My worst (recent) experience with peer review

My colleagues and I just published a paper on validation of genomic results in BMC Bioinformatics. It is “highly accessed” and we are really happy with how it turned out. 

But it was brutal getting it published. Here is the line-up of places I sent the paper. 

• Science: Submitted 10/6/10, rejected 10/18/10 without review. I know this seems like a long shot, but this paper on validation was published in Science not too long after. 
• Nature Methods: Submitted 10/20/10, rejected 10/28/10 without review. Not much to say here, moving on…
• Genome Biology: Submitted 11/1/10, rejected 1/5/11. 2/3 referees thought the paper was interesting, few specific concerns raised. I felt they could be addressed so appealed on 1/10/11, appeal accepted 1/20/11, paper resubmitted 1/21/11. Paper rejected 2/25/11. 2/3 referees were happy with the revisions. One still didn’t like it. 
• Bioinformatics: Submitted 3/3/11, rejected 3/1311 without review. I appealed again, it turns out “I have checked with the editors about this for you and their opinion was that there was already substantial work in validating gene lists based on random sampling.” If anyone knows about one of those papers let me know :-). 
• Nucleic Acids Research: Submitted 3/18/11, rejected with invitation for revision 3/22/11. Resubmitted 12/15/11 (got delayed by a few projects here) rejected 1/25/12. Reason for rejection seemed to be one referee had major “philosophical issues” with the paper.
  
• BMC Bioinformatics: Submitted 1/31/12, first review 3/23/12, resubmitted 4/27/12, second revision requested 5/23/12, revised version submitted 5/25/12, accepted 6/14/12.