The area of bio-molecular computing has recently witnessed a major paradigm shift. Rather then being used only as simple calculating units capable of solving hard combinatorial or numerical problems, DNA computers are increasingly becoming more tailored to operate like intelligent biological machines with unprecedented potentials. One example of applying DNA computers in such a new setting is in the area of logical control of gene expression levels. For this purpose, DNA computers are designed in such a way as to be able to diagnose some forms of cancer-related irregularities in a cell and release biological strands acting as inhibitors or activators of certain sets of genes. Such a control action can also be seen as a form of intra-cell cancer therapy, although it may also have other, more varied, purposes and goals. There are several important problems in the area of coding and network theory that arise in the context of developing DNA computers for controlling gene expressions. The two most important issues are that of minimizing diagnostics failure and of increasing the computational reliability of the system. The first question is intimately related to analyzing the operational principles of networks of gene interactions, while the second is concerned with relating combinatorial characteristics of single-stranded DNA sequences to their hybridization affinities and secondary structures. In this paper, we will describe the state-of-the-art results and present some new relevant combinatorial and coding theoretic problems in this area.