AnonNeuroGrad

A few of those programs are harder than you think to get into and I would probably move them into Reach programs namely NYU and Chicago possibly also BU (I might be biased but my interview cohort there were also interviewing at places like NYU, Northwestern, MIT, etc.). I think it doesn't have as prestigious of a reputation but it draws some of the same caliber of applicants as those applying to the two big name Boston schools (MIT and Harvard) who use it as their "back-up"; a lot of the people I met decided to go to places like UCSD, UCSF, Yale, Karolinska, etc but nevertheless you'd have to compete against them for a spot at the interview. We had >500 applicants, 40 interviewees (2 international), and 9 were in the cohort (2, like me, were swung into a different neuro program).
USC should not be reach imo. If you're looking at computational neuro, you should remove WSU and Yale.
You didn't ask but here's a list of schools I made for myself when applying. There's a lot of systems neuro mixed in here.
I hate lists because it is so much more nuanced than that. I focused my applications based on particular papers and research collaborations that stood out to me (which is what you should do as well). I'm about to tell you a list (in no particular order) of places that do great work in comp. neuro. but this shouldn't be taken as comprehensive and know that I am biased by groups doing systems work as well in what's called "latent space inference" or "manifold learning" in the United States. Look at who is presenting at Cosyne/CNS/CCN for a good idea of comp. neuro. I don't really make a distinction between many computational and systems neuro since they're so tightly integrated. Adam Calhoun has a great blog post on this and the network graph shows you the current who's whom of the field and their main collaborators. I've starred the "top five schools" imo. I'm intentionally making a long-list so that you can decide who are the top ones in your desired subfield. If I didn't give PIs, it's because I'm lazy. Here's my top ten list
Stanford* (Surya Ganguli, Krishna Shenoy, Dan Yamins, Scott Linderman, EJ Chichilnisky, Google guys like David Sussillo and Jon Shlens)
Princeton* (Jonathan Pillow, William Bialek, Carlos Brody, David Tank, Sebastian Seung)
NYU (Wei Ji Ma, Xiao-Jing Wang, Dmitri Chklovskii, Eero Simoncelli, Dora Angelaki)
Columbia* (John P. Cunningham, Mark Churchland, Liam Paninski, Stefano Fusi, Ken Miller, Randy Bruno, Niko Kriegskorte, Larry Abbott)
MIT (Mehrdad Jazayeri, James DiCarlo, Joshua Tenenbaum, Michale Fee, Mriganka Sur, Mark Bear, Haim Sompolinsky [half-time in Haifa, Israel])
Washington University in St. Louis (James Fitzpatrick, Adam Kepecs, Ilya Monosov, Camillo Padoa-Schioppa, Lawrence Snyder, Geoffrey Goodhill, Keith Hengen)
University of Washington (Adrienne Fairhall, Rajesh Rao, Eric Shea-Brown, [many Allen Institute scientists])
UC Berkeley (Hillel Adesnik, Jack Gallant, Bruno Olshausen, Fritz Sommer, Linda Wilbrecht)
Carnegie Mellon/Pittsburgh* (CNBC) (Brent Doiron, Rob Kass, Bard Ermentrout, Byron Yu)
University of Chicago (John Maunsell, Jack Cowan, David Freedman)
 
And an extended list including many systems people
UC San Diego (Tatyana Sharpee, Terry Sejnowski, Thomas Albright, Bradley Voytek)
Harvard University (Sam Gershman, Chris Harvey, Cengiz Pehlevan, Mackenzie Mathis, many others)
Caltech (Markus Meister, Doris Tsao)
Champalimaud Centre for the Unknown (Christian Machens, Zach Mainen, Leopoldo Petreanu)
UCLA (Jonathan Kao, Dario Ringach, Josh Trachtenberg)
UCSF (Massimo Scanziani, Vikas Sohaal)
ETH Zurich (Ben Grewe, Valerio Mante)
UCL* (Gatsby Unit and Sainsbury-Wellcome) (Matteo Carandini, Ken Harris, Maneesh Sahani)
Oxford (Tim Behrens, Tim Vogels, Adam Packer)
HHMI/Johns Hopkins (Janelia Farm) (Marius Pachitariu, Vivek Jayaraman, Davi Bock, Karel Svoboda, Reza Shadmehr)
Cold Spring Harbor Labs (shared students with SUNY Stony Brook sometimes) (Anne Churchland, Anthony Zador, Tatiana Engel, Adam Kepecs)
Boston University (Chandramouli Chandrasekaran, Ben Scott, Nancy Kopell, Mark Kramer, Uri Eden)
Toronto (Joel Zylberberg [affiliated through York])
Penn (Diego Contreras, Josh Gold, Konrad Kording)
University of Rochester (Adam Snyder, Thomas Howard, Greg DeAngelis)
Baylor (Andreas Tolias, Jacob Reimer)
Northwestern (Daniel Dombeck, Andrew Miri, Sara Solla)
Brandeis (Eve Marder, Gina Turrigiano)
Brown (Jerome Sanes, David Sheinberg, Wilson Truccolo)
UT Austin (Alex Huk, Dana Ballard)
Tons of Germans that I have no idea what universities they are at
EPFL
 
An extended extended list of places that still do this work and are up-and-coming or may be more systems oriented or I know less about but are worth applying to
Georgia Tech (Chethan Padarinath, Eva Dyer, Chris Rozell)
University of Oregon (Cris Niell, David McCormick, Yashar Ahmadian, Luca Mazzucato)
SUNY Stony Brook (shares with CSHL) (Memming Park, Giancarlo La Camera, Alfredo Fontanini, Braden Brinkman)
UC Davis
University of Southern California
Duke
UNC Chapel Hill
Yale
UT Houston
Rice
UCSB

So I actually go to BU and the vibe I got/have is not so much that the departments are competitive but that they just have different philosophies regarding training. Maybe that results in disagreements but I've only been here a week so I probably am not privy to them yet. Again, PM if you want more specific details but broadly,
GPN: This is the main neuro program available and is very heavy into systems neuroscience but seems to be the best funded and supported among the three. It is housed on the main campus with most faculty in either CILSE (the brand new beautiful tower for neuro and some bio) and LSE (life sciences building next door) with some at the medical center (30-45 min shuttle ride away). They seem fairly well-organized and put on programs/events for their 10-15 students a year. Their curriculum is highly programmed which is both good and bad: you get to take a lot of classes with your cohort but you have to take a lot of the classes they want you to take. This program also has access to the computational specialization but doing so will give you only two rotations instead of three (they rotate longer). Admissions for this department is very competitive.
BBC: This program is run through the Psychological and Brain Sciences department and sort of bunches you up with the developmental and clinical psych students. This program is *much* smaller than I think the other two: there are four people in my cohort and they admitted eight last year. Don't think of it so much as a cohort program but as more of a European-style process because you do not rotate and are directly admitted to the lab. Stipend I think is just short of GPN but maybe only a thousand less. There is far less programming put on by the department so I can only recommend this for the student that is able to make friends easily since no one is doing it for you. You also need to have a compelling fit with a PI to get admitted. I know about 10 students interviewed (no idea how many applicants) and 4 ended up joining. This program has a *very* flexible curriculum as only 2 classes are required (Stats for Psych) and the rest is up to you and your PI. I recommend this program for someone really who knows what to do and this comes with the benefit that you get to start researching and publishing earlier without a lot of program requirements. They have grown the department a lot lately with four newish hires (Ben Scott, Marc Howe, Chand Chandrasekaran, and Steve Ramirez) and are hiring another PI. I would also caution that this department has a traditional qualifying exam where you do a literature review and have to answer questions based on those each given to you over a few days (a lot of programs now are just taking an NRSA proposal plus thesis proposal). Not sure what the qualifying exam process is for GPN or A&N.
A&N: This program is much more heavily focused on, eponymously, neuroanatomy and clinical applications. It's based on the medical campus which might be a negative for some but they do seem to have a decent amount of programming (not as much as GPN but more than BBC) for their students and also seem to have far more masters students. I think they emphasize teaching more and their students run the gross anatomy labs for the med students. A lot (all?) of MD/PhD students are through this program. This one is the most foreign to me so I have no idea what the stipend, qualifying exam, or curriculum is like here but it should be easy enough to find. Cohorts are about medium sized and are 4-8 not including a similar number of masters students. 
 
