Saying this as someone with a 3.36, ya, you have a chance. I've been calling up directors of all the neuroscience programs I'm interested in and, amongst other topics of conversation, asking them about my chances at their programs. The feedback I've gotten from all of them, other than UCSD, has been very positive. Now, I do have more research than you, but my impression is that your 2.5 years is well good enough, especially if you can get those manuscripts in review. Perhaps genetics or developmental biology will garner a more competitive field of applicants than neuroscience, but I doubt it.
I don't know abut the quality of any genetics or developmental biology programs, but maybe Emory would be good to look into? They seemed the least concerned about my GPA of anyone. As in, they viewed it as a total non-issue. On the top end Harvard, Stanford, Yale, and Johns Hopkins were all very encouraging of my chances. With that said, other than Emory, they all said that my LORs, SOP, and GRE would be important, and perhaps more so than usual. Most said that I would need a GRE in the 70th to 80th percentile for them to feel truly comfortable with my low GPA. So, keep that in mind.