Schools Which Grad Schools Should I Apply to with My GPA and Research Experience?

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With a GPA of 3.1 overall and 3.55 in physics, strong GRE scores in the 90th percentile, and two years of undergraduate research with publications, the applicant is well-positioned for graduate school applications. Emphasis should be placed on applying to programs that align with their research interests rather than focusing solely on GPA. The applicant is considering whether to pursue a master's degree to improve prospects, but many believe that strong research experience and letters of recommendation can offset a lower GPA. It is important to highlight improvements in academic performance in the personal statement. Overall, the applicant has a solid foundation for applying to graduate programs despite concerns about GPA.
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Due to poor performance the first year or so of school, I have an overall GPA of 3.1 and a physics GPA of ~3.55. I've done pretty well otherwise, at least I think I have. Can someone tell me what range of schools to which I should be applying.

GPA: 3.5/3.1 Major/Overall (all As for the past three semesters)

Research: Two years undergraduate research. Two second-author publications. A couple of poster presentations and one small talk.

GRE: I am in the 90th percentile on the GRE and PGRE.

Other: Lab TA for two semesters. White American male.

I will have two very good letters or recommendation.

I know I can get in somewhere, I'm just not sure where I should apply.
 
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I would aim for departments that are doing research in areas that you're interested in rather than an apporiate "range" of schools. Academic pedigree doesn't count for nearly as much as people seem to think it does.
 
Thanks for the response. Yeah, I am planning on applying to places that have professors doing research in areas that I am interested.

The problem is, I can't apply to twenty schools. I didn't know if I would be able to weed some out based on my poor GPA.

Also, should I improve my prospects by pursuing a master's before a phd? I'm just worried about my GPA.
 
Firstly, as a caveat, I know nothing about the US system, but from what I've read of people's stats over the years here, your GRE, research and letters look to make up for a low(ish) GPA. If your transcript clearly shows that your poorer grades were in lower years, and you write a personal statement thing (or whatever it's called) that also highlights this, then I don't see why you'd be rejected because of that. Still, there may be some automatic lower limit that I don't know of. What are your publications like; are they in respected journals in your field? How much input did you have in them?
 
Yeah, the publications are in respected journals. I collected data for them and worked with my adviser on some of the experimental setup. I 'helped' him write one of them, but I think he could have done it without me, haha. My roommate seems to think that I won't have a problem getting into a school that I want, but I'm just worried I guess.
 
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