Let me know if you have any questions about these as I can relay them directly to a person in the program. Personally, I think the GPN is the best program for the average student but I liked the independence of the BBC (but really don't like that I essentially don't have a cohort but this isn't the biggest issue because I'm pretty gregarious and have a lot of Boston friends). For whichever professor you'd like to work with, just make sure they are affiliated with the right departments. If you have a lot of specific appeal with one professor, consider the BBC because all they require is for said professor to want you and have the funding available (plus a back-up professor). The GPN you need to appeal to the entire department and need to have three professors step forward and say they want to take you. 

A few of those programs are harder than you think to get into and I would probably move them into Reach programs namely NYU and Chicago possibly also BU (I might be biased but my interview cohort there were also interviewing at places like NYU, Northwestern, MIT, etc.). I think it doesn't have as prestigious of a reputation but it draws some of the same caliber of applicants as those applying to the two big name Boston schools (MIT and Harvard) who use it as their "back-up"; a lot of the people I met decided to go to places like UCSD, UCSF, Yale, Karolinska, etc but nevertheless you'd have to compete against them for a spot at the interview. We had >500 applicants, 40 interviewees (2 international), and 9 were in the cohort (2, like me, were swung into a different neuro program).
USC should not be reach imo. If you're looking at computational neuro, you should remove WSU and Yale.
You didn't ask but here's a list of schools I made for myself when applying. There's a lot of systems neuro mixed in here.
I hate lists because it is so much more nuanced than that. I focused my applications based on particular papers and research collaborations that stood out to me (which is what you should do as well). I'm about to tell you a list (in no particular order) of places that do great work in comp. neuro. but this shouldn't be taken as comprehensive and know that I am biased by groups doing systems work as well in what's called "latent space inference" or "manifold learning" in the United States. Look at who is presenting at Cosyne/CNS/CCN for a good idea of comp. neuro. I don't really make a distinction between many computational and systems neuro since they're so tightly integrated. Adam Calhoun has a great blog post on this and the network graph shows you the current who's whom of the field and their main collaborators. I've starred the "top five schools" imo. I'm intentionally making a long-list so that you can decide who are the top ones in your desired subfield. If I didn't give PIs, it's because I'm lazy. Here's my top ten list
Stanford* (Surya Ganguli, Krishna Shenoy, Dan Yamins, Scott Linderman, EJ Chichilnisky, Google guys like David Sussillo and Jon Shlens)
Princeton* (Jonathan Pillow, William Bialek, Carlos Brody, David Tank, Sebastian Seung)
NYU (Wei Ji Ma, Xiao-Jing Wang, Dmitri Chklovskii, Eero Simoncelli, Dora Angelaki)
Columbia* (John P. Cunningham, Mark Churchland, Liam Paninski, Stefano Fusi, Ken Miller, Randy Bruno, Niko Kriegskorte, Larry Abbott)
MIT (Mehrdad Jazayeri, James DiCarlo, Joshua Tenenbaum, Michale Fee, Mriganka Sur, Mark Bear, Haim Sompolinsky [half-time in Haifa, Israel])
Washington University in St. Louis (James Fitzpatrick, Adam Kepecs, Ilya Monosov, Camillo Padoa-Schioppa, Lawrence Snyder, Geoffrey Goodhill, Keith Hengen)
University of Washington (Adrienne Fairhall, Rajesh Rao, Eric Shea-Brown, [many Allen Institute scientists])
UC Berkeley (Hillel Adesnik, Jack Gallant, Bruno Olshausen, Fritz Sommer, Linda Wilbrecht)
Carnegie Mellon/Pittsburgh* (CNBC) (Brent Doiron, Rob Kass, Bard Ermentrout, Byron Yu)
University of Chicago (John Maunsell, Jack Cowan, David Freedman)
 
And an extended list including many systems people
UC San Diego (Tatyana Sharpee, Terry Sejnowski, Thomas Albright, Bradley Voytek)
Harvard University (Sam Gershman, Chris Harvey, Cengiz Pehlevan, Mackenzie Mathis, many others)
Caltech (Markus Meister, Doris Tsao)
Champalimaud Centre for the Unknown (Christian Machens, Zach Mainen, Leopoldo Petreanu)
UCLA (Jonathan Kao, Dario Ringach, Josh Trachtenberg)
UCSF (Massimo Scanziani, Vikas Sohaal)
ETH Zurich (Ben Grewe, Valerio Mante)
UCL* (Gatsby Unit and Sainsbury-Wellcome) (Matteo Carandini, Ken Harris, Maneesh Sahani)
Oxford (Tim Behrens, Tim Vogels, Adam Packer)
HHMI/Johns Hopkins (Janelia Farm) (Marius Pachitariu, Vivek Jayaraman, Davi Bock, Karel Svoboda, Reza Shadmehr)
Cold Spring Harbor Labs (shared students with SUNY Stony Brook sometimes) (Anne Churchland, Anthony Zador, Tatiana Engel, Adam Kepecs)
Boston University (Chandramouli Chandrasekaran, Ben Scott, Nancy Kopell, Mark Kramer, Uri Eden)
Toronto (Joel Zylberberg [affiliated through York])
Penn (Diego Contreras, Josh Gold, Konrad Kording)
University of Rochester (Adam Snyder, Thomas Howard, Greg DeAngelis)
Baylor (Andreas Tolias, Jacob Reimer)
Northwestern (Daniel Dombeck, Andrew Miri, Sara Solla)
Brandeis (Eve Marder, Gina Turrigiano)
Brown (Jerome Sanes, David Sheinberg, Wilson Truccolo)
UT Austin (Alex Huk, Dana Ballard)
Tons of Germans that I have no idea what universities they are at
EPFL
 
An extended extended list of places that still do this work and are up-and-coming or may be more systems oriented or I know less about but are worth applying to
Georgia Tech (Chethan Padarinath, Eva Dyer, Chris Rozell)
University of Oregon (Cris Niell, David McCormick, Yashar Ahmadian, Luca Mazzucato)
SUNY Stony Brook (shares with CSHL) (Memming Park, Giancarlo La Camera, Alfredo Fontanini, Braden Brinkman)
UC Davis
University of Southern California
Duke
UNC Chapel Hill
Yale
UT Houston
Rice
UCSB

I'm in BU BBC and I know a fair bit about all three programs (my lab is in A&N and I interviewed with GPN [but didn't get in') but you'll have to PM me if you want info and I'll give you my personal email.

