Nontraditional student with moderate GPA looking to enter grad school

On paper:
Institution and Major: U of I Urbana, Molecular and Cellular biology, minor in chemistry. Known for grade deflation
Overall GPA: 2.97
Major GPA: 2.90
400 level and up combined GPA: 3.11
3 years of basic science research in 2 different labs
1 publication in Nature Chemistry
Relevant work experience: Lab manager in top psychology lab
Letters of Rec: 1 from high prestige chem professor Havard MD/PhD and HHMI, 1 from a post-doc, and one from a bio course instructor
GRE: TBA but I predict a proportionally much higher score compared to GPA, e.g. >80 percentile
Numerous leadership activities including: AMSA, Phi Theta Kappa Honor society, and served on Campus Recreation policy committee.

Goals:
My goal is to get a PhD at a mid-upper tier research university studying cognitive control. I have not chosen which field to pursue this in but it will either be psychology or neuroscience. Some schools I have considered are UCSF, UIUC, University of Colorado, UM-Madison, Northwestern, and University of Maryland. UCSF is my top choice but I don’t know if my GPA will automatically disqualify me. They do not list a minimum GPA.

Circumstances:
As a non-traditional student I needed to maintain a steady job to help cover my living expenses. I worked around 30 hours per week and went through depression for a couple years, but was too stubborn to seek treatment. I took many high level biology courses that were not even required for my major. Classes that were more homework and participation intensive I consistently did much poorer than classes that were test based.

Taking postbac classes are not an option for me because I have no possible way of paying for them. I am looking to matriculate Fall 2016. Any advice or opinions would be greatly appreciated!

You will have to see how your GRE scores go but many schools have a 3.0/4.0 minimum for consideration. This is particularly true of the highly selective ones that have many, many applicants. If you have a supporter at UIUC you might have a better chance there than the others you have listed. Don’t get me wrong, you can probably get into a pretty good program if you apply to less selective programs that don’t triage based on GPA. You seem to have good research experience and the GPA is a bit better looking more closely at recent courses.

It would be better if all three of your letters are from professors. Postdocs can serve in a pinch.

The rest of your background is pretty good; the GPA seems to be the only ding, and your upper-level GPA is higher (although why start it at 400-level? Junior and senior classes are usually 300-level and up, unless UIUC does that differently. Most students will have only taken a few 400-level classes, so a GPA in just 400- and 500-level classes is kind of meaningless).

So really, there’s no way to predict…some professors might be too turned off by your GPA and other professors will be more open given the rest of your record. Personally were I choosing a student, I might be intrigued by your experience but wary about the low GPA. At top schools, there are unfortunately many other applicants who will look just as good as you do but have a better GPA. More mid-tier programs might be more forgiving, though. You should probably apply to a pretty wide range of places - some top, and some more mid-tier - to see what happens.

Also, you’d have better chances in a neuroscience program, unless you have significant coursework in psychology that you don’t mention here.