Research

Biological networks such as neural network, gene regulatory network, protein-protein interaction network, and metabolic network are ubiquitous in biological systems. The study of structure and function of biological network has a profound impact on our understanding of biological systems. Laboratory of Biological Network Computation focuses on applying computational approaches to study real biological networks including large-scale neural network and gene regulatory network in nervous system. We have two main research directions:

1. Analysis of large-scale neural networks

The study of neural networks in complex organisms has been the key to understand the neural basis of behaviors at the systems level. Currently, cutting-edge technologies including electron microscopy, light microscopy, and functional MRI have enabled the reconstruction of connectomes at microscopic, mesoscopic, and macroscopic levels in different species. In species such as zebrafish, it has become possible to monitor the neural activity of the whole larval brain at single neuron resolution. Therefore, there is an urgent need for the development of computational methods for processing and analysis of the large-scale connectomics data. We are working closely with the experimental labs to develop new strategies for network reconstruction best reflecting the causality in sequential neural activity data. We are analyzing the topological structures of the multi-scale whole-brain networks in order to link the function of neural network with its structure. From the analysis of large-scale neural network, we hope to unveil the overarching principle of neural basis of complex behaviors that can further inspire innovative computational models in artificial intelligence.

2. Analysis of gene regulatory network in nervous system

Circadian clock is an endogenous oscillator evolved to coordinate animal behavior and physiology according to the 24-hour daily rhythm of the environment. At the molecular level, the circadian clock is generated through the negative feedback loops consisting of core circadian genes. Circadian clock controls various aspects of physiological processes such as sleep-wake cycle, metabolism, and cell cycle through the gene regulatory networks in different tissues. Using a systems biology approach, we are studying the circadian gene regulatory networks in model organisms such as mouse and zebrafish. The reconstruction of gene regulatory network by the integration of circadian gene expression data and promoter analysis allows us to identify the novel components and modules in circadian gene regulatory networks. With a combination of computational and experimental approaches, we hope to reveal the circadian functions in the nervous system as well as peripheral tissues and identify crucial molecular links between circadian clock and neurodegenerative diseases.