Sure I just wanted to make sure you didn't only apply to top schools having heard the advice that "GPA doesn't matter if you have strong research" which I made the mistake of. If you're in NIH PREP/IRTA that's a big plus. Just make sure to appeal to at least 3 professors at each school you really want: I had a few PI's want me (and tell me as much) but because they were only 1 or 2 per school, I never ended up getting in (*cough* Carnegie Mellon *cough*); mea culpa. I have some specific recommendations regarding Columbia if you want to PM me and I can help you through which PI's to talk to or how BU works if you want as well.
Best of luck!!!

So I have some good information for you since I was in your exact position when I graduated (almost exact same stats) and probably would’ve had the same results. I’ll help walk you through what I did to compensate for low grades and what worked/didn’t work and how I did this application season.
i graduated from a regional SLAC with a 3.2 GPA in Biochemistry and Math with a minor in neuroscience. I had three years of undergrad experience but no pubs. I went on to take the GRE and got a 167/164/6.0 I think V/Q/W. I thought deeply about where I needed to compensate and how by following the advice of others and some good blog posts; my weakest areas were going to be my GPA, lack of publications, and letters of rec (no one knows of my recommenders). Thus, number one and two on my list were to enroll in an MS program with good grades and to get some publications. Also to find a job with some big names to write my letters.
I was actually fairly successful at everything: at the time of application, I was a quarter shy of finishing a masters in applied math with a 3.7 at a top-3 public school and I had been working 3.5 years at the premier neuroscience non-profit gaining 3 publications (3rd in Neurotox., mid in eLife, mid in eNeuro), 2 in review (mid in Nature, 2nd in PLOS ONE), and two more in prep (3rd and a 1st). My letter writers were all now former academics (not PIs though, postdocs) that were known in the community. I thought I did everything I could have almost as best as possible and all my mentors had told me that I should shoot very highly in terms of schools.
I applied to the following 14 schools: Harvard, Stanford, Columbia, Princeton, Carnegie Mellon/Pitt, UCSF, UCSD, Carnegie Mellon (Bio), University of Oregon, Boston University, Stony Brook University, MIT, and NYU. I also networked heavily and emailed 2-3 PIs at every school and corresponded with around a dozen extensively over email, over Skype, or in-person at SfN. I was feeling very confident I’d get interviews from around half my schools.
Now a few months later I was rejected from ten schools and received interviews from Carnegie Mellon (Bio), Stony Brook University, University of Oregon, and Boston University. I was admitted to both University of Oregon and Stony Brook University with fellowships about $5k a year each for three years. I’m still waiting to hear back from Carnegie Mellon (Bio) and am waitlisted for Boston University (GPN).
Some takeaways,
I should’ve asked my letter writers to address my grades and I should’ve talked more at length about why my grades were so low (undiagnosed sleep disorder [DSPD], and trauma with my best friend dying in a car accident). Admissions committees didn’t care that I got a 3.7 in my masters it felt like and this didn’t offset my undergrad grades as far as I could tell The admissions process is tightly controlled at a lot of schools by a single-person or a small committee and even though I was invited to interview (even being rated first in the cohort by a professor), it once again came down to grades and I suppose fit which was disappointing. I had believed that once I interviewed, the schools already wouldn’t care about grades and thought I was a good fit. as far as fit goes, I was a bit too specific and I suppose seemingly inflexible during interviews: I thought being a very good specific fit for two or three professors was the way to go but I’m thinking it’s better to have broad appeal. I wasn’t able to get un-pigeonholed as a “biology” or “computational” guy in different contexts. Some PIs expressed doubt as to whether I would even want to do experiments while others didn’t comment on my 5 years of programming or my masters in math. my publications didn’t matter. I never got a single comment on any of them and a lot of interviewees seemed like they had pulled up my CV in their computer a minute before the interview. I think the only sort of pub that matters is a 2nd or 3rd author in a high-tier journal or a 1st in a mid-tier journal. my work experience didn’t matter per se. I had a lot of friends get admitted to schools I got rejected from when they had only 2 years of experience and I had very nearly 7. The only difference between us was GPA so I think the advice “research experience is more important than grades” is false. it matters tremendously who is writing your letters. I’ve seen students with a 3.4 gpa and mediocre scores/experiences with letters from HHMI or NAS members get into every school in the top10.  If I were to do it all again, 
I would have addressed my grades more directly and had my letter writers do so as well I would have not done the MS (or done a 1-year full-time) and then focused two years on getting one or more first-authorships. In retrospect, I had all the experimental and analytic skills to do so but I was just intimidated by the idea of it. I would have chased after working with big names in the field to get a recommendation from them. It matters more than it should. I wish I knew that everyone who was giving me advice that was last in admissions 5 years ago has outdated information. It's at least twice as competitive now and 1st-authorships are now going from unheard of to uncommon. I should've worked like my life depended on it and that's saying a lot because there were many weeks I was working 60-80 hours with work and homework combined. Neuroscience is the hardest life sciences field right now (except clinical psych PhDs) and possibly all of science save except some fields like ML/CS but, unless you talk to someone who's recently applied or is on admissions, you wouldn't know it. BU got >500 applications for 40 interview spots and 8 spots in their incoming class. I networked a ton but I should've networked even more. Really making sure these PIs were invested in having me. One PI at each Boston and CMU had told me explicitly they "golden buzzered" me into interview which I would've never gotten otherwise. Most of my schools were top-20 so I needed this sort of help for each one but even one isn't a guarantee especially if their admissions process is more committee based. BU's seemed to give more power to individual PI's while others were tightly controlled and voted on by each committee. I had a chat for 30 min in-person with the director at Harvard and he said he liked my skillset and would look for my application but alas I never got in (I should've been upfront about my grades). I should've applied to lower-ranked but still very good schools like Pitt, Northwestern, Rochester, UT Austin, Georgia Tech, etc. Very important: I should have applied to more biology programs. They're easier to get into and the only difference is in curriculum (work with all the same professors). Several neuro interviewees I was with at sort-of mid-level institutions also had interviews at top20/10 biology programs. I'm also going to disagree with the advice that getting an acceptance after interview is "yours to lose" because at several of my interviews the acceptance rate was below 50% and so it came down to fit mostly even if you were a wonderful person. One school told me they wanted to see at least three PI's throw their hat in the ring for you. At several of my interviews, all of us were confident, knowledgeable about our work, skilled, and driven no question but yet more than half of us will not receive an offer. This does vary though as I know of one top school that routinely offers every interviewee that passes the "is this person at least normal" test.
Your grades aren't as bad as mines but I feel like for those with the same grades, the only way out is to have something that makes the reviewers go "holy shit" i.e. one or more glowing recs from big names in the field or having first-authorship. That's all I can think up right now but let me know if you have any questions.

Good luck to you all! So many memories, so many tears; I miss it in some sick way.

Good luck to you all! So many memories, so many tears; I miss it in some sick way.

Good luck to you all! So many memories, so many tears; I miss it in some sick way.

Good luck to you all! So many memories, so many tears; I miss it in some sick way.

