This is how I write science papers

Growing up in Venezuela, I really wanted to be a writer. I loved writing short stories with fictional characters named Petunia who overcame challenges and provided a moral in the end. I remember writing one story in which one of the characters tragically dies. My mom (a psychotherapist) thought it reflected a hidden trauma and sent me to one of her colleagues for evaluation. Fortunately, the therapist concluded (correctly, if I may add) that I was just being creative.

At the time, it never crossed my mind to become a doctor. This sentiment persisted through adolescence; when discussing my future in my college application essay, I stated: “I do not want to become a doctor or a lawyer.” And yet they still accepted me!

Twenty years after that essay was written, I am that which I never thought I would be—a doctor. But only recently have I realized that I may not have landed too far from a career in writing. Being a doctor requires a lot of writing: patient notes, emails to other providers, letters to insurance companies, etc.  In academic medicine, in particular, my career depends on my writing. To advance professionally, I need to write research articles, book chapters, editorials, and any other type of written work (preferably stuff that is cited on PubMed) that earns me regional, national, or even international acclaim. Unfortunately, blogging or tweeting do not count for promotion…yet!

Conducting research also means applying for grants, which require a TON of writing. I just submitted a grant this week that was 14 single-spaced pages (with 0.5-inch margins, Arial font, size 11), not including the supplemental documents such as budget, CV, timelines, etc.

Thus, I have spent several years writing science papers and have refined a system that (I think) works pretty well. More than advancing my career, I found that writing has helped me to learn, grow, and reflect (I’ve previously discussed the value of writing and reflection).

What follows is a description of my process of writing science papers (I will not address how to write the content of such papers). By “science papers” I mean any document that requires working with references and managing citations, including grants, book chapters, research and review articles. I will reveal the strategies, tools, and software that I use to write.

This post is part of a series of articles where I reflect on the process of doctoring, such as Mastering the Inpatient Consult Service and  This is what it’s like to be a physician.

Start writing

I remember learning how to write a 5-paragraph essay in my high school English class:

  1. Research a topic.
  2. Create an outline of what you want to write.
  3. Write it.

It turns out, however, that I don’t work that way (and many people don’t, either). It is through writing that I figure out what I’m thinking. Basically, I write to learn. It seems premature to create an outline of what I’m going to write about before knowing what I think!

So, step one is sitting down to write. Step two is taking a break. A trick I’ve learned recently is the value of leaving the document unfinished for a few days. This allows my subconscious to come up with ideas when I’m otherwise distracted (the diffuse mode of thinking). When I return to my writing, I’m full of creative ideas that make it much easier to complete the manuscript…it basically writes itself! This technique also works well for making presentations and other creative projects.

I’m currently using Ulysses, a Markup-based text editor that I’m still learning how to use. However it’s pretty clean and simple, and focuses me on the writing (it automatically saves my document—including prior versions—which prevents a lot of potential grief!). I also have it on my iPhone and iPad, and it syncs my documents between devices instantly.

I previously used Apple’s Pages which no longer supports the use of Papers (read below), which was a deal-breaker for me.


In order to figure out what to write about, what’s already been said, and where the limits of our knowledge lie, I read a lot of papers. My favorite way of finding relevant articles is by using Google Scholar, an online database that does a great job of ranking the most useful articles for my research needs (typically by presenting me with the most cited articles based on my search criteria). Google Scholar is linked to my university’s library, which allows me to get full PDFs of the papers with just one click (if the PDF is available. Otherwise I have to go through my library’s PubMed or access the journal directly from my library’s collection). The downside of the ease of downloading articles is that I often find myself, like Alice in Wonderland, falling down a never-ending tunnel, chasing reference after reference, often forgetting the topic I’m supposed to be researching!

Organize the papers

To manage the many articles that I download for every manuscript, I need an efficient system for storing and organizing these files. For many years I have been using Papers, a wonderful tool to find and store PDFs of scientific articles (in a similar way that iTunes stores music). It also allows me to search for new articles when it is linked to my local library, although I find it more flexible to find new articles with Google Scholar, and then add them to Papers manually (a quick drag-and-drop). The app is available for the Mac, iPhone, and iPad and automatically syncs through the cloud, keeping each device up to date. Over the years, I’ve managed to collect 2,305 articles in my Papers library. Whenever I add a PDF to Papers, it magically matches the paper with its citation (including authors, journal name, volume, issue, pages, dates, and even an abstract of the article). This is incredibly useful when I want to find a specific paper (e.g., what was that great 1987 JAMA article about arthritis?) or all of my downloaded papers about a certain topic (show me all the articles I’ve read about recurrent fevers).

