PhD Admissions Importance: Research vs. Grades I have read and been told that research is the single most important factor for applying for PhD programs in STEM fields. But, I also hear that GPA and GRE scores are the first cutting point for adcoms. 

What is actually more important, grades or research? Will committees look at applicants with low GPAs?

In my scenario, I have a ~3.4 GPA overall, ~3.7 in Major (CS). This is not stellar. But what I do have is 1 first-author conference publication (Best Paper Award at conference) and 1 first-author journal publication as a Junior, with more other work/papers in progress. And my GREs are 158V/170Q/4.5W.

I'm very interested in top schools, but I'm worried my GPA will hold me back.

Will admissions throw away my application at sight of my GPA? Or will they take the time to review my whole application?
Graduate admissions committees should, in principle, be able to review all of the applications they receive in full; this is not like undergraduate admissions, where a small team may be responsible for 10,000 or 20,000 applications. That said, some of the larger graduate departments may receive several hundred applications per year, and it may be necessary to do a preliminary screening before deciding which applications will be examined in further detail. However, what gets through such a screen can vary strongly from school to school and department to department. For instance, if you're at a school whose alumni regularly go on to graduate schools and have a track record of success, that can also be a "plus" factor. If you're near the top of your class, that can also mitigate "weak" grades somewhat (because it indicates that your school resists grade inflation). 

I would hope that graduate admissions flag applications with publications listed, but it depends on whether or not the database reports that summarize applications actually can do a screen for the presence of publications. 

Your specific case, however, is unfortunately in the "no man's land"—not a clear "read no matter what," but also not an automatic "throw away," either. It is probable that you will have a tough time if you look only at "top 5" or "top 10" departments, but you should be able to get considered by many good programs.