Several faculty are working actively in the area of Bioinformatics, and we are encouraging students to work in the area. The primary faculty advisor is in CS, but students also work closely with faculty in several bio/medical departments.
For information on applying to the Ph D Program in the CS department at the University of Chicago, see the following web page.
It is also possible to specialize in bioinformatics via the Computational Mathematics track at the University of Chicago.
The new Ph D program in Biophysics is another way to work in bioinformatics at Chicago with a significant experimental component.
See my bibliography for areas of research in which I have been involved. I am a member of the Institute of the Biophysical Dynamics (IBD) and the Computation Institute (CI), both of which have a focus on computuational/theoretical biochemistry/biophysics.