I have been tasked to analyze a rich dataset consisting of transcriptomics, proteomics and metabolomics. I want to take a systems biology approach and explore the data and find some new questions to test. I am new to the field of systems biology, and I am trying to find some resources to help me on my endeavor. I have found a few papers using correlation networks for transcriptomics and I have a copy of An Introduction to Systems Biology by Uri Alon in the mail. But I have yet to find any papers that actually use all three types of data in an analysis. And I am struggling to find a resource on how to practically carry out such an analysis, especially on the proteomics and metabolomics side of things. Any recommendations for good systems biology papers and examples of software/pipelines that would be useful in my case would be much appreciated.