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?