Academic Publishing, Part III:

How to Write a Research Paper (So That It Will Be Accepted) in a High Quality Journal

Clifford B. Saper, MD, PhD

Department of Neurology, Program in Neuroscience, and Division of Sleep Medicine

Beth Israel Deaconess Medical Center, Harvard Medical School

Boston, MA 02215

Address correspondence to:

Dr. C.B. Saper, Dept. of Neurology, Beth Israel Deaconess Medical Center, 330 Brookline
Avenue, Boston, MA 02215
Email:csaper@bidmc.harvard.edu

This article has been accepted for publication and undergone full peer review but has not been
through the copyediting, typesetting, pagination and proofreading process which may lead to
differences between this version and the Version of Record. Please cite this article as an
‘Accepted Article’, doi: 10.1002/ana.24317
This article is protected by copyright. All rights reserved.
 Annals of Neurology Page 2 of 7

Since I began reading the scientific literature when I was a student, I have had a bucket
list of journals that published work I admired, and in which I eventually wanted to see some of
my own work published. Getting papers into some of those journals (no, I have not yet
completed the list…) has been a very satisfying part of my career. Along the way, as an author,
reviewer, and editor, I have learned a great deal about how to prepare a paper so that it has the
best chance of making it into my journal of choice. In the first two segments of this series, we
explored the peer-review process and how to choose a journal in which to publish your work. In
this article, we will discuss the process of writing a research paper to maximize the chance of its
being accepted in your first-choice journal.

Write for the journal to which you plan to submit

It may seem axiomatic that your paper will have the best chance of being published in a
journal if you prepare it specifically for that publication. However, it is surprising how often
authors do not do this. In Part II in this series, I advised that writers should choose the journal in
which the work would best fit, based on what they typically publish. Reading typical papers in
that journal should also give you a good idea of what the editors are looking for in style and
organization.
Different journals have specific formats. Annals uses the classic style of a separate self-
contained Abstract, followed by an Introduction, Methods, Results, and Discussion. Some
journals make the first paragraph of the Introduction serve as an Abstract, place the Methods at
the end of the article, or combine some components of Results and Discussion. While the
remainder of this article will address the writing of a manuscript that is organized in the format
used by Annals, you should be sure of the format used by your target journal, and write your
paper in that style.
Another key difference between journals is how they position themselves in the
“intellectual space” of their fields. For example, some high-visibility journals are looking for
papers that are particularly newsworthy. Simply providing a paper of high scientific quality may
not be good enough for them. Other journals have a predilection for papers of a certain type
(e.g., basic science, clinical trials, case reports, etc.) or for work in a certain subfield (e.g.,
cognitive, demyelinating disease, neuromuscular, etc.). These preferences are often driven by
the taste of their editors, so it can be useful for authors to review the list of editors and members
of the editorial board, whose own work often defines the intellectual space in which that journal
is most comfortable.
While your work will, of course, define its own field, it is often possible to target it for a
specific journal, by deciding which components of the study to put into that manuscript, what
types of analyses you want to present, and which ideas you want to emphasize in your paper.
Writing your paper specifically for that audience of editors is a key strategy in getting your paper
accepted. On the other hand, if you find that the intellectual space of the target journal is
different from what your paper addresses, it is generally better to find a more hospitable journal
than to try to push your work into a less welcoming environment.

Make your writing concise and state each point only once
Many new authors start laying out their Results section, or their figures. They then back
into writing an Introduction, which is often rambling because it seeks to cover every point in the
Results, and then a Discussion, which often repeats points made in the Introduction. This leads
to a paper that is too long, making it difficult for a reader to glean the key points. Experienced

