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PROFIE_EVALUATION: PhD in CS, Fall-2020 (computational biology/bioinformatics)

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[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.
My profile:
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 [20]
2. Johns Hopkins University [25]
3. Pennsylvania State University [30]
4. New York University [30]
5. University of California--Irvine [30]
6. University of Virginia [30]
7. Virginia Tech [40]
8. University of California--Davis [37]
9. University of Colorado--Boulder [40]
10. Stony Brook University--SUNY [40]
11. Michigan State University [55]
12. Indiana University--Bloomington [55]
13. Iowa State University [61]
14. University of California--Riverside [61]
15. Case Western Reserve University [68]
16. George Mason University [68]
17. Florida State University [82]
18. University of Central Florida [82]
19. CUNY Graduate School and University Center [82]
20. University of Connecticut [83]
21. University of Texas-San Antonio [119]
 
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:
[1] What usnews ranking ranges could be considered as ambitious, moderate and safe based on this profile?
[2] Could you suggest any safe schools for this profile?

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I think you should put off picking school at this moment and first seriously think about how to get a PhD program first. 

Let me guess you are international and from a non-English speaking country? (more than half of schools on accept several international students per year, the competition is very brutal because there might be thousands of international applicants and likely more than half of them are not worse than you, and be honest, even on domestic loose standard, you are not very competitive)

TOEFL speaking score is very important especially for those low rank schools because they need you do TA more than RA, so you might be screen off in the first round.

GRE and GPA are fine, but still not very competitive, can not be a reason to accept you when there are tons of cheaper domestic students and international with higher GPA, GRE and schools. 

You should definitely do a master first, and even though you need to low down your expectation quit a lot to make sure be accepted.  

Apply rank ~100 master program and some backups. 

 

 

 

 

 

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