Current Bioinformatics - Volume 18, Issue 10, 2023

Background: The expression of secretory proteins is involved in each stage of biomass from fetal development to the immune response. As an animal model for the study of human diseases, the study of protein secretion in pigs has strong application prospects.Objective: Although secretory proteins play an important role in cell activities, there are no machine learning-based approaches for the prediction of pig secretory pro Read More

Introduction: It is expected that certain driver mutations may alter the gene expression of their associated or interacting partners, including cognate proteins.Methods: We introduced DEGdriver, a novel method that can discriminate between mutations in drivers and passengers by utilizing gene differential expression at the individual level.Results: After being tested on eleven TCGA cancer datasets, DEGdriver substa Read More

Background: Understanding the subcellular location of proteins is essential for studying molecular and protein functions. Intracellular proteins must interact with appropriate molecules at the right time and in the right subcellular location to fulfill their functions. Therefore, the precise prediction of protein subcellular location can help elucidate complex cellular physiological response processes and is of great importance to resear Read More

Introduction: Numerous clinical data and animal models demonstrate that many patients with neuropathic pain suffer from concomitant depressive symptoms.Methods: Massive evidence from biological experiments has verified that the medial prefrontal cortex (mPFC), prefrontal cortex, hippocampus, and other brain regions play an influential role in the comorbidity of neuropathic pain and depression, but the mechanism Read More

Background: Spinocerebellar ataxia type 3/Machado-Joseph disease (SCA3/MJD) is a clinically heterogeneous and progressive condition. Evaluation of its progression will contribute to clinical management and genetic counseling.Objective: The objective of this study was to provide a visualized interpretable prediction of the progression of SCA3/MJD based on machine learning (ML) methods.Methods: A total of 716 patients with Read More

Background: Prostate cancer (PCa) is a kind of malignant tumor with high incidence among males worldwide. The identification of novel biomarker signatures is therefore of clinical significance for PCa precision medicine. It has been acknowledged that the breaking of stability and vulnerability in biological network provides important clues for cancer biomarker discovery.Methods: In this study, a bioinformatics model by characteri Read More

Background: New drugs are costly, time-consuming, and often accompanied by safety concerns. With the development of deep learning, computer-aided drug design has become more mainstream, and convolutional neural networks and graph neural networks have been widely used for drug128;“ target affinity (DTA) prediction.Objective: The paper proposes a method of predicting DTA using graph convolutional netw Read More