How to Publish Your First Bioinformatics Paper

Publishing your first bioinformatics paper is settled by four decisions, not by writing talent: whether the work is a paper at all or a portfolio project, who meets the ICMJE authorship criteria, which venue you send it to, and whether you post a preprint first. Get those right and the writing is the easy part.

Most students worry about the writing. The writing is the part that goes least wrong, because a supervisor will correct your prose and a reviewer will tell you what is missing. What goes wrong is upstream and offstage: a project that was never a paper gets sent anyway, an author list gets decided by seniority, a journal gets chosen from an email, and nobody tells the student that rejection is the ordinary outcome rather than a verdict on them.

There is also one piece of advice on almost every Indian how-to-publish page that is now out of date, and it matters enough to deal with early. The StemSkills Lab team has spent more than ten years in sequence and structural bioinformatics, drug discovery and design, and multiscale molecular modeling, and this guide follows the published guidance for each decision rather than lab folklore. If you want the background definitions first, our FAQs about bioinformatics journals cover those separately; this guide is about what to do.

Is your project a paper, or is it a portfolio project?

Ask this before anything else, and accept that for most MSc dissertations the honest answer is the second one. A portfolio project is not a failure state. It is a different asset with a different job: it proves you can do the work, it can be inspected by anyone in an afternoon, and it does not need a reviewer’s permission to exist. A paper claims that something is now known that was not known before. Those are different claims and they survive different kinds of scrutiny.

The test is whether a reader outside your lab learns something from your result that they could not get from the papers you cited. Re-running a published pipeline on the same data teaches you a great deal and teaches the field nothing. The signals below sort most student projects quickly.

If the table lands you on the right-hand column, build the project properly instead. Our guides on computational biology project ideas for MSc students and on building a bioinformatics portfolio cover that route, and a verifiable credential from our free certifications sits beside it well on an application.

Who belongs on the author list?

Authorship is not a reward, a courtesy, or a function of who paid. It is defined, and the definition is public. The ICMJE recommends that authorship be based on the following 4 criteria, quoted here in full because students are routinely told a shortened version:

1. “Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND”
2. “Drafting the work or reviewing it critically for important intellectual content; AND”
3. “Final approval of the version to be published; AND”
4. “Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.”

The rule that follows is the one that settles arguments: “All those designated as authors should meet all four criteria for authorship, and all who meet the four criteria should be identified as authors.” Those who do not meet all four are acknowledged instead. The ICMJE also states that an author “should be able to identify which co-authors are responsible for specific other parts of the work”, which is a useful question to ask out loud in a group meeting.

A four-person student project, worked through criterion by criterion

Take a typical dissertation: you designed and ran an epitope screen, a labmate ran one of the servers for you on a day you were away, your supervisor set the question and revised the manuscript, and the head of department would like to be included.

• You. Design, analysis, drafting, approval, accountability. All four criteria. Author, and on this project usually first author.
• Your supervisor. Conception of the question, critical revision, approval, accountability. All four criteria. Author.
• The labmate who ran one server. That is a contribution to acquisition of data, so criterion 1 can be met, but criteria 2, 3 and 4 are not met by running a tool. The wrong move is to drop them silently. The ICMJE is explicit that the criteria “are not intended for use as a means to disqualify colleagues from authorship who otherwise meet authorship criteria by denying them the opportunity to meet criterion #s 2 or 3.” So offer the review and the approval. If they take it up, they are an author. If they decline or never respond, they are acknowledged, and now you can say why.
• The head of department who did not take part. Criterion 1 is not met, so authorship is not available. This is the hardest one to hold as a student, and the practical defence is not an argument in a corridor: it is the journal’s own authorship declaration, which the corresponding author has to attest to at submission. Point at the form, not at the person.

Why is the UGC-CARE list no longer the filter you were told to use?

Because it stopped. The UGC-CARE site itself now carries this notice: “The UGC-CARE List has not been updated since October 2024 and will not be updated further, as per the UGC Public Notice dated February 11, 2025. The website is available for information purposes only.” The UGC-CARE home page says so in its own words, and the same page still reports that “No journals were included in the UGC-CARE list in its 16th Quarter update (January 2023 to March 2023).”