Add citations

Unlike most of what happens in politics these days, scientific papers should be backed up by evidence. The best way of doing this is with a citation manager to facilitate this process. Fortunately, Papers is highly qualified to do this. It’s remarkably easy to use: when I want to insert the citation within Ulysses (or Word, or whatever program I’m using), I click the Command key (⌘) twice and a Papers pop-up appears.

I search for the citation that I want to insert, click a button, and it automatically adds it to my document like this: {Hausmann:2014dh}.
After I’m done writing, it will automatically change all of my citations into whatever format that I specify (eg. superscript numbers, Author-date, etc). But don’t do this yet! There are more steps to go through.

Collaborate and get feedback

Many of the articles and book chapters that I’ve published have been written with co-authors. As such, it’s essential to receive feedback on my writing from my collaborators. If I’m working with only one other author, I export my Ulysses document to Word and email it to my co-author for editing (it takes precisely 3 clicks to do this from Ulysses). If there are several authors, I prefer using Google Docs, which allows multiple people to view and edit the same document at the same time. This prevents the common mistake of sending the document to multiple people, who will either all correct the same mistake (a waste of time for them), or who will work on different versions of the document (a real headache for me!).

Once I receive the document from my co-authors, I continue all future edits on Word or Google Docs; I don’t copy the text again into Ulysses. At this point, the article is almost complete and just needs some polishing.

Clean up my grammar with Grammarly

I have been using Grammarly for the last few months (after learning that MacSparky is a fan) and have been pleasantly surprised. I first started using it shortly before sending a manuscript to a major journal. Even after the 7 authors of the paper re-read it multiple times, Grammarly still found a couple of major grammatical errors (which I fixed) and it also provided me with suggestions on improving the writing (which were great!). These edits, by themselves, made the subscription to this service worth it. Despite our brilliant prose, our article was still not accepted, although it was just sent for peer review at another journal.


The formatting is the last piece of the puzzle when writing articles. This is where I format the article according to the guidelines provided by the journal (eg. double-spaced, 12-point font, 1-inch margins, etc.) as well as change the Papers references {Hausmann:2014dh} according to the journal preferences.

Before formatting the references, I always save a copy of the unformatted document (eg. SciencePaperUnformatted.doc). You’ll see why below.

Papers makes it really easy for me to format my manuscript—I just tell it the journal that I’m submitting the article to (or type of formatting I’d like, such as MLA or AMA) and it will format the citations within the text as I requested, also providing me with a beautiful references section at the end of my manuscript, in the appropriate order.

I usually tweak the references after it’s done, such as by adding commas in between references, but this typically takes just a few minutes. I also double-check the references at the bottom to make sure that they are complete.

Saving my work

This has been a challenge for me over the years. When I used to use Pages, I would save all the Pages documents within the Pages folder in my iCloud Drive. However, because most projects had different types of documents related to them (eg. Word documents, PDFs, etc), they would all end up in different folders and it made it difficult to find them later.

I’m currently creating a folder dedicated to each project within my Dropbox, which contains all the documents related to the submission (the unformatted and formatted Word versions, submission instructions, PDFs, etc). This is working much better and forces me to be better organized with my files.

Ulysses automatically saves my documents in a Ulysses folder in iCloud Drive, so they are not in my Dropbox project folder. However, once I convert a Ulysses file to Word, I don’t need to go back to the Ulysses version.


After doing this entire process, I often have to edit my documents again. For one recent submission, I didn’t realize that the word limit was 3800 including references! I’ve also had to edit my document after feedback from peer reviewers, who wanted me to provide additional information or to adjust my conclusions.

If I ever need to do substantial edits on my manuscript, I always work on the unformatted document (not the one with the citations in place). That way, if I delete or move a reference, it’s no big deal. Once I’m done, I just format the references again using Papers. Trying to edit the document with citations in place is a nightmare—adding or deleting one citation will wreak havoc on the numbering system…trust me, I learned that the hard way!


And voila! That’s how I write papers.

It wouldn’t be fitting to finish this article about writing science papers without a proper conclusion where I reflect on the work above and present suggestions for the future. After writing this, I noticed that I still enjoy the creative process of writing and, hopefully, after reading this blog post, you will too.

Good luck with all of your submissions, and keep writing!


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