Recent advances in high-throughput technique enables the generation of a large amount of omic data such as genomics, transcriptomics, proteomics, metabolomics, glycomics etc. Typically, differential expression analysis (e.g., student's t-test, ANOVA) is performed to identify biomolecules (e.g., genes, proteins, metabolites, glycans) with significant changes on individual level between biologically disparate groups (disease cases vs. healthy controls) for cancer biomarker discovery. However, differential expression analysis on independent studies for the same clinical types of patients often led to different sets of significant biomolecules and had only few in common. This may be attributed to the fact that biomolecules are members of strongly intertwined biological pathways and highly interactive with each other. Without considering these interactions, differential expression analysis could lead to biased results. Network-based methods provide a natural framework to study the interactions between biomolecules. Commonly used data-driven network models include relevance network, Bayesian network and Gaussian graphical models. In addition to data-driven network models, there are many publicly available databases such as STRING, KEGG, Reactome, and ConsensusPathDB, where one can extract various types of interactions to build knowledge-driven networks. While both data- and knowledge-driven networks have their pros and cons, an appropriate approach to incorporate the prior biological knowledge from publicly available databases into data-driven network model is desirable for more robust and biologically relevant network reconstruction. Recently, there has been a growing interest in differential network analysis, where the connection in the network represents a statistically significant change in the pairwise interaction between two biomolecules in different groups. From the rewiring interactions shown in differential networks, biomolecules that have strongly altered connectivity between distinct biological groups can be identified. These biomolecules might play an important role in the disease under study. In fact, differential expression and differential network analyses investigate omic data from two complementary perspectives: the former focuses on the change in individual biomolecule level between different groups while the latter concentrates on the change in pairwise biomolecules level. Therefore, an approach that can integrate differential expression and differential network analyses is likely to discover more reliable and powerful biomarkers. To achieve these goals, we start by proposing a novel data-driven network model (i.e., LOPC) to reconstruct sparse biological networks. The sparse networks only contains direct interactions between biomolecules which can help researchers to focus on the more informative connections. Then we propose a novel method (i.e., dwgLASSO) to incorporate prior biological knowledge into data-driven network model to build biologically relevant networks. Differential network analysis is applied based on the networks constructed for biologically disparate groups to identify cancer biomarker candidates. Finally, we propose a novel network-based approach (i.e., INDEED) to integrate differential expression and differential network analyses to identify more reliable and powerful cancer biomarker candidates. INDEED is further expanded as INDEED-M to utilize omic data at different levels of human biological system (e.g., transcriptomics, proteomics, metabolomics), which we believe is promising to increase our understanding of cancer. Matlab and R packages for the proposed methods are developed and available at Github (https://github.com/Hurricaner1989) to share with the research community. / Ph. D. / High-throughput technique such as transcriptomics, proteomics and metabolomics is widely used to generate ‘big’ data for cancer biomarker discovery. Typically, differential expression analysis is performed to identify cancer biomarkers. However, discrepancies from independent studies for the same clinical types of samples using differential expression analysis are observed. This may be attributed to that biomolecules such as genes, proteins and metabolites are members of strongly intertwined biological pathways and highly interactive with each other. Without considering these interactions, differential expression analysis could lead to biased results. In this dissertation, we propose to identify cancer biomarker candidates using network-based approaches. We start by proposing a novel data-driven network model (i.e., LOPC) to reconstruct sparse biological networks. Then we propose a novel method (i.e., wgLASSO) to incorporate prior biological knowledge from public available databases into purely data-driven network model to build biologically relevant networks. In addition, a novel differential network analysis method (i.e., dwgLASSO) is proposed to identify cancer biomarkers. Finally, we propose a novel network-based approach (i.e., INDEED) to integrate differential expression and differential network analyses. INDEED is further expanded as INDEED-M to utilize omic data at different levels of human biological system (e.g., transcriptomics, proteomics, and metabolomics) to identify cancer biomarkers from a systems biology perspective. Matlab and R packages for the proposed methods are developed and shared with the research community.