I had a 3.1 cGPA with a 2.8 in my math major and a 2.9 in my biochem major; I got four interviews (BU, Carnegie Mellon, UO, and Stony Brook) and into BU, UO, and Stony Brook. I'll be attending BU which is just about in the top-20 nationally and one of the stronger ones for computational neuroscience (which is my interest). I will say that, first of all, you can still not only go to grad school but also a good one but it won't be easy by any means. I took four years off and I had a bit higher GPA and did 3 years of research in undergrad so, for you, probably expect to take at least that long. One of my undergrad projects turned into a 3rd author publication and then I was able to secure an RA position after college in neuroscience research. I spent that time getting two more publications and an MS over the four years; although I didn't get interviewed for most top schools I applied to, the PI's I met were super enthusiastic about having me there because of my past experience and MS.
So I guess this is to say that it can still be done and hopefully neuro won't get significantly harder in a few years. PM me if you have any questions but I almost never am on here! I have Discord at the same screen-name so find me there if you have questions.

NYU has very strong computational work but a lot of their scientists do old school stuff and have had their time in the sun (sorta Buzsaki, Movshon, Rinzel) and I doubt Yann LeCun would have time to work with anyone. Rumor has it also that XJ Wang is leaving but I didn't tell you that. Simoncelli, Chklovskii, and Wei Ji Ma are all good options still but their research is somewhat different. It is a Swartz center though and NYC is awesome! They just hired Christine Constantinople who has some good systems ideas using automated behavior training for rats I think.
UCL is obviously excellent with leaders in both theory (Sahani, Latham, Hyvärinen, Botvinick, Pouget) and systems (Harris, Carandini, Mrsic-Flogel) and I'd rate it #1 in the world for combining these approaches. Not sure how Brexit will affect things though and being so close to DeepMind means good industry connections (and also that faculty are harder to keep).
I will once again plug CMU/Pitt's PNC program: they're planning on growing CMU's integration of neuroscience and machine learning through a new Institute of Neuroscience (headed by Barbara Shinn-Cunningham) while still maintaining the joint venture (the CNBC means effectively Pitt and CMU are combined and it's funded by a T32). The work of Byron Yu, Brent Doiron, Bard Ermentrout, and Robert Kass needs no introduction but I've heard (from a postdoc who interviewed in ML) that they are trying to double the size of their ML department which is already #1 in the world. The CMU side of things will also be hiring more neuroscientists for collaborative work and they just built a new business school for tech transfer.

I visited Boston and I think you should take into consideration that the city is pervasively academic what with Harvard next door and Boston University across the river not to mention Tufts, Northwestern, Boston College, and the numerous biotechs all in close proximity. I personally loved that atmosphere whereas I've heard that Pasadena is a bit out there. Given the choice, I'd pick MIT as the ability to go over to Harvard, BU, or the medical campuses is not to be discounted in terms of the ability to network.

So I have some good information for you since I was in your exact position when I graduated (almost exact same stats) and probably would’ve had the same results. I’ll help walk you through what I did to compensate for low grades and what worked/didn’t work and how I did this application season.
i graduated from a regional SLAC with a 3.2 GPA in Biochemistry and Math with a minor in neuroscience. I had three years of undergrad experience but no pubs. I went on to take the GRE and got a 167/164/6.0 I think V/Q/W. I thought deeply about where I needed to compensate and how by following the advice of others and some good blog posts; my weakest areas were going to be my GPA, lack of publications, and letters of rec (no one knows of my recommenders). Thus, number one and two on my list were to enroll in an MS program with good grades and to get some publications. Also to find a job with some big names to write my letters.
I was actually fairly successful at everything: at the time of application, I was a quarter shy of finishing a masters in applied math with a 3.7 at a top-3 public school and I had been working 3.5 years at the premier neuroscience non-profit gaining 3 publications (3rd in Neurotox., mid in eLife, mid in eNeuro), 2 in review (mid in Nature, 2nd in PLOS ONE), and two more in prep (3rd and a 1st). My letter writers were all now former academics (not PIs though, postdocs) that were known in the community. I thought I did everything I could have almost as best as possible and all my mentors had told me that I should shoot very highly in terms of schools.
I applied to the following 14 schools: Harvard, Stanford, Columbia, Princeton, Carnegie Mellon/Pitt, UCSF, UCSD, Carnegie Mellon (Bio), University of Oregon, Boston University, Stony Brook University, MIT, and NYU. I also networked heavily and emailed 2-3 PIs at every school and corresponded with around a dozen extensively over email, over Skype, or in-person at SfN. I was feeling very confident I’d get interviews from around half my schools.
Now a few months later I was rejected from ten schools and received interviews from Carnegie Mellon (Bio), Stony Brook University, University of Oregon, and Boston University. I was admitted to both University of Oregon and Stony Brook University with fellowships about $5k a year each for three years. I’m still waiting to hear back from Carnegie Mellon (Bio) and am waitlisted for Boston University (GPN).
Some takeaways,
I should’ve asked my letter writers to address my grades and I should’ve talked more at length about why my grades were so low (undiagnosed sleep disorder [DSPD], and trauma with my best friend dying in a car accident). Admissions committees didn’t care that I got a 3.7 in my masters it felt like and this didn’t offset my undergrad grades as far as I could tell The admissions process is tightly controlled at a lot of schools by a single-person or a small committee and even though I was invited to interview (even being rated first in the cohort by a professor), it once again came down to grades and I suppose fit which was disappointing. I had believed that once I interviewed, the schools already wouldn’t care about grades and thought I was a good fit. as far as fit goes, I was a bit too specific and I suppose seemingly inflexible during interviews: I thought being a very good specific fit for two or three professors was the way to go but I’m thinking it’s better to have broad appeal. I wasn’t able to get un-pigeonholed as a “biology” or “computational” guy in different contexts. Some PIs expressed doubt as to whether I would even want to do experiments while others didn’t comment on my 5 years of programming or my masters in math. my publications didn’t matter. I never got a single comment on any of them and a lot of interviewees seemed like they had pulled up my CV in their computer a minute before the interview. I think the only sort of pub that matters is a 2nd or 3rd author in a high-tier journal or a 1st in a mid-tier journal. my work experience didn’t matter per se. I had a lot of friends get admitted to schools I got rejected from when they had only 2 years of experience and I had very nearly 7. The only difference between us was GPA so I think the advice “research experience is more important than grades” is false. it matters tremendously who is writing your letters. I’ve seen students with a 3.4 gpa and mediocre scores/experiences with letters from HHMI or NAS members get into every school in the top10.  If I were to do it all again, 
I would have addressed my grades more directly and had my letter writers do so as well I would have not done the MS (or done a 1-year full-time) and then focused two years on getting one or more first-authorships. In retrospect, I had all the experimental and analytic skills to do so but I was just intimidated by the idea of it. I would have chased after working with big names in the field to get a recommendation from them. It matters more than it should. I wish I knew that everyone who was giving me advice that was last in admissions 5 years ago has outdated information. It's at least twice as competitive now and 1st-authorships are now going from unheard of to uncommon. I should've worked like my life depended on it and that's saying a lot because there were many weeks I was working 60-80 hours with work and homework combined. Neuroscience is the hardest life sciences field right now (except clinical psych PhDs) and possibly all of science save except some fields like ML/CS but, unless you talk to someone who's recently applied or is on admissions, you wouldn't know it. BU got >500 applications for 40 interview spots and 8 spots in their incoming class. I networked a ton but I should've networked even more. Really making sure these PIs were invested in having me. One PI at each Boston and CMU had told me explicitly they "golden buzzered" me into interview which I would've never gotten otherwise. Most of my schools were top-20 so I needed this sort of help for each one but even one isn't a guarantee especially if their admissions process is more committee based. BU's seemed to give more power to individual PI's while others were tightly controlled and voted on by each committee. I had a chat for 30 min in-person with the director at Harvard and he said he liked my skillset and would look for my application but alas I never got in (I should've been upfront about my grades). I should've applied to lower-ranked but still very good schools like Pitt, Northwestern, Rochester, UT Austin, Georgia Tech, etc. Very important: I should have applied to more biology programs. They're easier to get into and the only difference is in curriculum (work with all the same professors). Several neuro interviewees I was with at sort-of mid-level institutions also had interviews at top20/10 biology programs. I'm also going to disagree with the advice that getting an acceptance after interview is "yours to lose" because at several of my interviews the acceptance rate was below 50% and so it came down to fit mostly even if you were a wonderful person. One school told me they wanted to see at least three PI's throw their hat in the ring for you. At several of my interviews, all of us were confident, knowledgeable about our work, skilled, and driven no question but yet more than half of us will not receive an offer. This does vary though as I know of one top school that routinely offers every interviewee that passes the "is this person at least normal" test.
Your grades aren't as bad as mines but I feel like for those with the same grades, the only way out is to have something that makes the reviewers go "holy shit" i.e. one or more glowing recs from big names in the field or having first-authorship. That's all I can think up right now but let me know if you have any questions.