John Wiley & Sons

This article is protected by copyright. All rights reserved.
Page 3 of 7 Annals of Neurology

reviewers often report back that a paper reads as if it were written “by a graduate student or a
resident” (i.e., a neophyte).
The key to avoiding this syndrome is to plan your paper in advance. The hardest part,
and the part that deserves the most amount of thought, is how you frame the problem you are
studying intellectually. This choice should be driven by the work itself, of course, but should
also match the style of the target journal. For example, a given study may report a novel
scientific finding that has implications for human health. For a high-visibility scientific journal,
the authors may choose to emphasize the biological novelty of their findings and the implications
for further work; for a clinical journal, the authors may want to re-write the paper to emphasize
the relevance to human disease and its treatment.
Once you have decided how to frame your work, you need to look back at the results, and
organize them in a way that fits that emphasis. For example, you may want to include some
findings that have interesting neurobiological implications for a basic science journal, but
perhaps remove those and instead emphasize the disease-related aspects for a more clinical
journal. You will find that you can (and almost always will) leave some components of your
study on the cutting room floor. What you choose to include and what you leave out will depend
in part on the way you frame your problem, and the journal for which you are preparing the
paper.
When you have identified the components of your results that you want to include, it is
time to lay out the points that you want to make in your Introduction and Discussion. We will
discuss below the types of material you may want to include in each. However, at this point, it is
important to emphasize that each major point should be discussed in detail only once. It is
important to decide if the detail will be in the Discussion (where it usually fits best) or in the
Introduction (if it is needed to set up the scientific problem).

The Introduction should concisely frame the problem; avoid using too many abbreviations
The Introduction should be written for a general reader in the overall field of the journal
for which you are writing. If you are writing about a disease for a general neuroscience
audience, it may require a much more substantial introduction to the disease than it would for a
general neurology audience, and the latter may require more introduction than for a subspecialty
clinical journal. On the other hand, the amount of introduction given to the scientific method
used to study the disease may have the opposite requirement (e.g., less detail needed to introduce
2-photon confocal microscopy to a scientific audience, but a very detailed introduction for a
clinical subspecialty audience).
While the opening lines may give a general introduction to the field, the text should move
as quickly as possible to the specific problem that the paper addresses. It is important here to sell
your audience on the importance of answering the scientific question your study poses. This will
draw in the reviewer of your paper, who will pay more attention to your subsequent results. A
reviewer who finishes your Introduction without a strong sense of why your results will be
important is not likely to be as impressed with the rest of your paper.
At the same time, it is important not to state your results and conclusions in the
Introduction. Many neophyte writers do this, hoping that this precis will entice the reader to go
on to the remainder of the paper. Not only is this unnecessary, but it may well set up the reader
(who may not yet be convinced of the premise) to want to find flaws in your study, before
actually reading it in detail. Let the Abstract provide the lead-in. The Introduction should end
with a delineation of how you intend to go about solving the problem you have posed.

John Wiley & Sons

This article is protected by copyright. All rights reserved.
 Annals of Neurology Page 4 of 7

A common error made by inexperienced writers is to use too many abbreviations. A few
abbreviations are necessary for long, bulky names that are repeated frequently in the text, but if
you find yourself using more than about six abbreviations for the entire paper, you are probably
using too many. A good test is to look at the last paragraph of the Abstract or Introduction. If it
reads, to a naïve observer, as if it were written in code, you are using too many abbreviations.

The Methods should allow an investigator in your field to repeat the study
The Methods in many journals have been relegated to second-class status. Some put
them at the end of the published text, as if they are a distraction that can be kept for later, if
necessary. Some high-visibility journals banish the Methods entirely to online supplementary
material. While the Methods do take up valuable page space, the Editors of Annals continue to
believe that it is not possible to really interpret Results unless you understand how they were
obtained. For that reason, we have kept the Methods in the traditional position, between the
Introduction and the Results.
Regardless of the style of the journal that you choose, it is still important to make sure
that the Methods you give would allow a reasonably skilled competitor in your field to replicate
the work you present. This may seem to be a bother, and some writers hesitate to give away too
many of their “trade secrets” to their competitors. However, if the result is important, other
investigators in your field are going to want to repeat it. If they fail, your reputation may be
damaged.
The Methods should include very specific information about key equipment and reagents,
down to the company from which they were purchased and the catalog number if appropriate.
The information should be provided in a series of paragraphs on specific methods or types of
experiments that will be described. Be sure to include a paragraph on the methods of analysis,
including statistical tests, and a paragraph on participant recruitment and consent, for studies
involving human subjects.

