What are alternatives to Journal of Theoretical Biology?
There are quite a few journals where you can publish theoretical work in this area. Here are a few suggestions (the distinction is based on my perception and knowledge of what they've published, I'll let others chip in if they disagree):

For more theoretical work:


The IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB).
The Journal of Computational Biology.
The Journal of Mathematical Biology.
The Bulletin of Mathematical Biology


For more applied work:


Bioinformatics.
BMC Bioinformatics. (open access)
Algorithms for Molecular Biology. (open access)
PLoS Computational Biology. (open access)


This is not exhaustive of course, and I suggest you discuss these "candidates" with your collaborators.

EDIT: I marked some of them "open access" because they advertise(d) so. This does not mean that the others do not offer that option, you'll have to check.