Question: Suggestions regarding bioinformatics journal
gravatar for pixie@bioinfo
2.6 years ago by
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

Hello, First of all, apologies for this lengthy post. If it is found to be inappropriate, kindly remove it. I have learnt my bioinformatics from this community and hope to get some valuable suggestions from here.

This year, we had sent our manuscript to a reputed plant science journal. Our 1.5 yrs work mostly comprised of large-scale data mining using on publicly available transcriptomics data on rice. We used network-based approach along with protein-protein interactions and gene-association information to construct the networks. Finally we used clustering approaches and extensive manual curation to analyse and validate the various processes indicated by the data.

Rice has more than 50K genes and only a small percentage have known functions associated with them. Moreover, the GO annotations assigned are very generic and pathway-based information is even less. Hence we felt that network-based topological analysis of important nodes (genes) in our network can provide important cues to identify potential biomarkers for the particular condition we studied, which can be further validated by the scientific community

We submitted in April, 2017 and after several delays and mess-ups by the journal, they rejected it few days back. Two reviewers were assigned and they endorsed the manuscript and the handling editor provisionally accepted it after which it went for a technical validation. To our surprise, the review was re-activated and it went to a third reviewer who basically had a problem with bioinformatics itself and insilico analysis. We performed additional analysis to validate our work and after we responded to him, the reviewer withdrew without giving any replies or further comments. Our paper was stuck in this state for 2 months. Then after repeated mails to the journal, the specialty editor (who seems to be above the handling editor) made a comment in the portal that the manuscript seems fine and comments of the reviewers are based on their respective backgrounds. The consensus is in favor of the MS and it should be accepted. After this, the paper again went for a technical validation for a month! We then receive a mail from the chief editor, that the MS is rejected based on the comments of the third reviewer. We were shocked, as it was seen from the portal, the third reviewer had 'withdrawn' . So how a paper can be accepted once and rejected again (on the basis of a reviewer who left the review process) is what we fail to understand. Moreover, they held up our paper for so long, and none of the editors or the other two reviewers had demanded for a wet-lab validation.

So basically, I am in a frustrated state of mind, and would like to have suggestions from this community as to where we can submit the MS again and expect to have a fair and transparent review-process. It need not be a plant-based journal.

bioinformatics • 1.3k views
ADD COMMENTlink modified 2.6 years ago by markus.riester500 • written 2.6 years ago by pixie@bioinfo1.4k

The publication and peer review process is broken. It is biased towards those universities that have good reputations, which is itself mainly driven by income and not related to actual quality of research or capacity of the researchers. Researchers neither have sufficient time to adequately review all of these publications, and one frequently encounters the situation where a paper under peer review is more a target of some reviewer's frustrations at other things as opposed to the quality of your work under review.

I have worked at many diverse institutions, ranging from those that don't even make the university rankings to what was #1 at the time I was there.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by Kevin Blighe63k

Hi Kevin, completely agree with you. The funny thing is one of the editors had recently published a similar work in the same journal. But like you said, he is from a well-known university...

ADD REPLYlink written 2.6 years ago by pixie@bioinfo1.4k

No further comment! ;)

ADD REPLYlink written 2.6 years ago by Kevin Blighe63k

sorry to hear about your ms journey. Unfortunately, that is how things work, be it publications, grants, appointments and so many other things in research and every where else. Have a big heart, don't get side tracked and keep pushing your paper. Good luck :)

ADD REPLYlink written 2.6 years ago by cpad011213k

Thanks. Yup, the show must go on :)

ADD REPLYlink written 2.6 years ago by pixie@bioinfo1.4k
gravatar for genomax
2.6 years ago by
United States
genomax87k wrote:

You may want to look at GigaScience. It is an open-access, open-peer review journal. So you would exactly know who reviewed your paper and what their comments were. I believe one of the requirements they have is that you make your entire dataset available.

You should also consider putting the paper up on bioRxiv to ensure that you get credit for this work, especially if others publish similar studies while your paper is under review.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by genomax87k

Okay, point noted :)

ADD REPLYlink written 2.6 years ago by pixie@bioinfo1.4k
gravatar for pfs
2.6 years ago by
pfs270 wrote:

I would post the article on a non-peer reviewed site first so you get your work out there and claim the space. See In your situation I would just submit the article to another journal.

ADD COMMENTlink written 2.6 years ago by pfs270

Thanks, yes we are going to do that now.

ADD REPLYlink written 2.6 years ago by pixie@bioinfo1.4k
gravatar for Carlo Yague
2.6 years ago by
Carlo Yague5.0k
Carlo Yague5.0k wrote:

A sadly typical story...

I don't know if this fits the scope of your paper, but regarding the review process, elife is pretty nice. Briefly, the editors are 'real' scientists, and the reviewers have to actually talk to each other.

Our goal is to make peer review constructive and collaborative: initial decisions are delivered quickly; working scientists make all editorial decisions; and revision requests are consolidated following an open, internal consultation among reviewers to deliver a single, concise set of the essential revisions. Post-review decisions and author responses for published papers are available for all to read.

They have a plant biology section.

ADD COMMENTlink written 2.6 years ago by Carlo Yague5.0k

Thanks for the suggestion, I'll look it up

ADD REPLYlink written 2.6 years ago by pixie@bioinfo1.4k
gravatar for EagleEye
2.6 years ago by
EagleEye6.6k wrote:

I had very good experience with BMC bioinformatics. The editor’s response to email queries were very quick and sensible. I would recommend you to go for this journal.

Meanwhile as per genomax recommendation put it in biorxiv.

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by EagleEye6.6k

Thank you, will look into this

ADD REPLYlink written 2.6 years ago by pixie@bioinfo1.4k
gravatar for markus.riester
2.6 years ago by
markus.riester500 wrote:

If the critique of reviewer 3 has absolutely no merit, I would consider an appeal. It was probably a very tough decision for the editor as well, so he might be willing to hear your case again. Be nice, admit the flaws in presentation etc.

8 months until rejection is a worst case scenario, but still happens to everybody - independent of affiliation. Appears you gambled by submitting to a high impact journal and this time you unfortunately might have lost. Try to understand what reviewers didn't like and address it in the next round. Send it to people for comments. Know when it's time to move on and bury the work in a low impact journal or when it's worth doubling down, polishing and submitting again to a similarly ranked journal.

ADD COMMENTlink written 2.6 years ago by markus.riester500
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