Writing Manuscripts

The following is an outline of my preferred steps, (generally) in order, for preparing a manuscript for publication. While everyone’s preferences for writing will evolve to be different (that’s ok and expected!) this is a process that has worked well for me and I am providing to you as a baseline to ensure you get appropriate practice/training and feedback, should you (generally) follow it.

Figure story 

This should be made VERY early on in the project and either sent to me for feedback or discussed in 1-1 meetings. Your figure story should consist of the figures that you plan to include in a manuscript, including captions. Think of this as your vision for what you want to tell the world about your project. Ask yourself some questions:

• • • • What is the most important result?

      • What information should you include to help guide the reader to understand what you have done?

      • What are the key pieces of data you need to convince yourself (and, therefore, others) that your results are valid?

      • What do you need in SI figures to back up the claims you are making in the main text figures?  

  • Your figure story can be made long before you have real data. In fact, I encourage “storyboarding” by simply drawing out the figures you anticipate including in the publication – this will help you to identify what data you need to collect. As you do collect data, you can update these drawings with real figures and change the story as necessary if/when the project twists and turns (as research does!).

Paper outline 

this should come a little later in the process compared to your figure story, but not by much! This is where you expand a bit more on the story you want to tell. I recommend starting with a bullet list of points you plan to touch on in both the introduction and in the results/discussion. This is mostly for you as a starting point to organize your thoughts when you start writing

Initial paper draft 

This should also not wait until you have “all the data”! Start writing early, this will help you identify holes that you didn’t know you needed to fill (either with a main text figure or with an SI figure) to back up some of the claims you want to make. Keep in mind that your first draft will (1) likely be the hardest and (2) not be the final draft! Don’t get too hung up on wording, etc in this draft, just focus on getting your story into words.

Edit to improve 

Once you have an initial draft, now it’s time to go back and improve to make your story more clear – I emphasize here that this should be a story; it may read more like a lab report the first time around as you’re just trying to be sure all of your technical points get included, but once you go back and reread, try to analyze with the mindset of guiding the reader to the main points and connections you want them to make. For me, this is easiest if I put my initial draft away for a few days and then come back with a fresh mind and more of a “reader” perspective rather than the “writer” perspective.

Identify initial journal 

This can be a challenging task and something that we will decide on together. The journal we choose will depend on a few different aspects of the story, such as intended audience, scope of the work, breadth/depth of the study, etc. Regardless of journal, we will always write our papers to include the most comprehensive data set necessary to validate the work we are trying to communicate. However, publishing something in Nature may mean we do this with a much broader scope of work than publishing in a journal like Polymer Chemistry. By the end of your graduate studies, it is my goal for you to be able to confidently identify an appropriate journal for your research and put together a body of work that you are proud of submitting. I believe it is also important for you to be able to discern what additional work it would take to submit to the next “level up” of journal class and whether that is appropriate or meaningful for a given study.

Solicit feedback from other students/postdocs and coauthors 

This should be done when you have a “complete” draft, but you shouldn’t revise numerous times before sending your draft to someone else for review. One strategy I like to take as a first round of “editing” is simply sending to someone who is relatively unfamiliar with the work and asking them to skim the writing briefly and give me a summary of what they think the point of the paper is. If it matches what I was trying to convey, I continue on; if not, I have work to do! Beyond general reviews of this initial draft, any coauthors involved in major contributions to the work should have a chance to edit and contribute to the draft as well before sending to me for feedback. 

Iterate with me 

Once you’ve written a complete draft that you believe tells your story, it should be sent to me for review. Note, this is different than a final draft – we will likely iterate numerous times before it is considered finalized and ready to submit. However, figures should be submission-quality and all sections of the manuscript should be at least drafted at high quality. The less time I need to spend commenting on your figure quality and fixing grammar errors, the more time I can spend on critically evaluating the work and editing as such. This is not to say you can’t leave comments on sections you’re uncertain about or need help with, or highlight areas where you’d appreciate a second opinion on phrasing/content, etc – I strongly encourage these things! I don’t know what you need/want from me in terms of help in your writing unless you tell me. The process that I will follow for iterating on paper drafts with you will generally look like this, with some phases being repeated (or perhaps even skipped) as appropriate:

• • Phase 1 – high-level feedback only. I will provide comments, but no direct edits to the text. I do this because I want you to think about why I am suggesting these changes and have the chance to practice addressing these comments and improving the writing yourself before I step in. Remember, your PhD is a great time for you to practice and develop confidence in communicating your science – this is one of the many fun parts of our work!

  • Phase 2 – minor edits with more feedback. I’ll directly edit a few small sections as an example of how I would address some of the changes that need to be made; otherwise, I will add another round of comments highlighting sections where I’d like you to make changes.

  • Phase 3 – full edits. By this point, the manuscript is in a state where we both are satisfied with the story and content. In this phase, I’ll make direct edits to the full text, which will likely be mostly edits relating to phrasing or paragraph structure, not scientific content. My expectation is that, once I return this edited draft to you, you will also parse through my edits and evaluate them critically – “reject change” is an option and you should feel empowered to use it (thoughtfully)! My way is not necessarily always the best way, and I may make mistakes of my own or misinterpret what you were trying to say in the initial phrasing.

Circulate the “final” draft with coauthors and once more with me 

Once given my approval to do so after iterating on the manuscript, you will be responsible for sending our “final” draft and the SI file to collaborators and soliciting their feedback/edits. You must get formal, written approval for submission from each author on the manuscript before submission. Once you have incorporated all edits from coauthors, the manuscript and SI should both be sent back to me for a final review and approval for submission.

Submit the manuscript 

You, as the first author, will be responsible for providing the necessary information for the submission of the manuscript and any supplementary information. You’ll need to draft a cover letter as well (ask me for examples if you have not done this before!) and identify suggested reviewers (I am happy to provide suggestions for this, but would love your opinions, too!).

Addressing reviews and/or resubmission

Once your manuscript has come back from peer review, schedule time with me (or plan to use your 1-1 time) to go through the reviewer comments and outline a plan for addressing them in a timely manner. Keep in mind that every reviewer comment was made due to some impression that our manuscript left on the reviewer, so it is important that we make an effort to address every point. In some cases, this may mean making additions or edits to the manuscript itself, and other times it may mean simply providing an explanation in the point-by-point response. As part of the resubmission process, we will be required to submit a point-by-point response to reviewers; you will be responsible for drafting this and I will edit along with the final draft of the revised manuscript. If the reviews require additional experiments, you will be responsible for either performing the experiments yourself or coordinating any necessary effort from collaborators. You will also be responsible for editing the manuscript and coordinating any necessary contributions from coauthors in this respect. If substantial modifications are made to the manuscript, you should circulate the draft with coauthors once more before sending to me for final edits and resubmission.

• • If the manuscript submission was rejected, with or without reviews provided, you should still schedule time with me to discuss next steps and identify our plan for resubmission to a different journal.

Reviewing proofs

Once your manuscript is accepted 🥳, we will receive proofs for review before publication. You will be responsible for an initial review and edit of these proofs. Once you’ve completed your review, let me know and I will also do a quick review before submitting for publication.

Celebrate! 

Be sure to take some time to celebrate the publication of your work! This is a big deal, and I will be looking forward to celebrating with you! You have put a lot of time and effort into teaching the world something new, and you should be so proud of the work you have done.