Read that carefully before you act on it. It does not mean the journals on the old list became bad. It means a list that was frozen cannot tell you anything about a journal’s behaviour since it froze, and that checking a title against it is no longer a safety check. We are not stating what replaces it, because the notice does not say and we have not verified a replacement. What it changes for you is that the screening has to be done on the journal itself, which is the rest of this section.

Start with the question of whether the journal is where your readers are. For open access titles there is a usable public index: a request to the Directory of Open Access Journals public API at doaj.org/api/search/journals returned a total of 23,570 indexed journals on 1 October 2026. That is the method, not just the number, so you can repeat it on the day you need it and get the current figure. Being in DOAJ is evidence a journal has described its own practices to a third party; absence from it is a question to answer, not a verdict.

Where should you send your first paper?

Send it where the people who would cite it already read, and decide that before you finish writing. This is Bourne’s advice almost verbatim: “Rule 9: Decide early on where to try to publish your paper.” (Bourne PE, “Ten simple rules for getting published”, PLoS Computational Biology 2005, 1(5):e57, PMID 16261197, PMC1274296). The venue sets the length, the structure and the expected depth of validation, so choosing late means rewriting.

The last row is the one students underuse. Your supervisor’s publication record is a map of venues that accept work of your shape, with a person beside you who has been through the process there.

Screening an invitation that arrives in your inbox

You will get these as soon as your name appears anywhere. Work through the email itself before you look at the journal:

1. Does it describe your actual work? A real invitation names a specific paper or talk of yours and the field correctly. Generic flattery and a field that is not quite yours are the first signal.
2. Does it promise a decision quickly, in the email? Speed advertised up front is a claim about review, and review is the thing you are buying.
3. Is the editorial board real and checkable? Pick two names and find their institutional pages and their other papers. Boards are sometimes listed without the person’s knowledge.
4. Do the articles have registered DOIs? Take a DOI from a recent article and look it up at Crossref. A registered DOI resolving to the right article is a minimum, not a recommendation.
5. Are the policies written down? Peer review process, corrections and retractions, and copyright. A journal that will not say how it reviews cannot be assessed.
6. Does submission happen by replying to the email? A manuscript sent as an email attachment has no record you can point to later.

Three further resources are worth using here even though we are not linking them, because they block automated requests and we only link pages we can read: Think. Check. Submit. offers a checklist of exactly this kind, COPE publishes the standards journals claim to follow, and Sherpa Romeo records what each publisher lets you do with your own manuscript. Search those names in a browser.

Should you post a preprint first?

Usually yes, and the reason is specific rather than ideological: a preprint date-stamps your work as yours before review begins, which protects a student whose manuscript is sitting on a slow supervisor’s desk. Check your target journal’s policy first, then post.

Understand what you are getting and what you are committing to. On bioRxiv, “all articles are screened on submission for plagiarism, non-scientific content, inappropriate article types, and material that could potentially endanger the health of individual patients or the public”, and “authors are solely responsible for the content posted”. That is a screen, not peer review, and you should describe it that way on your CV.

The commitment is permanence, and this is the part students miss. bioRxiv’s FAQ states that posted manuscripts “receive DOI’s and thus are citable and part of the scientific record. They are indexed by services such as Google Scholar and Crossref, creating a permanent digital presence independent of bioRxiv records. Consequently, bioRxiv’s policy is that papers cannot be removed.” Authors may withdraw an article if they no longer stand by its conclusions or find fundamental errors, with a statement posted explaining why. Revisions post under the same DOI and earlier versions stay visible in the article’s history.

So post the version you would defend, not the version you are still arguing with your co-authors about. A preprint is a publication step, not a draft folder.

What should happen before the manuscript leaves your group?

One internal round, deliberately hostile, and it is the cheapest improvement available to you. Zhang’s rules for writing research papers put this at Rule 9, “Test the Water in Your Own Backyard” (Zhang W, “Ten simple rules for writing research papers”, PLoS Computational Biology 2014, 10(1):e1003453, PMID 24499936, PMC3907284), sitting beside Rule 8, “Be Your Own Judge”.

