Understanding the interactions between microorganisms and their impact on bacterial behavior at the community level is a key research topic in microbiology. Different methods, relying on experimental or mathematical approaches based on the diverse pr...
Proteins are used in various biotechnological applications, often requiring the optimization of protein properties by introducing specific amino-acid exchanges. Deep mutational scanning (DMS) is an effective high-throughput method for evaluating the ...
Cellular communication relies on the intricate interplay of signaling molecules, forming the Cell-cell Interaction network (CCI) that coordinates tissue behavior. Researchers have shown the capability of shallow neural networks in reconstructing CCI,...
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA b...
Biochimica et biophysica acta. General subjects
Mar 14, 2024
BACKGROUND: Abiotic stresses pose serious threat to the growth and yield of crop plants. Several studies suggest that in plants, transcription factors (TFs) are important regulators of gene expression, especially when it comes to coping with abiotic ...
N6-methyladenosine (m6A) is the most prevalent, abundant, and conserved internal modification in the eukaryotic messenger RNA (mRNAs) and plays a crucial role in the cellular process. Although more than ten methods were developed for m6A detection ov...
RNA-protein interaction (RPI) is crucial to the life processes of diverse organisms. Various researchers have identified RPI through long-term and high-cost biological experiments. Although numerous machine learning and deep learning-based methods fo...
Interdisciplinary sciences, computational life sciences
Mar 8, 2024
As one of the most important post-translational modifications (PTMs), protein phosphorylation plays a key role in a variety of biological processes. Many studies have shown that protein phosphorylation is associated with various human diseases. There...
Neural networks : the official journal of the International Neural Network Society
Mar 5, 2024
Convolutional neural networks (CNNs) have gained immense popularity in recent years, finding their utility in diverse fields such as image recognition, natural language processing, and bio-informatics. Despite the remarkable progress made in deep lea...
RNA modification, a posttranscriptional regulatory mechanism, significantly influences RNA biogenesis and function. The accurate identification of modification sites is paramount for investigating their biological implications. Methods for encoding R...
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