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I am looking to publish a paper in computational biology. However, I have no affiliation (I have been affiliated with some institutions in the past, but am not currently affiliated with anyone now). I am also looking for a journal that will publish with no charge as I am low on funds.

I understand I should be able to publish a paper when my work is evaluated solely for its quality. However I have been unable to find any non-predatory and at least semi-legitimate computational biology journals that use double-blind review and are free to publish in.

I will submit my manuscript to bioRxiv, but would really like to publish in a journal. I am unsure how to proceed - should I try and submit to a single-blind journal and mark my affiliation as "independent scholar" or try some other way to publish to a double-blind computational biology journal?

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Well, you have the following options:

  • Write up and publish your article as an independent researcher. If your work is theoretical and mathematically provable then, there is a high chance that the lack of affiliation doesn't affect the way the editor approach your paper. However, if you are using a large volume of data and providing surprising results, then there is a high chance that your lack of credit (if I may assume it.) discourages the journal from publishing your work. The fact is that most of the journals cannot dig down and verify the reproducibility of large-scale analyses so their best bet is relying on the credential of institutes.

  • Approach a PI in a related field to review your work and see if he can provide some feedback/comments on that. You can revise your manuscript based on your mutual discussions and add some potential experiments up and then publish it together. You probably would save a huge amount of money as you can depend on their funding resources.

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It can't be denied that there is some sociological element in the peer review process, so the list of authors, their qualifications (some journals require this), the institution- all these shouldn't matter, but sadly they sometimes do. This is not to discourage you, but rather so you accept the finite probability that this could work against you.

Double-blind review is also not immune to this, because the editor will have your details, and he/she could also develop a negative opinion. So my suggestion would be to not look for too many double-blind journals, and submit to the wide range of single blind, free publishing journals one by one. Remember, this element is based on probability, so if you are willing to try several journals, you are automatically improving your chances (not to mention, potentially getting helpful reviews).

Another possibility is to work on the paper with someone you have been affiliated with in the past, and submit it as a joint publication. If that works out, some of your misgivings will be taken care of.

In any case, please don't hold back and not submit, getting a chance to publish is a universal right, even if you're not presently at an institution.

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    This answer is essentially the same as that of @CoderInNetwork, which I didn't see until I submitted. :) – user153812 Apr 2 '18 at 5:21
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Yeah, sure, just submit. You don't have to be at an institution to submit something. Is uncommon but not vanishingly rare. If you are worried about your work being stolen or your contribution downplayed than watch out. But realize this can happen if you are at an institution also.

  • Thank you! So a reviewer wouldn't just look at my paper, see I am an "indepedent scholar" and reject it? – user90757 Apr 2 '18 at 4:15
  • @user90757: No, they won't. No way. Unless your discipline is totally nuts and everybody is taking exotic drugs. – einpoklum - reinstate Monica Apr 2 '18 at 16:51
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The review process can be political, but I think you are overestimating the risk of people rejecting your work out of hand because of your (lack of) affiliation. Bioinformatics actually has a couple of famous independent researchers, like Robert C. Edgar, who developed MUSCLE. I think your odds of getting work published as an unaffiliated single author are actually much better in computational biology than in most of the life sciences.

As far as price goes, reputable OA journals often waive publication fees on a need-based, case by case basis. You request a waiver at submission and will get an answer within a week or two. Here's a link to info about fee waiver requests for PLoS and BMC. Out of OA journals, I would consider PLoS Computational Biology and the BMC journals (BMC Bioinformatics, Genomics, etc. as appropriate for the topic), and maybe Nucleic Acids Research if your work fits their call for research.

You could also submit to Bioinformatics and not pay for the immediate OA option (the default is to embargo the paper for several months), though having your work be easily accessible could help it be more widely disseminated, especially as an unaffiliated scholar who is presumably not routinely presenting about the work. Also you would need to be more careful about self-archiving since in that case the bioRxiv policy is different.

  • Why would the lack of affiliation have any effect? I mean, ok, it would mean more scrutiny of claimed laboratory research, since if you're not affiliated, how do you have lab access. But beyond that? – einpoklum - reinstate Monica Apr 2 '18 at 16:53
  • I think OP is concerned that the lack of affiliation will make reviewers quicker to assume the author is a crank. It's not a totally irrational fear: some scientists are obsessed with status or are very proprietary about their subfield, and some of those get asked to review papers. But in practice these attitudes aren't that prevalent, one nasty review doesn't typically sink a paper at the journals I listed (especially if the editor can see the reviewer's being unreasonable), the risk would be ~= for a junior PI at a small institution, and this field has high-profile independent scientists. – Patrick B. Apr 2 '18 at 19:37
  • Addendum: by "obsessed with status" above I really mean "equate status with competence" or "use status as a short-cut to evaluate competence." – Patrick B. Apr 2 '18 at 19:44
  • If he writes a paper claiming to have found the cure for cancer, then maybe, but if it's a paper on, say, cell membrane dynamics, it's not the type of thing cranks are interested in publishing. – einpoklum - reinstate Monica Apr 2 '18 at 20:13
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    You'd think, but I've reviewed papers on topics at that level of granularity that I'd nevertheless describe as crankery: grandiose unsupported claims, idiosyncratic and opaque writing style, obvious lack of familiarity with well-established previous work, etc. – Patrick B. Apr 3 '18 at 3:08

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