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Computational Biology

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Advanced vision transformers and open-set learning for robust mosquito classification: A novel approach to entomological studies.

PLoS computational biology
Mosquito-related diseases pose a significant threat to global public health, necessitating efficient and accurate mosquito classification for effective surveillance and control. This work presents an innovative approach to mosquito classification by ...

Identification and verification of the optimal feature genes of ferroptosis in thyroid-associated orbitopathy.

Frontiers in immunology
BACKGROUND: Thyroid-associated orbitopathy (TAO) is an autoimmune inflammatory disorder of the orbital adipose tissue, primarily causing oxidative stress injury and tissue remodeling in the orbital connective tissue. Ferroptosis is a form of programm...

S-PLM: Structure-Aware Protein Language Model via Contrastive Learning Between Sequence and Structure.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Proteins play an essential role in various biological and engineering processes. Large protein language models (PLMs) present excellent potential to reshape protein research by accelerating the determination of protein functions and the design of pro...

Novel machine learning model for predicting cancer drugs' susceptibilities and discovering novel treatments.

Journal of biomedical informatics
BACKGROUND AND OBJECTIVE: Timely treatment is crucial for cancer patients, so it's important to administer the appropriate treatment as soon as possible. Because individuals can respond differently to a given drug due to their unique genomic profiles...

The significance of long chain non-coding RNA signature genes in the diagnosis and management of sepsis patients, and the development of a prediction model.

Frontiers in immunology
BACKGROUND: Sepsis is a life-threatening organ dysfunction condition produced by dysregulation of the host response to infection. It is now characterized by a high clinical morbidity and mortality rate, endangering patients' lives and health. The pur...

Integration of biological data via NMF for identification of human disease-associated gene modules through multi-label classification.

PloS one
Proteins associated with multiple diseases often interact, forming disease modules that are critical for understanding disease mechanisms. This study integrates protein-protein interactions (PPIs) and Gene Ontology data using non-negative matrix fact...

DeepPD: A Deep Learning Method for Predicting Peptide Detectability Based on Multi-feature Representation and Information Bottleneck.

Interdisciplinary sciences, computational life sciences
Peptide detectability measures the relationship between the protein composition and abundance in the sample and the peptides identified during the analytical procedure. This relationship has significant implications for the fundamental tasks of prote...

PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms.

Nature communications
Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards p...

Integration of bulk/scRNA-seq and multiple machine learning algorithms identifies PIM1 as a biomarker associated with cuproptosis and ferroptosis in abdominal aortic aneurysm.

Frontiers in immunology
BACKGROUND: Abdominal aortic aneurysm (AAA) is a serious life-threatening vascular disease, and its ferroptosis/cuproptosis markers have not yet been characterized. This study was aiming to identify markers associated with ferroptosis/cuproptosis in ...

An exploration into the diagnostic capabilities of microRNAs for myocardial infarction using machine learning.

Biology direct
BACKGROUND: MicroRNAs (miRNAs) have shown potential as diagnostic biomarkers for myocardial infarction (MI) due to their early dysregulation and stability in circulation after MI. Moreover, they play a crucial role in regulating adaptive and maladapt...