So I have some good information for you since I was in your exact position when I graduated (almost exact same stats) and probably would’ve had the same results. I’ll help walk you through what I did to compensate for low grades and what worked/didn’t work and how I did this application season.
i graduated from a regional SLAC with a 3.2 GPA in Biochemistry and Math with a minor in neuroscience. I had three years of undergrad experience but no pubs. I went on to take the GRE and got a 167/164/6.0 I think V/Q/W. I thought deeply about where I needed to compensate and how by following the advice of others and some good blog posts; my weakest areas were going to be my GPA, lack of publications, and letters of rec (no one knows of my recommenders). Thus, number one and two on my list were to enroll in an MS program with good grades and to get some publications. Also to find a job with some big names to write my letters.
I was actually fairly successful at everything: at the time of application, I was a quarter shy of finishing a masters in applied math with a 3.7 at a top-3 public school and I had been working 3.5 years at the premier neuroscience non-profit gaining 3 publications (3rd in Neurotox., mid in eLife, mid in eNeuro), 2 in review (mid in Nature, 2nd in PLOS ONE), and two more in prep (3rd and a 1st). My letter writers were all now former academics (not PIs though, postdocs) that were known in the community. I thought I did everything I could have almost as best as possible and all my mentors had told me that I should shoot very highly in terms of schools.
I applied to the following 14 schools: Harvard, Stanford, Columbia, Princeton, Carnegie Mellon/Pitt, UCSF, UCSD, Carnegie Mellon (Bio), University of Oregon, Boston University, Stony Brook University, MIT, and NYU. I also networked heavily and emailed 2-3 PIs at every school and corresponded with around a dozen extensively over email, over Skype, or in-person at SfN. I was feeling very confident I’d get interviews from around half my schools.
Now a few months later I was rejected from ten schools and received interviews from Carnegie Mellon (Bio), Stony Brook University, University of Oregon, and Boston University. I was admitted to both University of Oregon and Stony Brook University with fellowships about $5k a year each for three years. I’m still waiting to hear back from Carnegie Mellon (Bio) and am waitlisted for Boston University (GPN).
Some takeaways,
I should’ve asked my letter writers to address my grades and I should’ve talked more at length about why my grades were so low (undiagnosed sleep disorder [DSPD], and trauma with my best friend dying in a car accident). Admissions committees didn’t care that I got a 3.7 in my masters it felt like and this didn’t offset my undergrad grades as far as I could tell The admissions process is tightly controlled at a lot of schools by a single-person or a small committee and even though I was invited to interview (even being rated first in the cohort by a professor), it once again came down to grades and I suppose fit which was disappointing. I had believed that once I interviewed, the schools already wouldn’t care about grades and thought I was a good fit. as far as fit goes, I was a bit too specific and I suppose seemingly inflexible during interviews: I thought being a very good specific fit for two or three professors was the way to go but I’m thinking it’s better to have broad appeal. I wasn’t able to get un-pigeonholed as a “biology” or “computational” guy in different contexts. Some PIs expressed doubt as to whether I would even want to do experiments while others didn’t comment on my 5 years of programming or my masters in math. my publications didn’t matter. I never got a single comment on any of them and a lot of interviewees seemed like they had pulled up my CV in their computer a minute before the interview. I think the only sort of pub that matters is a 2nd or 3rd author in a high-tier journal or a 1st in a mid-tier journal. my work experience didn’t matter per se. I had a lot of friends get admitted to schools I got rejected from when they had only 2 years of experience and I had very nearly 7. The only difference between us was GPA so I think the advice “research experience is more important than grades” is false. it matters tremendously who is writing your letters. I’ve seen students with a 3.4 gpa and mediocre scores/experiences with letters from HHMI or NAS members get into every school in the top10.  If I were to do it all again, 
I would have addressed my grades more directly and had my letter writers do so as well I would have not done the MS (or done a 1-year full-time) and then focused two years on getting one or more first-authorships. In retrospect, I had all the experimental and analytic skills to do so but I was just intimidated by the idea of it. I would have chased after working with big names in the field to get a recommendation from them. It matters more than it should. I wish I knew that everyone who was giving me advice that was last in admissions 5 years ago has outdated information. It's at least twice as competitive now and 1st-authorships are now going from unheard of to uncommon. I should've worked like my life depended on it and that's saying a lot because there were many weeks I was working 60-80 hours with work and homework combined. Neuroscience is the hardest life sciences field right now (except clinical psych PhDs) and possibly all of science save except some fields like ML/CS but, unless you talk to someone who's recently applied or is on admissions, you wouldn't know it. BU got >500 applications for 40 interview spots and 8 spots in their incoming class. I networked a ton but I should've networked even more. Really making sure these PIs were invested in having me. One PI at each Boston and CMU had told me explicitly they "golden buzzered" me into interview which I would've never gotten otherwise. Most of my schools were top-20 so I needed this sort of help for each one but even one isn't a guarantee especially if their admissions process is more committee based. BU's seemed to give more power to individual PI's while others were tightly controlled and voted on by each committee. I had a chat for 30 min in-person with the director at Harvard and he said he liked my skillset and would look for my application but alas I never got in (I should've been upfront about my grades). I should've applied to lower-ranked but still very good schools like Pitt, Northwestern, Rochester, UT Austin, Georgia Tech, etc. Very important: I should have applied to more biology programs. They're easier to get into and the only difference is in curriculum (work with all the same professors). Several neuro interviewees I was with at sort-of mid-level institutions also had interviews at top20/10 biology programs. I'm also going to disagree with the advice that getting an acceptance after interview is "yours to lose" because at several of my interviews the acceptance rate was below 50% and so it came down to fit mostly even if you were a wonderful person. One school told me they wanted to see at least three PI's throw their hat in the ring for you. At several of my interviews, all of us were confident, knowledgeable about our work, skilled, and driven no question but yet more than half of us will not receive an offer. This does vary though as I know of one top school that routinely offers every interviewee that passes the "is this person at least normal" test.
Your grades aren't as bad as mines but I feel like for those with the same grades, the only way out is to have something that makes the reviewers go "holy shit" i.e. one or more glowing recs from big names in the field or having first-authorship. That's all I can think up right now but let me know if you have any questions.

