B- in a Major Class Last 60 Credits (Mathematics) I'm a mathematics undergraduate at a research university, and recently got a B- in Advanced Calculus I this semester as a junior. I would like to know how much this could affect my chances for getting into graduate school for a PhD in applied mathematics.

The reason is simple: time management. I received a research scholarship in Biology and spent too much time on this commitment (it was my first major project). However, my mentor is confident this project will get me a first authored publication within a decent journal.

My other classes that semester were straight A's. As a result my overall GPA is now 3.79 and my major GPA 3.72. I completed an AA in high school, so all of my electives have been in statistics, maths, computer science and graduate level genetics.

However, this is not my first bad grade: I also go a B- in physics and withdrew from a chemistry course my freshman year but was quickly diagnosed with Asperger's syndrome and given reduced course load + double test time. These are the conditions under which I got my B- in Advanced Calculus I. 

I would greatly appreciate an expert opinion (I'll also talk to my math adviser next semester). My research interests lie within gene expression/regulation, so I really want to enter a PhD program in applied mathematics that is also associated with a NIH funded center for System's Biology (such as UC Berkeley, Stanford or MIT).

Next semester I'm taking Advanced Calculus II under the same professor, a course in C++ and a 6000 level PhD track course in Genomics/Proteomics/Transcriptomics with 3 exams and 4 semester projects (I have a 4.0 in all the prerequisites). Any advice?
Any advice?


Yes.  Since you have a designated adviser, I recommend talking to them about it.  They can guide you through the rest of your program.  You can talk to them when classes resume, which is fine, because you have  long term considerations in which absolutely no action is needed or helpful over the semester break.

Your question here is not really practical or answerable.  Yes, it is better to get higher grades than lower ones: you heard it here first.  Obviously if you could retroactively increase your B- grade, then your hypothetical PhD application would be at least slightly stronger.  No one B- is going to make or break a PhD application.  If you are having time management issues, then you should take steps to address them...starting with talking to your adviser.  You might consider delaying taking the sequel to the course you got a B- in to shore up your knowledge, acquire better time management skills, or both.  On the other hand you might need to take this course right away in the context of your program as a whole.

Finally, I notice that you seem to have more success with biology than mathematics: compare a likely first-authored publication with a B- grade in an intermediate level course.  If you apply to a program in mathematics, then your math skills will be compared against others whose interests are solely or primarily in math.  If you apply to a program in biology then your math skills will likely be found to be very strong and set you apart from many of the other candidates.

Enjoy the holiday break.