The Results should lay out the findings in clearly demarcated paragraphs; avoid the
“travelogue” approach
A common mistake made by inexperienced writers is to be led by the organization of the
figures. The text then becomes a series of expanded figure legends (“Figure 1 shows that…”).
This is similar to the travelogue presented by those who come back from a trip with a load of
photographs to show their friends (“The next slide shows...”). Some presenters at scientific
meetings also use this approach, which is a sure way to lose your audience. If you find yourself
repeating details of the figure legends in your text, or vice versa, you are making an error in one
of those two places (or both of them).
No one wants to be fed a series of graphs or photographs. They want to hear a story.
Make your story organized, so it builds to make a point. Do not get lost in digressions (save
those data for another paper) or confuse your audience with more detail than is necessary.
Leaving out some details is difficult. By the time you get around to writing up a project, they are
like your children, and you do not want to leave anyone behind. But you have to be ruthless in
writing a paper, and focus your attention on the goal, not on the cloud of data you collected that
eventually led to that goal.
Another common error is to put the results into chronological order. This is fine, if the
logical order of presenting your findings also is in that order. But quite often, the results were
obtained in a different order from that which provides the best and clearest story. In one high-

John Wiley & Sons

This article is protected by copyright. All rights reserved.
Page 5 of 7 Annals of Neurology

impact paper that I published, the results were presented in exactly the opposite order to that in
which they were obtained. That was because we had backed into the final result and
conclusions, not expecting them when we started the project. However, once we knew what that
result would be, it was simpler to explain the story when presented in the reverse order of the
way in which the events actually unfolded. That surprise, which for us occurred at the end of the
study, was exactly what made the result compelling enough to publish in a high-visibility
journal, and it belonged at the beginning of the printed publication, to frame the rest of the
experiments properly.

The Discussion should highlight the most significant aspects of your work, identify its
limitations, and discuss its meaning for the field
The first paragraph of the Discussion section should concisely reprise the major findings
of the study. This is your opportunity to put the spin you want on the observations you have
collected, and paint the big picture for your reader. If you cannot make a case here for how your
work has advanced the field, you are unlikely to do so, and many readers will stop there.
It is a good practice next to write a paragraph on the limitations of your work. All work
has limitations, both in the ways in which the research was conducted and the ways in which the
results can be interpreted, and you should make those clear. If you do not, the reviewers of the
paper will do so, and your work will very likely not be published. If you address this first, and
provide proper indications of the value of the work despite these limitations, you will have the
upper hand in that discussion.
The remainder of the Discussion should be broken up into paragraphs that address
important issues you want to address with respect to your data. Again, you are trying to tell a
story, or a series of stories, about how your data change the field. This is the place to review the
problems in the field, and to identify the place of your own observations in resolving some of
those problems.
Many writers include some sort of a résumé at the end of the discussion. This is not
really needed, because your Abstract provides that. Instead, it is worthwhile devoting some
space to projecting out into the future, identifying the new avenues of investigation opened up by
your observations.

Write the Abstract last to make sure that it matches the intent of the rest of the paper
Many writers try to prepare the Abstract first because it is the first thing a reader will see
when encountering the paper. However, if the writer has done a good job on the rest of the
paper, it may have developed in ways that might have been unexpected when the data were first
collected. Some data that turned out to be a distraction may have been dropped. Or the results
may have been put in a different order to emphasize a certain set of findings. It is often easier to
write a compelling abstract that will cause the reader to want to read the rest of the paper only
after the rest is already written.

“There is no such thing as good writing, only good re-writing.”

