Network-based computational systems biology, an emerging area focusing on various biomolecular networks, is a multidiscipline intersection of mathematics, computer science and biology. To elucidate the essential principles and fundamental mechanisms of cellular systems, study on biomolecular networks is increasingly attracting much attention from several academic communities, such as mathematics, information science and life science. A major challenge in computational biology is to investigate how cellular systems facilitate biological functions and achieve complex lives by various interactions (pathways and networks) between genes, proteins and metabolities. In contrast to the study on individual molecules, I will demonstrate our recent works on the area of network biology, including topics on inferring and analyzing biomolecular networks in cellular systems based on available experiment data, in particular stressing on the aspects of network, system, integration and engineering at molecular level.