Reddit reviews Systems Biology: Properties of Reconstructed Networks
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It sounds like you might be interested in systems biology, which emphasizes the use of simulation based on physical models of biological systems. A major goal within the discipline is to bridge the gap between genotype and phenotype.
Check out any of the techniques associated with modeling metabolism, such as flux balance analysis and metabolic flux analysis. Also, Bernhard Palsson has written some good books on the subject. I highly recommend looking at his groups publications.
If you're interested in image analysis, check out the last chapter in PLOS computational biology's online collection: translational bioinformatics. I think the collection really highlights the variety of subdiciplines within computational biology/bioinformatics.
I'm personally excited about developments in proteomics and metabolomics - fields that should provide a better understanding of the chemical processes that are responsible for phenotype.
I hope any of these fields spark your interest!