Hi Febear,
I think your case is very strong although you are a Ph.D. student.
I think you missed the most important part "orginality".
For EB1A, a larger number of publication does not equalto "originality". In this case, some letters from big guys all around the world are very important. Although you have many publications, but if you don't have enough citations,
the impact of your work becomes very weak. In this case,
referlence letters are dominant.
For sure, you should appeal. Remember to get more Big letters.
It may be good to look at some suggestions from
http://immigrationportal.com/showthread.php?t=177432
http://www.immigrationportal.com/showthread.php?t=148088&highlight=alien_simba