Writing Stress.jpg

Week 4: Paper writing resources, strategies, and tips

By Jennifer Kong

Greetings! Like many of your out there sheltering in place, I am trying to use this time to write papers. There are many strategies to tackle paper writing, here are some resources and tips that I hope you find helpful.

Online Resources

  • “How to prepare a manuscript” is a series of three articles written by Angel Borga (PhD) and published by Elsevier connect. While the original papers were written in 2014, they were updated in 2019. All the information is relevant and really helped me to organize my writing process and clean up early paper drafts. Definitely check these out!

  • Ten simple rules for structuring papers. A PLOS computational biology article written by Brett Mensh and Konrad Kording.
    This article really provides solid advice on how to create a narrative and logical flow in your papers. Instead of telling you how to write a paper, this resource provides insight into how to better craft each section of the paper. One concept I really liked was their CCC scheme, based on the idea that each paragraph should include a context, content, and conclusion. Also a must read!

  • Unit 2 - Writing scientific papers. Scitable by Nature Education.
    A resource provided by the journal Nature that was actually prepared for ESL (English as a second language) scientists. However, I think it is informative for all scientists. This resource breaks down the paper writing process and describes what should be included in each of the four major sections (abstract, introduction, body, and conclusion). In addition, this resource teaches you how to construct effective sentences, how to write in an active voice, and even provides a list of verbs that express research actions — the article is short, but worth it verb resources.

  • How to write a first-class paper. A Nature career feature written by Virginia Gewin.
    An entertaining read. Six pieces of advice from experts in the field on how to create a compelling and publishable manuscript.

  • How to write like a scientist. Written by Adam Rubin.
    Strictly an entertaining read by the author of “Surviving your stupid, stupid decision to go to grad school.” Light reading if you need a break.

major paper components

  • Presubmission inquiry letter (optional)

    • Journal dependent. Typically includes a title, abstract, and an explanation of the significance of your paper and its broad interest to your field or science in general.

  • Cover letter

  • Abstract

    • How to write a scientific abstract. Written by Karen McKee and published by the Wiley publishing company. A short, but well written article about how to write the scientific abstract.

  • Introduction

  • Results

  • Discussion

  • Figures

    • Main figures, supplementary figures, tables, other supplementary files

  • Figure legends

  • Materials and methods

  • Acknowledgements, funding sources for all authors, and author contributions.

  • References

writing styles

Before the pandemic, I interviewed a few postdocs and PIs and asked them about their paper writing strategies. I was shocked by some of the responses. In general, I feel like you can catagorize paper writers into two categories: machines and mortals.

  • Paper writing machines: Some researchers (yes, mostly PIs) just attack the task of paper writing and kill it. In a linear fashion, they start with the introduction, move onto the results, and then write up the discussion. In 3-5 days, they have a first draft done. The secret to the success of paper writing machines is that they know the field incredibly well and have kept up with recent findings and publications. Thus, going into the paper writing process, machines have a firm sense of the major scientific problems, what is unknown in the field, what the data contributes to the field, and the implications this has on the field. With all this knowledge, machines are able to just look at your data (or in some cases just recall data from lab meetings) and start writing.
    Writing order: Introduction -> Results -> Discussion

  • Paper writing mortals: Most researchers (including myself) are paper writing mortals. We know our data very well, but struggle at times to communicate the impact of our findings to a larger audience (i.e. to researchers outside of our field). Instead of starting with the introduction, most paper writing mortals start with the figures. We collect and organize all of the data we have, generate figures for the paper, then write up the results, then the discussion, and finally the introduction.
    Writing order: Collect and organize data -> Figures -> Results -> Discussion -> Introduction

my self directed paper writing plan

This is the paper writing plan that I followed to write a full scientific article. Feel free to modify it to your needs.