So I have some good information for you since I was in your exact position when I graduated (almost exact same stats) and probably would’ve had the same results. I’ll help walk you through what I did to compensate for low grades and what worked/didn’t work and how I did this application season.
i graduated from a regional SLAC with a 3.2 GPA in Biochemistry and Math with a minor in neuroscience. I had three years of undergrad experience but no pubs. I went on to take the GRE and got a 167/164/6.0 I think V/Q/W. I thought deeply about where I needed to compensate and how by following the advice of others and some good blog posts; my weakest areas were going to be my GPA, lack of publications, and letters of rec (no one knows of my recommenders). Thus, number one and two on my list were to enroll in an MS program with good grades and to get some publications. Also to find a job with some big names to write my letters.
I was actually fairly successful at everything: at the time of application, I was a quarter shy of finishing a masters in applied math with a 3.7 at a top-3 public school and I had been working 3.5 years at the premier neuroscience non-profit gaining 3 publications (3rd in Neurotox., mid in eLife, mid in eNeuro), 2 in review (mid in Nature, 2nd in PLOS ONE), and two more in prep (3rd and a 1st). My letter writers were all now former academics (not PIs though, postdocs) that were known in the community. I thought I did everything I could have almost as best as possible and all my mentors had told me that I should shoot very highly in terms of schools.
I applied to the following 14 schools: Harvard, Stanford, Columbia, Princeton, Carnegie Mellon/Pitt, UCSF, UCSD, Carnegie Mellon (Bio), University of Oregon, Boston University, Stony Brook University, MIT, and NYU. I also networked heavily and emailed 2-3 PIs at every school and corresponded with around a dozen extensively over email, over Skype, or in-person at SfN. I was feeling very confident I’d get interviews from around half my schools.
Now a few months later I was rejected from ten schools and received interviews from Carnegie Mellon (Bio), Stony Brook University, University of Oregon, and Boston University. I was admitted to both University of Oregon and Stony Brook University with fellowships about $5k a year each for three years. I’m still waiting to hear back from Carnegie Mellon (Bio) and am waitlisted for Boston University (GPN).
Some takeaways,
I should’ve asked my letter writers to address my grades and I should’ve talked more at length about why my grades were so low (undiagnosed sleep disorder [DSPD], and trauma with my best friend dying in a car accident). Admissions committees didn’t care that I got a 3.7 in my masters it felt like and this didn’t offset my undergrad grades as far as I could tell The admissions process is tightly controlled at a lot of schools by a single-person or a small committee and even though I was invited to interview (even being rated first in the cohort by a professor), it once again came down to grades and I suppose fit which was disappointing. I had believed that once I interviewed, the schools already wouldn’t care about grades and thought I was a good fit. as far as fit goes, I was a bit too specific and I suppose seemingly inflexible during interviews: I thought being a very good specific fit for two or three professors was the way to go but I’m thinking it’s better to have broad appeal. I wasn’t able to get un-pigeonholed as a “biology” or “computational” guy in different contexts. Some PIs expressed doubt as to whether I would even want to do experiments while others didn’t comment on my 5 years of programming or my masters in math. my publications didn’t matter. I never got a single comment on any of them and a lot of interviewees seemed like they had pulled up my CV in their computer a minute before the interview. I think the only sort of pub that matters is a 2nd or 3rd author in a high-tier journal or a 1st in a mid-tier journal. my work experience didn’t matter per se. I had a lot of friends get admitted to schools I got rejected from when they had only 2 years of experience and I had very nearly 7. The only difference between us was GPA so I think the advice “research experience is more important than grades” is false. it matters tremendously who is writing your letters. I’ve seen students with a 3.4 gpa and mediocre scores/experiences with letters from HHMI or NAS members get into every school in the top10.  If I were to do it all again, 
I would have addressed my grades more directly and had my letter writers do so as well I would have not done the MS (or done a 1-year full-time) and then focused two years on getting one or more first-authorships. In retrospect, I had all the experimental and analytic skills to do so but I was just intimidated by the idea of it. I would have chased after working with big names in the field to get a recommendation from them. It matters more than it should. I wish I knew that everyone who was giving me advice that was last in admissions 5 years ago has outdated information. It's at least twice as competitive now and 1st-authorships are now going from unheard of to uncommon. I should've worked like my life depended on it and that's saying a lot because there were many weeks I was working 60-80 hours with work and homework combined. Neuroscience is the hardest life sciences field right now (except clinical psych PhDs) and possibly all of science save except some fields like ML/CS but, unless you talk to someone who's recently applied or is on admissions, you wouldn't know it. BU got >500 applications for 40 interview spots and 8 spots in their incoming class. I networked a ton but I should've networked even more. Really making sure these PIs were invested in having me. One PI at each Boston and CMU had told me explicitly they "golden buzzered" me into interview which I would've never gotten otherwise. Most of my schools were top-20 so I needed this sort of help for each one but even one isn't a guarantee especially if their admissions process is more committee based. BU's seemed to give more power to individual PI's while others were tightly controlled and voted on by each committee. I had a chat for 30 min in-person with the director at Harvard and he said he liked my skillset and would look for my application but alas I never got in (I should've been upfront about my grades). I should've applied to lower-ranked but still very good schools like Pitt, Northwestern, Rochester, UT Austin, Georgia Tech, etc. Very important: I should have applied to more biology programs. They're easier to get into and the only difference is in curriculum (work with all the same professors). Several neuro interviewees I was with at sort-of mid-level institutions also had interviews at top20/10 biology programs. I'm also going to disagree with the advice that getting an acceptance after interview is "yours to lose" because at several of my interviews the acceptance rate was below 50% and so it came down to fit mostly even if you were a wonderful person. One school told me they wanted to see at least three PI's throw their hat in the ring for you. At several of my interviews, all of us were confident, knowledgeable about our work, skilled, and driven no question but yet more than half of us will not receive an offer. This does vary though as I know of one top school that routinely offers every interviewee that passes the "is this person at least normal" test.
Your grades aren't as bad as mines but I feel like for those with the same grades, the only way out is to have something that makes the reviewers go "holy shit" i.e. one or more glowing recs from big names in the field or having first-authorship. That's all I can think up right now but let me know if you have any questions.

