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Protein Interaction Maps

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Applying 12 machine learning algorithms and Non-negative Matrix Factorization for robust prediction of lupus nephritis.

Frontiers in immunology
Lupus nephritis (LN) is a challenging condition with limited diagnostic and treatment options. In this study, we applied 12 distinct machine learning algorithms along with Non-negative Matrix Factorization (NMF) to analyze single-cell datasets from k...

Machine Learning Identify Ferroptosis-Related Genes as Potential Diagnostic Biomarkers for Gastric Intestinal Metaplasia.

Technology in cancer research & treatment
BACKGROUND: Gastric intestinal metaplasia(GIM) is an independent risk factor for GC, however, its pathogenesis is still unclear. Ferroptosis is a new type of programmed cell death, which may be involved in the process of GIM. The purpose of this stud...

Identification of diagnostic genes and drug prediction in metabolic syndrome-associated rheumatoid arthritis by integrated bioinformatics analysis, machine learning, and molecular docking.

Frontiers in immunology
BACKGROUND: Interactions between the immune and metabolic systems may play a crucial role in the pathogenesis of metabolic syndrome-associated rheumatoid arthritis (MetS-RA). The purpose of this study was to discover candidate biomarkers for the diag...

Machine learning and bioinformatics analysis of diagnostic biomarkers associated with the occurrence and development of lung adenocarcinoma.

PeerJ
OBJECTIVE: Lung adenocarcinoma poses a major global health challenge and is a leading cause of cancer-related deaths worldwide. This study is a review of three molecular biomarkers screened by machine learning that are not only important in the occur...

Identification of molecular subtypes of dementia by using blood-proteins interaction-aware graph propagational network.

Briefings in bioinformatics
Plasma protein biomarkers have been considered promising tools for diagnosing dementia subtypes due to their low variability, cost-effectiveness, and minimal invasiveness in diagnostic procedures. Machine learning (ML) methods have been applied to en...

INTREPPPID-an orthologue-informed quintuplet network for cross-species prediction of protein-protein interaction.

Briefings in bioinformatics
An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated 'wet lab' experiments. In silico PPI inference methods are ideal tools t...

Screening of Secretory Proteins Linking Major Depressive Disorder with Heart Failure Based on Comprehensive Bioinformatics Analysis and Machine Learning.

Biomolecules
BACKGROUND: Major depressive disorder (MDD) plays a crucial role in the occurrence of heart failure (HF). This investigation was undertaken to explore the possible mechanism of MDD's involvement in HF pathogenesis and identify candidate biomarkers fo...

MAGICAL: A multi-class classifier to predict synthetic lethal and viable interactions using protein-protein interaction network.

PLoS computational biology
Synthetic lethality (SL) and synthetic viability (SV) are commonly studied genetic interactions in the targeted therapy approach in cancer. In SL, inhibiting either of the genes does not affect the cancer cell survival, but inhibiting both leads to a...

Identification of COL3A1 as a candidate protein involved in the crosstalk between obesity and diarrhea using quantitative proteomics and machine learning.

European journal of pharmacology
BACKGROUND: Increasing epidemiologic studies have shown a positive correlation between obesity and chronic diarrhea. Nevertheless, the precise etiology remains uncertain.

New GO-based measures in multiple network alignment.

Bioinformatics (Oxford, England)
MOTIVATION: Protein-protein interaction (PPI) networks provide valuable insights into the function of biological systems. Aligning multiple PPI networks may expose relationships beyond those observable by pairwise comparisons. However, assessing the ...