Methods in molecular biology (Clifton, N.J.)
Jan 1, 2022
Drug-target residence time, the duration of binding at a given protein target, has been shown in some protein families to be more significant for conferring efficacy than binding affinity. To carry out efficient optimization of residence time in drug...
BACKGROUND: Cell-surface proteins have been widely used as diagnostic and prognostic markers in cancer research and as targets for the development of anticancer agents. So far, very few attempts have been made to characterize the surfaceome of patien...
The lack of explainability is one of the most prominent disadvantages of deep learning applications in omics. This 'black box' problem can undermine the credibility and limit the practical implementation of biomedical deep learning models. Here we pr...
Glioblastoma (GBM) is a common malignant brain tumor which often presents as a comorbidity with central nervous system (CNS) disorders. Both CNS disorders and GBM cells release glutamate and show an abnormality, but differ in cellular behavior. So, t...
The identification of hidden responders is often an essential challenge in precision oncology. A recent attempt based on machine learning has been proposed for classifying aberrant pathway activity from multiomic cancer data. However, we note several...
RAGE signal transduction via the RAGE-NF-κB signaling pathway is one of the mechanisms of inflammatory reactions that cause severe complications in diabetes mellitus. RAGE inhibitors are promising pharmacological compounds that require the developmen...
Clinical definitions of asthma fail to capture the heterogeneity of immune dysfunction in severe, treatment-refractory disease. Applying mass cytometry and machine learning to bronchoalveolar lavage (BAL) cells, we find that corticosteroid-resistant ...
Current studies of cell signaling dynamics that use live cell fluorescent biosensors routinely yield thousands of single-cell, heterogeneous, multi-dimensional trajectories. Typically, the extraction of relevant information from time series data reli...
It is well known that the development of drug resistance in cancer cells can lead to changes in cell morphology. Here, we describe the use of deep neural networks to analyze this relationship, demonstrating that complex cell morphologies can encode s...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
Bioinformatics tools and resources are valuable for the analysis of data sets focusing on programmed cell death. This chapter discusses methods for the generation of gene sets as well as enrichment analysis using publicly available databases.
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