BeakerBreaker

There's nothing wrong with getting academic professors as some of your LORs, and it is true that schools in general do not accept recommendations from grad students/technicians/postdocs. It sounds like you still have time (~6 months before applications are due?) to familiarize your PI with who you are and what you have been doing in their lab, and you may choose to ask them to write a LOR early which may lead them to rely on the advice of your actual day-to-day mentors (the grad students). It is often the case that PIs have someone else write the recommendation letter for better or worse... The issue of whether or not you need to take time off comes down entirely to how sure you are that you want to get a PhD in general. A Master's is almost always a waste of time and money as graduate classes don't necessarily further your ability to work in the lab, and it's incredibly expensive unless paid for by someone else. I think you should apply to a PhD this cycle provided 1) you are sure you want to do it and 2) you can get decent LORs in the time between now and your application dates. If not, consider working for 1-2 years in a university as a research assistant/technician with the goal of getting better LORs and experience.

I suspect that's your issue right there. The chance that you get an offer after they spend $$$ to fly you out for an interview is generally fairly high. Your stats are otherwise decent to good and it kind of precludes a letter of recommendation tanking you.

Every relationship is different. Without knowing why you feel your relationship needs to be saved, my general advice is: if this relationship was "the one," it wouldn't need you to transfer to save it. I've skipped job offers and delayed my career for a year to try and maintain a relationship. It fell through. It wasn't the end of the world, but I believe these kinds of sacrifices are generally a bad idea, regardless of the outcome.

The only thing that stands out is your quantitative GRE is probably what would get your application screened out at most schools. Focus on improving that score when you retake it. There really is no such thing as a "safety school" when it comes to grad school so don't pick places that you think are mediocre simply because you think it will be easier to get in. Research experience (which you've been working on) is probably the biggest thing that will contribute to helping you get in aside from the GRE.

You might want to look at some of the individual schools. WUSTL recently dropped the GRE requirement for about half of their biomed programs but I don't know if that's the case anywhere you are applying (will save on the GRE transfer fee at least)

I'm not sure what you would get out of staying an additional year in your postbac, and I have no idea why they are advising you to stay. You have enough of everything on your CV from the looks of it to have a shot at those schools. I say just go for it this year. Umbrella vs. neuroscience doesn't matter unless you have zero experience in neuroscience. You should definitely apply to a decent selection of best/good schools and see how it goes if it wouldn't be a financial burden to do so.

The challenge for your application is that the schools will want to know what the chance is that you can handle the quantitative courses and that you will be able to successfully do graduate level work in biostats/informatics/comp bio. On paper it is basically impossible to tell if you are capable of doing that sort of work, whereas you have better demonstrated you can handle molecular bio. Knowing a bit of programming languages and self-taught math is a start but won't measure up against people who spent their undergrad focusing on it, and those people will generally be your competition as an applicant to those schools. There is no such thing as a "safe" school, but certainly the ones you have listed are going to be among the most critical of your application. You will have an uphill battle to prove you are capable of doing that sort of work. That said, you can certainly do it. I went the mol. bio -> bioinformatics route and worked hard to show I could handle statistics and computational approaches. Some of the umbrella programs like WashU will definitely allow you to work in whatever kind of lab you want, but that's only an option after you've been accepted.

You were working ~40 hours/week as a technician while finishing undergrad? That would be a good bit of experience. I think you should shoot for the top. Your GPA isn't stellar but won't prevent you from getting into good schools. Having good LORs will certainly help, but otherwise you look good to go. For your personal statement, you want to be able to express clearly why you want to do research full time at the doctoral level (so, independent thinking), what kind of projects you are interested in working on, and why the school you are applying to is the right fit. Grad schools want to see someone who knows what they are getting themselves into and has a clear and realistic vision for what they want to do with their career, and project someone who will thrive in a graduate environment. All of this is crucial. For the rest -- you can work in the hardship statements, but don't be defensive about yourself. Graduate school is basically a job interview and you don't want them looking at you like a charity case. If you expound on your medical issues, you sound like a liability -- this is not a good thing and they don't need to know. On the other hand, if work your family situation into it (don't make this the focus, though), you will sound like someone with grit which is one of the most important characteristics an incoming grad student can have. Do you have a good sense of the sorts of things you want to study? You should be going through the labs of the programs you might be interested in and seeing who you might want to work for. As a general rule of thumb, find schools with multiple options for mentors so you don't put all of your eggs in one basket. Start with the top schools and make a spreadsheet of programs/labs and just work your way down until you feel like you have a large list, then whittle it down to ~10 schools for applications at the very least. On the coasts, places like UCSF/MIT/Harvard/UWashington/Etc... Mix some of those with schools in the middle-brackets. Think about what those environments might be like. The classes won't be the challenge, but the atmosphere/culture will be demanding and require hard work. You should be able to get some financial assistance for the application fees themselves. Anyway, you sound pretty inspirational. If you want further advice on whittling things down, narrowing down the choices, or crafting the personal statement, poke around here or shoot me a PM. Good luck!

