Dos & Don'ts When Publishing a Scientific Manuscript

By Guest Blogger

This post was contributed by Maaike Pols, PhD, a Developmental Editor at F1000Research. 

With many changes taking place in the world of science publishing, and an ever increasing number of journals and publishers to choose from, it gets very confusing for scientists writing research articles. What should you take into account when writing up your research?

What type of journal should I choose?

writing a scientific manuscriptWriting a research paper for publication in a scientific journal requires several considerations. First, it is important to establish the type of audience you want to reach with your paper. Is it the wider scientific community, or are you writing for a specific subgroup of researchers in your area of expertise? Sometimes, the funders of your research may stipulate that your article must be published in an open access journal or by using the open access option in a conventional journal. Publishing via open access means that your manuscript will be available to anyone who wishes to read it, without them needing a subscription to the journal. An increasing number of funding bodies insist that the research data resulting from their funding should also be published. All these factors will influence your choice of journals to submit your work to.

Before submitting your paper to your preferred  journal, it is important to check the journal’s guidelines to authors and see whether your paper is in scope for the journal’s coverage. These guidelines also provide information on a journal’s house style and the things you need to include in your manuscript.

What information do I need to include in my paper?

More and more journals are asking for detailed information on lab resources, such as catalogue numbers and manufacturers’ details for antibodies, plasmids (like your Addgene plasmid #), and other reagents. F1000Research, among many other journals, has joined a pilot project from the Neuroscience Information Framework (NIF) called the Resource Identification Initiative. During this project, authors are asked to add an identifier (a bit like a GenBank ID) to all antibodies, animal models, and software tools in the Materials and methods section of their manuscript to make resources easier to identify, find back, and share.

Depending on the type of manuscript you are writing, it may be useful to consult the checklists that many journals use to verify whether a manuscript contains all the necessary information to be of maximal use to the scientific communities. The ARRIVE guidelines for the reporting of laboratory animals during in vivo research and the CARE guidelines for case reports are two sets of guidelines frequently used by editors. Providing all this information makes your manuscript more valuable to the research community. It also makes it more likely that researchers have enough information to replicate your experiments, making research more reproducible and your results more valuable.

Some journals, including F1000Research, also ask for the raw data behind the figures and results. This is a relatively new development, and it allows reviewers and other researchers to access the data and make up their own minds on whether the data analysis has been of good quality and whether they agree with the conclusions of the article. These initiatives are another way in which journals and their scientific communities aim to significantly improve the reproducibility and reliability of science publications.

Peer reviewing

To make sure your manuscript is perceived as a reliable source of information, it is best to submit it to a journal that uses a peer review system. Peer review in traditional journals happens before the manuscript is accepted for publication and is, in most cases, blind (meaning you don’t know who the reviewers are). If the reviewers and the editor decide that your manuscript needs to be revised before it can be published, this can delay publication and manuscripts may go through several rounds of revision before acceptance. F1000Research uses a novel form of peer review that occurs post-publication and is completely open; the reviewer’s name and affiliations, and the entire referee report are permanently attached to the published article. In addition, authors and readers are able to comment on the referee reports. If the reviewers suggest that the manuscript requires revisions, the authors can publish a new version of the article, while the first version and the referee reports remain available online. Open-peer reviewing is beneficial for both the referees (as they get credit for their time and effort) and the scientific community, as the reports can be very informative as to how a paper is received by other researchers in the field.

Dos and don’ts when publishing a scientific manuscript


  • Make sure your paper fits the scope of the journal you are sending it to. It’s wasting everybody’s time if you don’t.

  • Add a clear cover letter to your submission, briefly summarizing the conclusions of your paper. This will help the editor handling your manuscript decide on whether your manuscript fits the scope and the interest of the journal.

  • Be sure to check the Author Guidelines of the journal you are submitting to and make sure your manuscript fits the house style and prerequisites of the journal.

  • Ask colleagues (preferably native English speakers) to proofread your manuscript and help you correct any language- and spelling mistakes. A manuscript that is well written looks more professional than one full of typos.


  • Submit your manuscript to random journals or as many journals as possible at the same time. Take your time picking the appropriate journal and explain in your cover letter why you think your manuscript is appropriate for that journal.

  • Argue with an editor or reviewer over their decision. If you do object, do so in a respectful and professional manner. Arguing will make you look unprofessional and doesn’t help your chances of getting your manuscripts published in the future.

  • Disregard reviewer’s comments without explaining why. If it looks like you have ignored their comments, they will not be inclined to approve your paper.

  • Rush your submission or revision. A sloppy submission, missing files or a manuscript full of spelling errors will not have a great chance of getting published.

In summary, it is a good idea to take some time and look into which journal would be best suited for your paper. Always check the journals Author Guidelines to make sure that your paper fits with the journal’s house style and check that all required information is provided. The clearer you write your paper and the more information you provide on data, materials, and methods, the more valuable your paper will be to the scientific community.

Now, go on and get writing! Let us know if you have any other questions about writing and publishing your manuscript, or add your own tips below.

Thank You to Our Guest Blogger!

Maaike Pols F1000 Research

Maaike Pols is a Developmental Editor for F1000Research, responsible for assessing the scientific content of manuscripts submitted for publication. Holds a PhD in Cell Biology and a Masters degree in Infection and Immunity from Utrecht University. 



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Topics: Scientific Sharing, Scientific Publishing

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