Abstract
Signal transduction systems are known to widely regulate complex biological events such as cell proliferation and differentiation. Although numerous biological analyses have revealed many of the key molecules and events involved in cell signaling, an integrative view of this complicated system cannot provide a fundamental theory on the regulation of the entire network without analyzing the dynamic behavior of these molecules and events at the system level. Recent technological advances in mass spectrometry-based proteomics and bioinformatics have enabled us to obtain a networkwide description of signaling dynamics through the large-scale identification and quantification of phosphorylated molecules. Accordingly, computational modeling on the basis of dynamic proteomics data has also been applied to the network analysis of representative signaling systems such as the epidermal growth factor receptor pathway. This review focuses on the current status of quantitative proteomics technology for temporal studies of signal transduction and on the application of comprehensive signaling dynamics data to mathematical analyses of regulatory networks. The perspective on proteomics data-driven systems biology is also discussed.
Keywords: Signal transduction, quantitative proteomics, systems biology, LC-MS/MS, computational modeling
Call for Papers in Thematic Issues
AI-Based Prediction of Functional Proteins
Functional proteins are vital molecules involved in a variety of physiological and pathological processes within the body. Understanding the relationship between protein structure and function is key to unraveling the mechanisms of life sciences, disease processes, and drug discovery. However, traditional experimental methods are often time-consuming, costly, and constrained by ...read more
Application of Large Language Models in Bioinformatics
Large language models (LLMs) are increasingly transforming the field of bioinformatics by enabling scalable, data-driven solutions to complex biological and biomedical challenges. Recent advances in domain-specific foundation models have shown strong performance across a wide range of applications, including protein structure and function prediction, gene annotation, drug discovery, multi-omics data ...read more
Hot Topics in Computational Genomics
Computational genomics has emerged since the beginning of the 21st century. Recently, along with the sequencing technology at single-cell level, computational genomics step forward to the level of singe-cell resolution. Several topics are well studied in this area. Several other topics are still challenging tasks for bioinformatics. This thematic issue ...read more
Related Books
Microbial Insights into Wastewater Treatment and Environmental Sustainability
Biological Control for Plant Protection: Recent Advances in Research and Sustainability
From Genes to Algorithms: Navigating the Biotechnology Data Revolution
Phytochemical Arsenal: Understanding Plant Defense Mechanisms Against Nematodes
Controlled Environment Horticulture: Where Plant Biotechnology Meets Sustainable Future
Genetic Diversity of Coronaviruses: From SARSCoV to SARS-CoV-2 – (Part 2)
Wild Vegetables: Morphology, Phytochemistry and Utility - (Part 2)
A Practical Approach to Molecular Cloning
Organoid Technology: Disease Modelling, Drug Discovery, and Personalized Medicine
Arid and Semi-Arid Zones of Mexico: A Comprehensive Exploration of Biodiversity, Ecology, and Conservation
6