can help elucidate the func...