[PROFILE EVALUATION POST]
[TL:DR: Need suggestion on graduate school selection]
Hello good people,
Hope you are doing well. I have found the resources available in this site really helpful and am on the verge of applying to graduate schools for PhD in CS.
I may have a below than the average profile due to a lack of publications or a slightly concerning GPA. I have prepared a VERY LONG list of programs that are aligned with my interest. However, most of the programs I found are from the top 50 universities and it seems their acceptance rates are very low.
I will try to apply to some of those ambitious schools.
But what I am stressing about is actually finding at least 2 or 3 safe or moderate programs. The deadlines are closing in and I would really appreciate it if anyone can give me any suggestion.
CGPA: 3.48/4.00, (institution is in top 10 of my country) GRE: 324 (Q165, V159, A4.0), Toefl: 104 ( R30, L: 25, S20, W:29), Research experience: Undergrad thesis on phylogenetic trees( relevant to computational biology) Publication: NONE, Job: 2 years in the software industry, Research Interest: Computational Biology, Bioinformatics, Advanced Algorithms, Theory of Computation.
LoR: 2 from university professors, 1 from former employer
Some universities I found aligned to my interest: (with their usnews ranking)
1. Rice University 
2. Johns Hopkins University 
3. Pennsylvania State University 
4. New York University 
5. University of California--Irvine 
6. University of Virginia 
7. Virginia Tech 
8. University of California--Davis 
9. University of Colorado--Boulder 
10. Stony Brook University--SUNY 
11. Michigan State University 
12. Indiana University--Bloomington 
13. Iowa State University 
14. University of California--Riverside 
15. Case Western Reserve University 
16. George Mason University 
17. Florida State University 
18. University of Central Florida 
19. CUNY Graduate School and University Center 
20. University of Connecticut 
21. University of Texas-San Antonio 
I have got only a few generic replies from some professors of these schools. But could not decide any. Some programs ask for a Master's degree for PhD admission and I only have BSc. Also, TOEFL speaking score is making me omit some programs from this list too. My Queries:  What usnews ranking ranges could be considered as ambitious, moderate and safe based on this profile?  Could you suggest any safe schools for this profile?