I'm hoping to get a dialogue going on what peoples experiences are (both good and bad) with various bioinformatics-focused journals. Which have you submitted to, plan to submit to, and why? If you know the impact factor of your journal of choice, please supply it, but also any personal reasons for choosing a journal may also prove useful to the rest of us. If we get enough nominations (for good ones) I will set up a poll and hopefully we can decide on our favorites.

Ryan

Hi Ryan,

I've had good experiences with BMC Bioinformatics , one bad experience with Bioinformatics, and mixed feelings about Biomedical Informatics.

BMC was great because the response time in terms of reviews and of getting your article up online is really fast. I'm debating resubmitting something that was rejected to Biomedical Informatics versus sending it over to BMC right now. Trouble is that it seems a bit easier to publish in BMC so I'm not clear how this will affect perception of the articles published there (and of course of me).

If I had to pick - and i guess I do, I'd pick BMC bioinformatics as my favorite journal to publish in. I think their philosophy of open access, only online content, and fast turnover times win the day. Ultimately I guess I don't think the journal really makes the paper anyway - if its good, it will be rewarded with citations regardless.

ramble ramble

My very first post! Yay! :-)

Most of my publications have been in cancer/genome type journals, but my first peer reviewed publication was in BMC Bioinformatics.

The fast response time that Ben speaks up was certainly not what I experienced. After about 2 months of my manuscript status being listed as 'With Reviewers,' I emailed the editor and who got back to me with a message basically stating that the reviews were sitting on her desk for the past month. This happened again after the first round of revisions :-(

Eventually, the manuscript was accepted, so I guess I can't complain. Furthermore, I first submitted the manuscript in mid to late November, so maybe there was a bit of the Christmas rush going on.

Regarding impact factors, at the time of this writing, BMC Bioinformatics is at 3.49, which isn't too bad, but I get the impression that it has become a bit of a dumping ground for rejected bioinformatics projects.

Anyone with experience publishing in PLoS Computational Biology or PLoS One?

A colleague of mine was telling me that it took forever (~ 3 months) for her to get the first round of reviews back for her PLoS One manuscript. Basically, the editor said that the work was so novel that it was difficult for them to find suitable reviewers....!

Never heard of that one before!

My advisor had a really bad experience with a submission to PloS One. He ended up with a reviewer that really clearly didn't understand the point of the manuscript at all and, after pointing this out to the editor received no support. This may sound like rotten eggs for a rejected paper, but I wasn't an author on this one and I can tell you the reviews looked like they were written by a not so bright high school student trying to look impressive.

I think these discussions of individual experiences aren't super relevant though.. As we all know by now the reviewing process has an unfortunately high amount of randomness in it in terms of the response times, the quality/helpfulness of the reviews, and the fairness of the reviews. Their are lots of things in the works right now that will change how the process unfolds in the future, but I'll suggest just one right now. I think a) reviewers should have to sign their reviews and b) the reviews should be made public along with each iteration of the paper. IMHO this would incentivise reviewers to do a good job by rewarding them with essentially a new form publication. It would also make it easier to open up dialogues between experts in the field where the paper is being published. Publishing the different drafts and associated reviews would also form an invaluable resource for training students about science and about writing.

I've thought about this a little before, but was convinced in a conversation with Vince Smith at a recent meeting at Google.

Ben,

Did the manuscript get accepted to PLoS One eventually? Even though your advisor went through a hard time with PLoS One, their idea of publishing anything that is scientifically sound and letting the scientific community determine its importance is still quite intriguing, but one concern from me is that it'll just become a dumping ground for bioinformatics papers rejected from PLoS Computational Biology.

I agree that making the review process open and including the reviewer's comments in the final paper would help students become better at writing and presenting their results. Biology Direct (published by BMC) is one journal that does this, although as far as I know, they only publish the final version of the paper.



Biology Direct Link

Nope. It was published in Briefings in Bioinformatics (without any real modification and with very positive reviews). Just goes to show that PloS One is not immune from the plague of uninformed reviewers blocking publications based on the nasty combination of ignorance of the subject area and the authoritarian power that the "quality control" system we have in place provides them with.

PloS a dumping ground? Hardly.. Publishing in science a horrendously broken system that seems to be designed to waste as much of the time of some of the most highly trained people on the planet as possible? Absolutely.

My suggestion.. Don't "publish". Post your findings on your blog, move on with your life. If they are important, people will find them and even cite them.. Here is an example of a blog post that has had powerful impact by any academic standard, including being cited more than 100 times, - Ontology is Overrated .

Implications of not going through formal peer review:
a) zero time wasted waiting for reviewer/editor responses
- Imagine how much more work could be done if this process was avoided
b) zero journal-based authority. Some people will not read/believe it because it wasn't validated through peer-review.
- This means that it has to stand on its own. Any arguments have to stand up without any support other than what is found in the article and any findings would need to be reproducible to be trusted (wow imagine that..)
c) in current approaches to academic career advancement.. your career ends.
- Who would want to join such a broken system anyway? There have to be better lives to lead and better ways to advance the scientific endeavor..