This quotation, which is variously attributed to Robert Graves or to Supreme Court
Justices Louis Brandeis or Oliver Wendell Holmes, Jr, remains as true for scientific writing as it
does for literature or judicial decisions. It is important to get your first draft down, but you
should plan to let it sit for a week or so, and then return to it ruthlessly, cutting and slashing to
improve both the flow of the paper and your prose. Ask a few trusted colleagues to read your

John Wiley & Sons

This article is protected by copyright. All rights reserved.
 Annals of Neurology Page 6 of 7

work, and to give you suggestions for how to improve it. It is best to have some senior mentors
who have experience as reviewers or editors, particularly early in your career. It is also
important to listen to them. One of my students, for example, had a tendency to write in a prolix
style. The first draft of one paper was 110 pages long! I used a red pen to mark up the draft on
paper, and cut it about in half. When it came back to me it was still over 100 pages. After
several rounds of this (and red pens), he became restless with my editing, and I told him to see
what would happen if he sent the paper in. He did submit it, and the first review came back:
“This paper would have been great in the day of Charles Darwin…”
Finally, plan to re-write and revise your paper multiple times, over a period of weeks.
Frequently, when I go back to a paper after a week or so off, I find that I can improve it
considerably. Always look for ways to streamline your text. A common complaint of reviewers
is that a paper is 20% or 30% too long, but I have never seen a referee complain because a paper
was too short! The classic paper in Nature by Watson and Crick on the structure of DNA was
two pages long. Your work will have the greatest impact if you can reduce the text to that which
is essential to make your point.

Make sure your figures and tables fit with the text, and are cited in order
The figures and tables should be used to document the key findings that you describe in
the text. It is just as important to edit these, providing only the clearest examples in your paper.
The usual standard for a photomicrograph is to show your “typical best case,” i.e., a case that
typifies the data most clearly and convincingly. It is very important to cite the figures and tables
in order of appearance, in the text. Do not number your figures until after you have actually
placed those citations, or things may get very confusing.
Read the instructions for figures for your target journal. Make sure that you provide them
in the format that is required. Generally, most journals use the same standard as Annals, in
which you submit the text, references, tables, and figure legends (in that order) as a single text
document, but then upload each figure as a separate file. Make sure that the figures have
sufficient resolution for publication. In general, you can do this by sizing them to the journal
page, and then submitting them at 300 dpi resolution at the size in which they would appear in
the printed journal.

A final word
Once you have finished your paper, it is critical that you submit it to your co-authors (and
those who are acknowledged) for their approval before it is sent in. Be sure to write a careful
cover letter, which should state (briefly!) the main point of your paper. You should suggest
some referees who are knowledgeable about the field. Some journals permit you to list referees
who you think should not be chosen as reviewers. Be careful here to list only those who have
real conflicts with you or your co-authors, not a list of everyone you think might give your work
a critical review. The latter often leads the editors to ignore your request (and wonder whether
the work will stand up to critical review).
After the paper goes in, you can relax, at least for a little while. In general, most journals
that operate efficiently take about five weeks on average to deliver a decision. The standard
deviation on that is about one and a half weeks, so if your paper is not returned in eight weeks or
so, you should feel justified in writing to the editor (but not before that). Some authors request
rapid review of their work. In my experience, this only works if the paper is groundbreaking
work of earthshaking importance. Trying to accelerate the review of a paper that the reviewer

John Wiley & Sons

This article is protected by copyright. All rights reserved.
Page 7 of 7 Annals of Neurology

will view as “average” in the field typically results in a reviewer who feels imposed upon, and
almost always leads to a worse review (and often a more prolonged wait for the review) than if
the process were just allowed to run its course.
Good luck with your paper, and if the review is not what you want, remember that there
are a lot of other journals out there. As I alluded to previously in this series, the sweetest
revenge when your paper has been turned down is to publish it somewhere else and have it
become a mainstay of the field.

John Wiley & Sons

This article is protected by copyright. All rights reserved.