I think you should be able to get into Emory so long as you get really good letters of recommendation from both your MS program and your undergraduate institute. Or, you can just get LoRs just from your MS program, especially if you've done collaborations or work in other labs (might even be a good idea to talk to your adviser about which route to go). I'm not sure what percentile your GRE scores are in, but if they're around the 80s you should be fine with those as well. Most schools just want someone who is competent at lab work and knows how to critically think about problems.
