Publishing your Research – Avoid Pitfalls and Delays by Understanding the Process

When I was a researcher, my main concern was getting interesting and reliable results from my experiments (and changing the world of course!). However, nine years ago, after making the move into scientific publishing, I realised that I also would have benefited from knowing more about the publishing process as a PhD student and postdoc. Most of all, how decisions are made on what gets sent to peer reviewers, how the peer review process works and how editors decide on what gets published.

I have pulled together some of the main things that I know now, but wish I knew then about what goes on behind the scenes. Hopefully this basic advice can save you budding research author’s from unnecessary delays after submission.


What’s the Story?

The first paper I published was primarily based on serendipitous findings acquired during the last year of my PhD. When writing it up, my supervisor guided me to focus the paper on its most interesting and useful aspects so that a clear rationale and narrative could be presented.

It was only after I moved into publishing that I realised how important this is. Journals and publishing platforms like F1000Research, receive many submissions and editorial staff work hard to provide responses to authors as soon as possible. All manuscript editors are looking to answer some key questions:

  • Why was this done (rationale)?
  • How was this done (methods and reporting)?
  • What did the authors find (results/analysis)?
  • What does this mean (discussion and conclusions)?


Clarity and Standards of Reporting

Over the years, I have come across many clearly presented submissions, but every now and again there have been some where key aspects, such as the rationale, methods and analysis, have been very ambiguous. In these circumstances, editors need to raise queries with authors, and often revisions are required until the manuscript is clear enough to be sent out to peer reviewers.

This can add significant delays, and can be easily avoided by providing all the necessary information the journal or publishing platform requires (be sure to check the instructions for authors and submission guidelines).

Also, following the appropriate reporting guidelines for your study (CONSORT for randomised controlled trials, for instance) ensures that you will provide all the necessary information required. Full lists of reporting guidelines for specific study designs can be found at the EQUATOR network.


Choose the Right Fit – Don’t be Dazzled by the Impact Factor

Sometimes authors make their choice on where to submit to, primarily based on the impact factor. Again, this can lead to unnecessary delays. Journals and publishing platforms select submissions based on how well it fits in with their aims and readership. If your work meets the requirement for threshold and scope, then it is likely to be considered. Otherwise the editors have no choice but to reject the manuscript.

Prior to submission you can make as many queries to as many journals or publishing platforms as you like. If unsure send a query to the journal editor or editorial office; editorial staff are always happy to answer your questions and it can save you a lot of time by making sure your manuscript is the right fit for that publishing venue.

Be aware though, once you have submitted you cannot submit elsewhere until you have received a decision. Submitting to more than one journal or publishing platform at the same time is a breach of publication ethics and can result in rejection of the submission.

Many researchers already have a list of journals they want to submit to, but if you are considering a journal or publishing platform you are unfamiliar with, it is a good idea to read through their editorial policies so you’re aware of any mandatory information that needs to be included (for example, will you be expected to share the raw data?).

If you are considering an Open Access journal you are unfamiliar with, then it is important to go through the checklist on Think Check Submit, so that you can ensure it is reputable.


Authorship – Consensus is Key

Occasionally after submission an authorship dispute erupts. If this happens prior to publication then the editors will usually halt the process and ask the authors and their institutions to come to a resolution before any further progress can be taken.

As such, it is important that all authors agree on the order of authorship and that they all fulfil the criteria for authorship. During the review and revision process it is possible that there will be changes in the author list (including the addition or removal of authors). If this happens it is also important to inform the editors, so that they can follow any verification processes they have. For example, at F1000Research we require all authors (including any removed) to confirm that they agree to the new author list.


Who will be the Point of Contact?

Throughout the submission and review process, it is essential to have a designated submitting author who agrees to take responsibility to be the point of contact with the journal or publishing platform. This does not necessarily need to be the same person who will be corresponding author on the published paper.

The role of the submitting author is to correspond with the editorial team, to answer queries on behalf of their co-authors and to relay any information back to their co-authors as necessary. This process ensures a clear communication channel and helps to avoid breaches in publication ethics, such as, multiple submissions to more than one journal or platform.


Publication Ethics and Policies

As part of the assessment process, editors also check that any submitted manuscripts have adhered to their editorial and publication policies. This includes, but is not limited to:


Many journals and platforms will run all submissions through a plagiarism checker, such as iThenticate. If significant parts of the text are found to match with published articles, then the editorial team will query this with the authors. In some cases, this can lead to rejection of the manuscript, so it is important to ensure your manuscript is original in content.

Data Availability

It is becoming more common for journals and publishing platforms to ask for availability of data underlying the results of study. For instance, at PLOS journals, F1000Research and Wellcome Open Research platforms this is mandatory, while some others may request this only for particular study types.

Ethical Approval and Consent

All studies involving humans, animals and even plants need to be conducted ethically, and where applicable formal ethical approval is required from an appropriate ethics committee prior to conducting the study. Therefore, one of the most consistent editorial policies across journals and publishing platforms, is the requirement to include a statement to outline where approval was obtained from. In addition, details about participants informed consent to be part of the study, and also consent to have any identifiable information published, also needs to be included. Typically, articles will not be published without this mandatory information.


If you are conducting a clinical trial, it should be registered in a publicly accessible registry before the trial has started. This is recommended by the ICMJE and many journals (for example, The BMJ ) will not publish trials that have been registered after participants have been recruited. Others may consider publication but with some conditions to ensure transparency. For instance, the date the study was registered must be included to make it clear what stage the trial was at when it was registered (e.g. BioMed Central journals, F1000Research and Wellcome Open Research).

Increasingly, journals and publishing platforms are also asking authors to prospectively register systematic reviews in the PROSPERO registry (or similar).


Useful resources:

For understanding peer review – If you have not experienced the peer review process before, it is a good idea to familiarise yourself with what reviewers are asked to look for. Most journals and publishing platforms will include information about their peer review process on their homepages, which will give you insight into what reviewers are asked to look for.



Learn how to become a peer reviewer – There are now some useful resources available to help inexperienced reviewers gain insight and experience. Publons has launched a training course via the Publons Academy, which can be particularly useful. In addition, there are some ‘how to peer review’ tutorials available in this BMC Medicine collection, which breaks down the role of the peer reviewer in more detail. General tips on peer review are also available in this guide from F1000Research. Sense about Science often run workshops for early career researches to introduce them to peer review.

Understanding Open Peer Review – There are various types of Open Peer Review, and some journals offer this as an option for authors (for example Nature Communications) or reviewers (for example PLOS journals). For some journals open peer review is mandatory, and they publish the pre-publication history with signed reviewer reports alongside the article (for example BMC Medicine), or will also include the editorial decision letter (for example The BMJ). Post-publication peer review publishing platforms such as F1000Research and Wellcome Open Research publish all content associated with an article – for instance, the submitted version including data, signed reviewer reports, author responses and revised articles.



General tips and writing tools – There are numerous resources available online, but a particularly comprehensive overview is available from Elsevier here. Various writing and collaboration tools are also available, such as F1000Workspace, Mendeley and Overleaf.