Just go for it and don't sell yourself short. Emphasize your research experience and other academic accomplishments (such as the conferences/publications). The 3.0 GPA requirement is mostly to make sure you don't bomb out of the Master's phase of PhD programs. Whether or not they value the GPA is very school- and program-specific and many will overlook it entirely. I'm not sure how much I'd focus on it during the application, but definitely be prepared to discuss the upward trend and your passion for research in interviews... if they bring it up. Good experience, LORs, and GRE scores will be likely be enough to get you in to some of those programs. Also, keep in mind there really is no such thing as a "safety" school in graduate applications.

I did my first rotation during that summer.

Here are a couple of anecdotes that have shaped my view on this: My mom has an MBA from Stanford, and even 40+ years after she graduated, she is still talking about how "it was okay that she went to the #2 school because she got into Harvard and turned them down." A close friend of mine was accepted into a Tier 1 law school, but also was accepted into a Tier 2 law school with full tuition paid, and this made her decision very difficult. The MBA/J.D./etc. worlds are just fundamentally different than what goes on in science. The prestige of the program has a huge impact on your ability to find internships or clerkships and further your career. Science is a little more meritocratic. Nobody is going to bat an eyelash if you present a keynote talk at a conference and happen to be from the University of South Dakota. Similarly, if you publish three papers in Nature, your career prospects are going to be fairly good no matter what institution you're coming from. I just think - and this is sincere - that using prestige metrics to shape your decision is going to be a mistake. A couple other issues that will greatly affect your success would be: 1) who would you be working with (even if you go to Harvard, not all Harvard labs are the same), and 2) will you be in an environment where you will thrive and be inspired/allowed to do your best work (such as umbrella program vs. specialized). The prestige of the lab (lab, not school in most likelihood) will be good for networking opportunities, but that is fairly limited in scope. If you do good work, your institution won't be a big factor. Definitely don't make the mistake of using the opinion of people outside the field either. I know you aren't doing this, but I just felt like adding a mini-rant section for all of the people who thought I was absolutely nuts to consider schools in the midwest like UT: SW, a "no-name" school, and turn down 3 Ivy league schools in the process. Anywho, I hope you find a good university that fits what you're looking for scientifically. The extent to which I used rankings was I opened up U.S. News to look at the top ~150 schools and make sure I hadn't missed anything noteworthy (like UT:SW, Scripps, Cold Spring Harbor) that I might have otherwise overlooked. I didn't apply to Harvard or Stanford, not because I thought I wouldn't get in, but because I didn't see enough labs there I thought would fit my research interests. I'd totally look into WUSTL, UW:M, and Emory more if you have even the slightest interest because you certainly can succeed at any of those three provided the schools turn out to be good fits for you.

This is a near pointless exercise to involve multiple people on this site. There will be no consensus on what the 20 "best" graduate programs are in a field. If you want the metrics, they are freely available online; otherwise, sites like US News use their own. You will be the best judge when it comes to appraising each program's value based on what you feel is important. WUSTL, UWM, and Emory are all good schools for MCB. You will probably find that there are other factors much more important to your decision among these high caliber schools than their absolute ranking in some subjectively influenced list.

To be honest, I don't think the GRE is good for much of anything >< But this is what we have to work with

I just wanted to say I think it's interesting that people think quantitative matters more for biology - mostly because I've never heard that before, and didn't have that impression originally. Also, most of the biologists I know are not particularly good at quant, nor do they ever seem to need it (making a vast generalization here). It's been my impression that verbal reasoning, whatever that is, is at least as important for the vast majority of biologists. It's actually quite embarrassing when you run into professors who suffer in that category - even more so when they have some god awful fixation with forcing their students to "learn to write," or "learn to speak," when in reality it's just a projection of their own deficits... *shakes fist* I've never seen a grad school biologist suffer because they couldn't do 8th grade-era math, but I have certainly seen them suffer because they don't know how to read or write decently.

Ivy schools aren't all in the same tier in terms of difficulty. Brown and Dartmouth are not nearly as hard for admission as Harvard and Princeton. Your stats are fine for Brown, so far as having a chance at it. Can't comment on UPenn as I don't know. As Bioenchilada said, your other stats will matter. Aim higher and not lower if you have the time and financial means to do so.