OK, so here is an idea.  A few of my fellow tweeps will be aware that Heng Li’s paper on BWA-MEM was rejected from Bioinformatics;  he wrote about his experience in an e-mail and a copy of that is here.  At present, I honestly have no idea if the reasons are justified or not.

I absolutely, 100% believe in the peer review process, and would never try and circumvent it.  However, I think we all can agree that, at times, it goes wrong.  I’m not saying that the BWA-MEM rejection is an instance of this; the reviewers could be fully justified, we’ll never know as the reviews remain hidden.

As you all know, I am also a huge supporter of open peer review – I think reviewers should be identified and I think reviews should be published.

So here is an idea about how we might be able to make a difference.  Here is a potential plan:

  1. A bunch of volunteers read and digest the BWA-MEM paper in detail (it’s here).  Note: those volunteers could (and perhaps should?) include the original reviewers.
  2. Using a platform such as PubPeer.com, those volunteers review the paper fully, as if they were actually reviewing for Bioinformatics.  These reviews would be signed and fully open
  3. The full review cycle is carried out in public, with Heng responding to comments and posting the updated paper online.
  4. If the final decision is that the paper should be accepted, we petition Bioinformatics and provide them with the evidence.  Alternatively, we invite a range of journals!
  5. If the final decision is rejection, then nothing is lost and Heng at least has some good feedback

What do you think?  Imagine if this happened and Bioinformatics decided to accept the public reviews?  Wouldn’t that be a real paradigm shift?