Advice on writing papers

The Joys of Paper Writing or Making your Name in the Field

Adapted from a Guide to grad. School by Erin Lavik


First rule of paper writing: it didn’t happen if it wasn’t published.

Second rule of paper writing: See first rule.

Since the Story is the Key, How do you Figure out What is the Story

There are options. People have different ways of figuring out their story.

Figures. Many people like to figure out the figures and feel that helps them figure out the story. This can work well if you know the gist of what you’re trying to convey.

Give a talk to your research group. It forces you to craft a story. It can help refine it.

Talk one on one with your PI/colleague. Have them play devil’s advocate. You’ll see what holds water and what doesn’t.

Do you have a paper?

Things work. Things don’t. There’s lots of grey area, and honestly, you need to graduate. So, what do you do?

Make a chart. What do you know. What do you not know (This is often the harder part.) Get the devil’s advocate involved. Take every piece of data. Note under each column what you know from this and what you don’t.  When you go through everything you’ve got, look at what you know. What is the most cohesive story based on this? What in the “you don’t know column” do you need to know to complete the story? How can you figure it out? How critical is it?

Remember, this doesn’t happen in a vacuum. Few papers are single author papers. Use the other authors, your colleagues, your team. Help each other.

Before you write a word, put your figures together and outline the story. Once you’ve got the story, writing a scientific paper is much easier.


Outline for a Scientific Paper



The purpose of the introduction is to give the reader the context for the results you will present. You need to answer the following:

Why does this work matter?

What is the application? How big is the need? What is currently being used? What are the limits on current technologies?

What has been done?

This is where one cites the relevant work in the field that applies to this experiment. Chances are that others have done something before you. What are strengths and what are the limitations that your system/approach/technology aims to address?

What have you done that is new?

This is that now infamous statement where you sum the whole thing up and say what in the paper matters (the last line of the intro in most cases—sometimes it is actually the entire last paragraph.)


Along with this, many people also cite the work of competitors who may review the manuscript. Once one submits a manuscript to a journal, the editor will send it to reviewers who are familiar with the area (hence your competitors are likely to be involved). Scientists sometimes request certain reviewers and request others not be used, but the review process is anonymous, and the editor can consider or ignore one’s request.



Typically, you want the reader to be able to identify the techniques quickly so you break them down by subheading. The purpose of the experimental section is to give the relevant details a scientist familiar with the techniques would need to replicate your work. Things like the ratios of antibodies, where they were from (NF, 1:200, Sigma) are important.


Here one can spell out any unique materials used in the work. Antibodies are usually found in the immunocytochem. Section, but they could be here instead. Make sure when you list anything with an abbreviation or acronym that you spell it out the first time. DCM means different things to different audiences.


The results explain what you found from doing the experiments. Typically, researchers put their figures together and then use that to guide the writing of the results.


I make sure that every experiment in the experimental has a matching component in the results.

Examples of figures:

Fig 1: SEM images of scaffolds or schematics of design

Fig 2: Examples of mech. Testing curves.

Fig 3: Quantification of mech results

Fig. 4: Histology


The figures go at the end of the paper after the references and figure captions unless the journal states that they should be in the text (ACS journals often ask for this).


This is where you say what it all means. What did you find? How does it relate to the big picture you described in the intro?


Many students avoid the discussion or are brief to the point of mute. I’ll admit, that when I am publishing in a new area, I am very cautious with making huge claims and pondering wildly on the results, but in the end, the discussion is the meat of things. A discussion that boils down to “Yep, this stuff is really important” stinks.

So, how to do you get beyond the – because my PI said I needed to publish so I wrote this up? It’s not easy, but hopefully, the following will help.

Ask yourself the following:

What if I never discovered what I know in this work? What would I be doing differently? Do my findings fit with what other people have seen in the field? How so, and how not? Where the findings fit, it is easy to say that it isn’t important. But, why did you study it to begin? It may be exciting that it is expected, but that doesn’t mean it isn’t important.

It’s always a bit tougher when things are unexpected because you now have to make a case to people in the field that your findings are real and important. Remember all those essays you wrote in high school where you had a thesis and had to use supporting evidence to aruge your case? Welcome to your discussion.

What’s your thesis? (What you found/assert based on what you found) What’s your supporting evidence? First, you have your data. Here’s where you really show that it supports your thesis. Second, you have the broader findings in the field. You need to include the data that supports your findings and address the data (good data) that contradicts them—why are the results different?



These are the endnotes. Editors don’t like footnotes. They have too many formatting issues. If you have access to the program, Endnote, it will revolutionize your creating bibliographies and references. ACS Chemworx is also pretty fantastic and free. Zotaro is extremely popular and free.

Figure captions

The captions come next. When a paper is published, the captions are placed below the figures and above the tables once they are set into the publication.

Many people ask what should be said in figure captions. In my experience, a large number of readers will look at the figures and, potentially, just glace at the text—my clinician colleagues often do this. Make sure your captions give enough context for someone to know what you’ve found without reading all of the results.


Example of figure caption with little context: GFAP expression (green) scale bar= 200 microns

Example of caption with context: GFAP expression (green) in the cortext of postnatal day 1 rats is consistent with B cell migration along the rostral migratory stream. Scale bar- 200 microns

I like figures where the labels are on the image so I don’t have to read the figure caption and fgure out what the 12 panels show. If a column involves images of GFAP expression, label that column GFAP. If all the images in a row are for postnatal day 1 label the row in the figure.

When in doubt, make it easier on your reader.


This is the meat. Everything that really matters, the data, should be here. It is your job to put together the figures so they tell a story. Make sure there is logic to them.

Label them. Make them as easy to understand as possible. Organize and guide the reader through them so they see the story you are telling. If your story is about comparing GFAP expression, make sure the images are aligned next to each other to highlight that comparison.


So you want to publish in Science? (Honestly, this is mostly true for any publication)


  1. Tell a good, compelling story
  2. Have a “money shot”—the image that tells the story. Along these lines, it should be noted that a good illustration has played a role in a number of papers getting published in high impact journals
    1. Money shot: beautiful, compelling image. Directly relevant to story. Rarely is this a graph although it can be a key image that represents what is quantified (eg rat walks versus doesn’t as opposed to graph quantifying it)
    2. Illustrations. It must not only tell the story, it must be incredibly cool. There are reasons that in the age of illustrator, graphic designers still have jobs.
  3. Write the cover letter of a lifetime.
    1. Many students think that the letter is the perfunctory, here’s my paper part of the process. WRONG.
    2. The letter is what makes an editor back an article. You need a friendly editor. A friendly editor is not just a friend today, they are a friend for life. Give them a reason to care, and give them ammunition to defend your article.
  1. What is super cool about your work? Tell them. Tell them how it is special
  2. Create the simple figure including the money shot that summarizes everything that’s fabulous about your article
  • Why would the audience of the journal (the very broad audience of a high impact one) care about this? Tell them explicitly.