Will a MS with ~3.7GPA with good research experience and strong recommendations offset my horrible U-GPA to get into PhD? My u-GPA is about 2.8 and GRE is 330, from now on is a hypothetical scenario as I haven't done my masters yet so if you could treat it as an actual case and give me subjective answers that would be great. For the masters I have found this growing researcher who is doing amazing work and is eager for me to join his lab from the start of the program. Assuming that by the end of the MS, I get ~3.7GPA, a couple co-authored pub and 1 first authored pub in reputed journals along with going to conferences to present my work, altogether getting strong recommendations from the advisor and his colleagues. Will this in any way offset my u-GPA. Also apart from research in masters I have had about 2 years of research experience during undergrad (in and out of school) and have published a paper in a peer-reviewed journal. 

I am looking to get into the biomedical engineering PhD programs at university of chicago, northwestern university, university of pittsburgh, john hopkins university, york university, and university of pennsylvania. Do you think that I am aiming too high? If so, what else should I look to do to improve my chances? Also if I start MS this Fall should I apply for PhD at Fall 2022 or Fall 2023?

Additional Info:


I did a decent undergrad thesis (not great, 8 months), soon after I did a 2 month internship a another research lab. During my undergrad I worked w/ a prof for 1.2 years (Got two papers out - one in a conf and another in a journal). Currently I am working in a top research lab, now remotely due to covid-19 outbreak.
Some people have mentioned other questions thinking that those had the same information that I wanted. But, they did not as the questions talked about how to get into "a/some" PhD Program after a low U-GPA and maybe decent masters. The schools that I have mentioned above are ranked pretty high and  would appreciate if you could tailor your answers to my specific question of getting into these schools.
I picked these school not to show of the "rank" or "prestige" which seems stupid honestly. I chose the because of the strength in the field (F1) that I'm looking to do research in. In one of my previous questions I had mentioned that I got a PhD offer from university of houston which does the research in F1 but it isn't very strong in other area such as: number of grants that they pull in to do amazing research on large patient populations, intellectual cohorts, and industrial connections and startup resources. I picked these schools as I believe them to be the best in F1 and NOT for the main purpose of prestige. So if you don't have anything to suggest I IMPLORE you to not ask me to look at other schools as I did not ask for alternatives but solutions or ideas
It is good to aim high. It is also good to have broad target. If you apply to only a few schools with very similar profiles then being rejected by one will probably have a similar outcome at the others. So, I recommend a range of schools if you really want a degree and not just bragging rights about a top 50 school. 

But, about your GPA. It isn't a plus, of course, but most (not all) people who evaluate your application will weight the more recent work as more important than the earlier work. Therefore, if your recent work is good and you have letters that attest to the quality of your work and your dedication, then the older numbers will be discounted by most. 

But, the competition is still very strong and the slots are few. If someone has to make a choice between two candidates, the choice has to be made and lower priority things may bear some weight. 

However, the only way to know whether you have a problem is to actually make application to some places and then evaluate the feedback. There are some questions, like this one, that can only be answered by actually trying. But, you will be more likely to get accepted somewhere if you don't target too narrowly.