Bourne’s Rule 7 is the companion habit: “Start writing the paper the day you have the idea of what questions to pursue.” For a computational project that is not a figure of speech. The methods section is the log of what you ran, and it is accurate on the day you run it and reconstructed from memory a term later. Write down versions, parameters, and the exact commands as you go, because a reviewer will ask and your future self will not remember.

For a bioinformatics manuscript specifically, give the internal reviewer three things to attack: can they rerun your analysis from your methods alone, do your figures support the claims in your abstract, and is every tool version and parameter stated. Our team’s published research comes from projects of exactly this shape, immunoinformatics pipelines built from the same tool steps our guides teach, which is the honest reason to believe a dissertation project can become a paper of that form.

What actually happens after you submit?

Something in this sequence, and none of these outcomes except the first is unusual.

• Desk rejection. The editor returns it without sending it to reviewers, usually because it is out of scope or too thin for the venue. This is fast and it costs you nothing except the submission. Read the one line they give you: it is scope advice, and the next venue down your list may be the right one.
• Sent for review. The editor finds reviewers in your area. There is nothing for you to do here, and emailing to ask is counted against you.
• Major revision. This is a good outcome and students misread it as a bad one. It means reviewers believe the work can be publishable here. Answer every point in a numbered response letter, say what you changed and where, and where you disagree, say so politely with a reason rather than quietly not doing it.
• Minor revision. Close to acceptance. Do not get careless with it.
• Rejection after review. The normal case, and the single most useful thing in this guide is that the primary literature says so plainly. Bourne’s Rule 5 is “Learn to live with rejection.” His Rule 3 is the companion: “Good editors and reviewers will be objective about your work.” Reviewer reports from a rejection are free expert criticism, usually the most detailed your work will ever get. Fix what they identified, then submit to the next venue.

Timelines vary so widely between fields and journals that any figure you read is nearly meaningless for your case. Ask your supervisor what their last submission to that journal was like, which is a real answer about a real venue.

A first paper is also not the only thing being assessed. The computational biology skills roadmap sequences the rest, our guide on applying for a bioinformatics PhD covers how a submitted or preprinted manuscript is described in an application, and writing a bioinformatics CV covers how to list a paper that is not accepted yet without overclaiming.

Frequently asked questions

Can I publish a bioinformatics paper without a supervisor?

Technically yes, and it is harder in every way that matters. You lose the critical internal read that Zhang’s Rule 9 asks for, the venue knowledge in a supervisor’s publication record, and the person who tells you the work is not ready. If you have no supervisor, a preprint plus a strong public repository is usually the better first move.

How do I list a paper that is only submitted or preprinted?

Describe its actual state. “Submitted to journal name” or “preprint, DOI, not peer reviewed” are both respectable; “in press” when it is not, or an implied peer review that did not happen, is the kind of thing an interviewer catches. Our guidance on writing a bioinformatics CV works through the wording.

Does the first author position matter for a PhD application?

Yes, because it signals who drove the work, and a committee reads the position alongside the paper. If you did the design, the analysis and the draft, make the case for first author using the ICMJE criteria rather than asking as a favour. Being able to say which co-author is responsible for which part is the strongest form of that case.

My labmate ran one script. Is that authorship?

Not by itself, because running a tool meets at most the first ICMJE criterion and authorship requires all four. The correct process is to offer them the chance to review the manuscript critically and approve it, as the ICMJE explicitly requires you not to deny that opportunity. If they take it up, they are an author. If not, acknowledge them.

Is it worth paying to publish faster?

Treat speed sold up front as information about the review, not about the service. The useful question is who vets the paper and whether the policies are written down, which we work through in the invitation checklist above. Answer that before any discussion of cost, and take the answer to your supervisor.

How long should I wait before asking the editor for an update?

Until the journal’s own stated handling time has passed, which is on its author pages and varies far too much to generalise. Then one polite enquiry from the corresponding author, not several. In the meantime, Bourne’s Rule 8 is useful advice for the gap: “Become a reviewer early in your career.”