So I have some good information for you since I was in your exact position when I graduated (almost exact same stats) and probably would’ve had the same results. I’ll help walk you through what I did to compensate for low grades and what worked/didn’t work and how I did this application season.
i graduated from a regional SLAC with a 3.2 GPA in Biochemistry and Math with a minor in neuroscience. I had three years of undergrad experience but no pubs. I went on to take the GRE and got a 167/164/6.0 I think V/Q/W. I thought deeply about where I needed to compensate and how by following the advice of others and some good blog posts; my weakest areas were going to be my GPA, lack of publications, and letters of rec (no one knows of my recommenders). Thus, number one and two on my list were to enroll in an MS program with good grades and to get some publications. Also to find a job with some big names to write my letters.
I was actually fairly successful at everything: at the time of application, I was a quarter shy of finishing a masters in applied math with a 3.7 at a top-3 public school and I had been working 3.5 years at the premier neuroscience non-profit gaining 3 publications (3rd in Neurotox., mid in eLife, mid in eNeuro), 2 in review (mid in Nature, 2nd in PLOS ONE), and two more in prep (3rd and a 1st). My letter writers were all now former academics (not PIs though, postdocs) that were known in the community. I thought I did everything I could have almost as best as possible and all my mentors had told me that I should shoot very highly in terms of schools.
I applied to the following 14 schools: Harvard, Stanford, Columbia, Princeton, Carnegie Mellon/Pitt, UCSF, UCSD, Carnegie Mellon (Bio), University of Oregon, Boston University, Stony Brook University, MIT, and NYU. I also networked heavily and emailed 2-3 PIs at every school and corresponded with around a dozen extensively over email, over Skype, or in-person at SfN. I was feeling very confident I’d get interviews from around half my schools.
Now a few months later I was rejected from ten schools and received interviews from Carnegie Mellon (Bio), Stony Brook University, University of Oregon, and Boston University. I was admitted to both University of Oregon and Stony Brook University with fellowships about $5k a year each for three years. I’m still waiting to hear back from Carnegie Mellon (Bio) and am waitlisted for Boston University (GPN).
Some takeaways,
I should’ve asked my letter writers to address my grades and I should’ve talked more at length about why my grades were so low (undiagnosed sleep disorder [DSPD], and trauma with my best friend dying in a car accident). Admissions committees didn’t care that I got a 3.7 in my masters it felt like and this didn’t offset my undergrad grades as far as I could tell The admissions process is tightly controlled at a lot of schools by a single-person or a small committee and even though I was invited to interview (even being rated first in the cohort by a professor), it once again came down to grades and I suppose fit which was disappointing. I had believed that once I interviewed, the schools already wouldn’t care about grades and thought I was a good fit. as far as fit goes, I was a bit too specific and I suppose seemingly inflexible during interviews: I thought being a very good specific fit for two or three professors was the way to go but I’m thinking it’s better to have broad appeal. I wasn’t able to get un-pigeonholed as a “biology” or “computational” guy in different contexts. Some PIs expressed doubt as to whether I would even want to do experiments while others didn’t comment on my 5 years of programming or my masters in math. my publications didn’t matter. I never got a single comment on any of them and a lot of interviewees seemed like they had pulled up my CV in their computer a minute before the interview. I think the only sort of pub that matters is a 2nd or 3rd author in a high-tier journal or a 1st in a mid-tier journal. my work experience didn’t matter per se. I had a lot of friends get admitted to schools I got rejected from when they had only 2 years of experience and I had very nearly 7. The only difference between us was GPA so I think the advice “research experience is more important than grades” is false. it matters tremendously who is writing your letters. I’ve seen students with a 3.4 gpa and mediocre scores/experiences with letters from HHMI or NAS members get into every school in the top10.  If I were to do it all again, 
I would have addressed my grades more directly and had my letter writers do so as well I would have not done the MS (or done a 1-year full-time) and then focused two years on getting one or more first-authorships. In retrospect, I had all the experimental and analytic skills to do so but I was just intimidated by the idea of it. I would have chased after working with big names in the field to get a recommendation from them. It matters more than it should. I wish I knew that everyone who was giving me advice that was last in admissions 5 years ago has outdated information. It's at least twice as competitive now and 1st-authorships are now going from unheard of to uncommon. I should've worked like my life depended on it and that's saying a lot because there were many weeks I was working 60-80 hours with work and homework combined. Neuroscience is the hardest life sciences field right now (except clinical psych PhDs) and possibly all of science save except some fields like ML/CS but, unless you talk to someone who's recently applied or is on admissions, you wouldn't know it. BU got >500 applications for 40 interview spots and 8 spots in their incoming class. I networked a ton but I should've networked even more. Really making sure these PIs were invested in having me. One PI at each Boston and CMU had told me explicitly they "golden buzzered" me into interview which I would've never gotten otherwise. Most of my schools were top-20 so I needed this sort of help for each one but even one isn't a guarantee especially if their admissions process is more committee based. BU's seemed to give more power to individual PI's while others were tightly controlled and voted on by each committee. I had a chat for 30 min in-person with the director at Harvard and he said he liked my skillset and would look for my application but alas I never got in (I should've been upfront about my grades). I should've applied to lower-ranked but still very good schools like Pitt, Northwestern, Rochester, UT Austin, Georgia Tech, etc. Very important: I should have applied to more biology programs. They're easier to get into and the only difference is in curriculum (work with all the same professors). Several neuro interviewees I was with at sort-of mid-level institutions also had interviews at top20/10 biology programs. I'm also going to disagree with the advice that getting an acceptance after interview is "yours to lose" because at several of my interviews the acceptance rate was below 50% and so it came down to fit mostly even if you were a wonderful person. One school told me they wanted to see at least three PI's throw their hat in the ring for you. At several of my interviews, all of us were confident, knowledgeable about our work, skilled, and driven no question but yet more than half of us will not receive an offer. This does vary though as I know of one top school that routinely offers every interviewee that passes the "is this person at least normal" test.
Your grades aren't as bad as mines but I feel like for those with the same grades, the only way out is to have something that makes the reviewers go "holy shit" i.e. one or more glowing recs from big names in the field or having first-authorship. That's all I can think up right now but let me know if you have any questions.