Modified from the paper writing plan generated for the 2020 Spring Grant Writing Bootcamp by Dr. Jennifer Wilson and the article “11 steps to structuring a science paper editors will take seriously” by Dr. Angel Borja.

Step 1:  Plan it out! Create a checklist of all the major paper components you need to write, make a weekly plan, and a final submission goal date. Think about what kind of paper you want to write and where you want to submit your paper. Look up the paper formatting requirements (i.e. number of figures allowed, length, etc) and keep these in mind as you begin to write your paper. Hold yourself accountable by joining a writing group where everyone checks in with each other.
Step 2: Figures — Collect and analyze all your data and begin to prepare your figures and tables.
Step 3: Figure legends — Start to move the figures around, create titles for your figures, and begin creating a narrative for your paper.
Step 4: Methods — Carefully go over your figures and write out the methods you used to generate the data.
Step 5: Results — With your figures in hand, start writing up the results. Start to layout your narrative by creating the result titles, then gradually start to fill in the paragraphs and create the main body of the paper.
Step 6: Discussion — Think about the implications of your results and where you would take this further. Address how this work has further the field.
Step 7: Introduction — Read through all the literature in the field. Think carefully about what your the core problems and what advances your study has made.
Step 8: Abstract — Typically less than 200 words (will vary depending on the journal). Short and concise analysis of the the major findings of the paper.
Step 9: Other paper components — Write up the acknowledgements, funding sources, and make sure that all the appropriate references are included.
Step 10: Cover letter and other submission documents — Don’t forget to compile a list of suggested reviewers.
Step 11: Share the manuscript draft with co-authors and colleagues.
Step 12: Make final edits and submit! (Optional: Think about submitting to a pre-print database like bioRxiv to get your paper out sooner — if you do this, don’t forget to check with the journal guidelines to make sure they are okay with pre-print submissions).

tips and tricks for paper writing

  • Do not endlessly work on your figures. As you collect your data and start making figures you will find holes, you will discover experiments that you wish you did, or you will have the desire to redo experiments to generate “prettier” results. As you cannot do any of these things at the moment, just put together what you have and move on with the writing. If you feel so inclined, you can leave empty boxes in your figures with notes about the data you want to insert there. The goal here is to complete a draft of a paper. At the end, you can decide to submit it or go back to lab and collect more data.

  • Start writing now even if you do not have enough for a complete paper. I am currently working on writing two papers, one is a complete story, the other is about 80-90% complete. Even though I lack the “final figure” for the second paper, I will use this time to write it up. I understand the reluctance. You may ask yourself, “how do I write the discussion, if I don’t know how it ends?” However, the goal here is to get a draft started. Compile the figures, write the results, write the discussion, and then use this draft to decide what more you need to do to experimentally to create a publishable piece.

  • To maximize my paper writing efforts, I split up my writing time into two phases: awake and sleepy.

    • Awake writing is the writing do when I am fresh and alert. I write best (more clearly) in the morning, so I reserve this awake writing time for difficult writing sections like the results, discussion, and introduction.

    • Sleepy writing is the writing I do when I am tired. I tend to write a lot late at night, but generally dedicate this sleepy writing time to easy writing tasks like the methods and figure legends.

A few final thoughts

  1. Paper writing styles vary, so what works for me may not work for you. The key here is to keep at it and modify as needed, incremental progress is still progress.

  2. Just like grant writing, paper writing is a skill that you build throughout your academic career. So, don’t get discouraged! When my PI edits my papers, the page is still covered in red and heavily modified. Then, when my PI and I thought we had a solid first draft, our collaborator suggested we rearrange the figures and in doing so change the narrative. Don’t take it personally, learn from this review process and know that the paper will be better at the end.

  3. Lastly, don’t be hard on yourself. Initially, I had planned to write two papers. Two months later, I am still making final changes to the first paper. These are not normal times, you should not feel the need to be hyper-productive. Be kind to yourself. Your priority should always be your physical and mental well-being. Happy writing!