I feel strangely qualified to help you right now. I'm also highly interested in computational biology - I've been pursuing a microbiology degree with minors in chemistry and bioinformatics. I've done research in three labs so far in a rather peculiar order.
Environmental Microbiology - Two Years with only one Summer included - Looked at Salmonella and several gene regulators in context of plant systems.
Computational Biology and Functional Genomics - One Summer (10-weeks) Internship - I don't want to go into detail because the professor can be tracked down very easily... But it was developmental biology work.
Bioinformatics (Ecological Microbiology) - One month before the summer internship and then I'll return for a year - Microbiomes of forest environments shared across continents to elucidate differences in microbial populations.
The computational biology was done at UPenn and it was a great experience. I learned so many different techniques and UPenn's mentality and faculty are excellent and down to Earth. If you're looking at brand name they are an Ivy League with VERY impressive facilities. If you're looking for faculty they have a biomedical graduate studies program with a whole computational biology department. They are an excellent choice. I recommend you try this one and all the grad students seem to really love their lives here and the communication among labs is clear and constant.