So I have some good information for you since I was in your exact position when I graduated (almost exact same stats) and probably would’ve had the same results. I’ll help walk you through what I did to compensate for low grades and what worked/didn’t work and how I did this application season.
i graduated from a regional SLAC with a 3.2 GPA in Biochemistry and Math with a minor in neuroscience. I had three years of undergrad experience but no pubs. I went on to take the GRE and got a 167/164/6.0 I think V/Q/W. I thought deeply about where I needed to compensate and how by following the advice of others and some good blog posts; my weakest areas were going to be my GPA, lack of publications, and letters of rec (no one knows of my recommenders). Thus, number one and two on my list were to enroll in an MS program with good grades and to get some publications. Also to find a job with some big names to write my letters.
I was actually fairly successful at everything: at the time of application, I was a quarter shy of finishing a masters in applied math with a 3.7 at a top-3 public school and I had been working 3.5 years at the premier neuroscience non-profit gaining 3 publications (3rd in Neurotox., mid in eLife, mid in eNeuro), 2 in review (mid in Nature, 2nd in PLOS ONE), and two more in prep (3rd and a 1st). My letter writers were all now former academics (not PIs though, postdocs) that were known in the community. I thought I did everything I could have almost as best as possible and all my mentors had told me that I should shoot very highly in terms of schools.
I applied to the following 14 schools: Harvard, Stanford, Columbia, Princeton, Carnegie Mellon/Pitt, UCSF, UCSD, Carnegie Mellon (Bio), University of Oregon, Boston University, Stony Brook University, MIT, and NYU. I also networked heavily and emailed 2-3 PIs at every school and corresponded with around a dozen extensively over email, over Skype, or in-person at SfN. I was feeling very confident I’d get interviews from around half my schools.
Now a few months later I was rejected from ten schools and received interviews from Carnegie Mellon (Bio), Stony Brook University, University of Oregon, and Boston University. I was admitted to both University of Oregon and Stony Brook University with fellowships about $5k a year each for three years. I’m still waiting to hear back from Carnegie Mellon (Bio) and am waitlisted for Boston University (GPN).
Some takeaways,
I should’ve asked my letter writers to address my grades and I should’ve talked more at length about why my grades were so low (undiagnosed sleep disorder [DSPD], and trauma with my best friend dying in a car accident). Admissions committees didn’t care that I got a 3.7 in my masters it felt like and this didn’t offset my undergrad grades as far as I could tell The admissions process is tightly controlled at a lot of schools by a single-person or a small committee and even though I was invited to interview (even being rated first in the cohort by a professor), it once again came down to grades and I suppose fit which was disappointing. I had believed that once I interviewed, the schools already wouldn’t care about grades and thought I was a good fit. as far as fit goes, I was a bit too specific and I suppose seemingly inflexible during interviews: I thought being a very good specific fit for two or three professors was the way to go but I’m thinking it’s better to have broad appeal. I wasn’t able to get un-pigeonholed as a “biology” or “computational” guy in different contexts. Some PIs expressed doubt as to whether I would even want to do experiments while others didn’t comment on my 5 years of programming or my masters in math. my publications didn’t matter. I never got a single comment on any of them and a lot of interviewees seemed like they had pulled up my CV in their computer a minute before the interview. I think the only sort of pub that matters is a 2nd or 3rd author in a high-tier journal or a 1st in a mid-tier journal. my work experience didn’t matter per se. I had a lot of friends get admitted to schools I got rejected from when they had only 2 years of experience and I had very nearly 7. The only difference between us was GPA so I think the advice “research experience is more important than grades” is false. it matters tremendously who is writing your letters. I’ve seen students with a 3.4 gpa and mediocre scores/experiences with letters from HHMI or NAS members get into every school in the top10.  If I were to do it all again, 
I would have addressed my grades more directly and had my letter writers do so as well I would have not done the MS (or done a 1-year full-time) and then focused two years on getting one or more first-authorships. In retrospect, I had all the experimental and analytic skills to do so but I was just intimidated by the idea of it. I would have chased after working with big names in the field to get a recommendation from them. It matters more than it should. I wish I knew that everyone who was giving me advice that was last in admissions 5 years ago has outdated information. It's at least twice as competitive now and 1st-authorships are now going from unheard of to uncommon. I should've worked like my life depended on it and that's saying a lot because there were many weeks I was working 60-80 hours with work and homework combined. Neuroscience is the hardest life sciences field right now (except clinical psych PhDs) and possibly all of science save except some fields like ML/CS but, unless you talk to someone who's recently applied or is on admissions, you wouldn't know it. BU got >500 applications for 40 interview spots and 8 spots in their incoming class. I networked a ton but I should've networked even more. Really making sure these PIs were invested in having me. One PI at each Boston and CMU had told me explicitly they "golden buzzered" me into interview which I would've never gotten otherwise. Most of my schools were top-20 so I needed this sort of help for each one but even one isn't a guarantee especially if their admissions process is more committee based. BU's seemed to give more power to individual PI's while others were tightly controlled and voted on by each committee. I had a chat for 30 min in-person with the director at Harvard and he said he liked my skillset and would look for my application but alas I never got in (I should've been upfront about my grades). I should've applied to lower-ranked but still very good schools like Pitt, Northwestern, Rochester, UT Austin, Georgia Tech, etc. Very important: I should have applied to more biology programs. They're easier to get into and the only difference is in curriculum (work with all the same professors). Several neuro interviewees I was with at sort-of mid-level institutions also had interviews at top20/10 biology programs. I'm also going to disagree with the advice that getting an acceptance after interview is "yours to lose" because at several of my interviews the acceptance rate was below 50% and so it came down to fit mostly even if you were a wonderful person. One school told me they wanted to see at least three PI's throw their hat in the ring for you. At several of my interviews, all of us were confident, knowledgeable about our work, skilled, and driven no question but yet more than half of us will not receive an offer. This does vary though as I know of one top school that routinely offers every interviewee that passes the "is this person at least normal" test.
Your grades aren't as bad as mines but I feel like for those with the same grades, the only way out is to have something that makes the reviewers go "holy shit" i.e. one or more glowing recs from big names in the field or having first-authorship. That's all I can think up right now but let me know if you have any questions.

I’m a bit of a special case but I can help you out. I have heard a few things from the program.
Feel free to PM me.

If you’re comfortable, you can PM me on the BU GPN GroupMe (I’m the guy who started it) else just PM here on grad cafe. I know a bit of the professors personally and have opinions about the schools I interviewed at that I can share privately. We were at the same interview. If you can’t tell who started the GroupMe, just look at the last names haha 

At least for biosciences, that "max" is completely meaningless. Many students are spending >50-60 hours per week on their research. Anything less than 40 and your PI is gonna be pissed.

To echo what MtnDuck said: the effect cascades. By your decision impacts hundreds of people indirectly, and at least one person directly. Your decline opens up a spot which enables someone to decline their lesser offers. If most shifting happens in April, there just isn't enough time for adcoms to go down the waitlist. If there is on average 3 day per offer turnaround, the adcomms can't get through 10 people on their waitlist in 3 days -- when the declines really happen.
Objections:
But they are willing to fly me out! This is a great opportunity to visit schools and network with professors I am interested in.
This is really an unfair tease. If you know you aren't taking their offer, then you're going on false pretenses, wasting their department's money, and making people wait for minimal gains. Is it really a good idea to use people to sight-see? It isn't like you're going to get a letter of recommendation. Just add them on PhilPeople for pete's sake. But if I decline that doesn't impact you. So what?
For some people, if they were given an offer before the 15th, they would accept your school's offer. You are literally impacting someone's ability to get into a school or get into a better school. It doesn't have to be about impacting anyone you know. The sooner the impact, the sooner others can impact others down stream. I am under no obligation to make any decision before April 15. If I wait, that's my prerogative.
True. Nothing is forcing you to make a decision, and definitely not to rush you. But if nothing will change your mind about the decision, then why take the time? If you are still unsure, that's one thing, but if you already have an obviously better offer, then this shows a character defect when you know this impacts other people's futures. Comparative harm account: you're harming people. You have a right to harm people, but that doesn't mean harming is right. Whatever my choice and whenever I decide to notify them, such course of action would be statistically normal. You cannot expect me to act otherwise.
Okay, I won't argue that it is obligatory, but clearly you don't see supererogatory actions as worthy of aspiration. I hope you're not working in ethics. It seems like it could be in my interest to hold onto the offer. I can use it as leverage.
Sure, if you think they are really comparable. But I'd argue it might even be in your interest to decline. The school might come back with a counter-offer that would not have been available if you didn't give them ample time to put together a more lucrative package.

Hi everyone,
I have finally finished interviews and have heard from all programs. I have narrowed my decision down to two programs: University of Virginia or University of Rochester. I just completed a Master's and I realized I would like to return to researching an interest of mine: any and all things glia (encompasses a lot I know).
The pros and cons of the institutions are both fairly weighted in my opinion (I won't bore you with the details but if you want to know I can rant hahaha). So, for those of you who are conducting research in neuroscience/glia which institution would you recommend for pursuing glia-related research interests? I also know my interests may change, so I feel both institutions have other areas and resources that could support a potential change of interest.
Thank you all! It's been a crazy admit season, I hope everyone is doing okay¬

Just got a call with an offer for the Brown Neuroscience PhD! With my gpa from undergrad being 3.27 (3.07 in major), i really wasn't too hopeful for this round of applications- But I'm ecstatic! 

I'd say 0% tbh. They seem to be winnowing it down slowly but I'd move on.
Edit: I told my friend in BCS that I hadn't heard anything and he didn't say "oh well you should keep waiting to see" but said "oh sorry you won;t be coming here" so I'm assuming they're done done except for exceptional cases (a lot of people decline invitations which won't/didn't happen)