From what I've heard (talking with my PI and other professors), LORs and research experience are the most important. If you have strong LORs despite low GPA and no publications, you still have a good shot. You're also applying to a variety of schools, so I definitely think you have a chance of getting at least a few interviews. Summer research fellowships also go a long way, so don't discount yourself yet! What I've learned this application season is that you never know exactly what the committees are looking for. They may need to balance the research interests of their incoming class, so if you have a strong synthetic bio background, it might work in your favor. Harvard Systems Biology interviews have already been sent out, but I believe most of your other schools haven't sent out invites, so there is still a chance!