Writing a journal manuscript

Publishing your results is a vital step in the research lifecycle

and in your career as a scientist. Publishing papers is necessary
to get your work seen by the scientific community, to exchange
your ideas globally and to ensure you receive the recognition for
your results. The following information is designed to help you
write the best paper possible by providing you with points to
consider, from your background reading and study design to
structuring your manuscript and figure preparation.

By the end of the tutorial you should know on how to:

 prepare prior to starting your research

 structure your manuscript and what to include in each section
 get the most out of your tables and figures so that they clearly
represent your most important results.
You will also have the opportunity to test your learning by
completing a quiz at the end.

Before you begin writing

A good research paper begins long before you start writing.
Giving some deep thought as to the topic you are researching,
the question you are answering and the study design, as well as
ensuring you follow appropriate research laws and regulations,
all contribute to making a publishable paper.

In the first half of the module we will cover:

 Identifying hot topics and background reading

 Study design
 Reference managers
 Types of journal manuscripts
 Identifying your research question
Making informed decisions about what to study, and defining
your research question, even within a predetermined field, is
critical to a successful research career, and can be one of the
hardest challenges for a scientist.

Being knowledgeable about the state of your field and up-to-

date with recent developments can help you:

 Make decisions about what to study within niche research areas

 Identify top researchers in your field whose work you can
follow and potentially collaborate with
 Find important journals to read regularly and publish in
 Explain to others why your work is important by being able to
recount the bigger picture
How can you identify a research question?
Reading regularly is the most common way of identifying a
good research question. This enables you to keep up to date with
recent advancements and identify certain issues or unsolved
problems that keep appearing.
Begin by searching for and reading literature in your field. Start
with general interest journals, but don’t limit yourself to
journal publications only; you can also look for clues in the
news or on research blogs. Once you have identified a few
interesting topics, you should be reading the table of contents of
journals and the abstracts of most articles in that subject area.
Papers that are directly related to your research you should read
in their entirety.

TIP Keep an eye out for Review papers and special issues in

your chosen subject area as they are very helpful in discovering
new areas and hot topics.
TIP: you can sign up to receive table of contents or notifications
when articles are published in your field from most journals or
publishers.
TIP: Joining a journal club is a great way to read and dissect
published papers in and around your subject area. Usually
consisting of 5-10 people from the same research group or
institute they meet to evaluate the good and bad points of the
research presented in the paper. This not only helps you keep up
to date with the field but helps you become familiar with what is
necessary for a good paper which can help when you come to
write your own.

If possible, communicate with some of the authors of these

manuscripts via email or in person. Going to conferences if
possible is a great way to meet some of these authors.
Often, talking with the author of an important work in your
research area will give you more ideas than just reading the
manuscript would.

Study design
You must have a good study design to get publishable results.
When designing an experiment, you will need to decide:
 What is your hypothesis or research question?

 What are the aim(s) of your study?

 What are the best methods for achieving your aims?

 Do you have the necessary resources to carry out your

methods?
 Which positive and negative controls will you use?

 Do you have the required ethics and

regulatory permissions? For example, if your experiment
will have animal subjects, you will probably need approval
from your institution’s review board. If you are publishing
a clinical trial, then you need register it in a clinical trials
 registry. Not getting the correct permissions will stop you
from publishing your work in reputable journals.
 Will your experiment have enough statistical power to
give useful results? Is your sample size large enough to
draw valid conclusions? Which statistical tests will you
use for your analysis? If you are not sure, consult a
statistician; they can provide you with expert advice that
may save you a lot of time.

Reference managers
Reference managers (or reference formatting software such as
BibTeX for LaTeX documents) make it easy to organize and
format citations. They can also assist with managing libraries
containing citations, PDFs, and image files by organizing
important documents by subject and allowing you to search your
library using keywords. Add and organize any papers that are
relevant to your research as you read them. This will help you
remember to appropriately cite articles that you have read.
Some widely used reference management and formatting
software applications are:
BibTeX
EndNote
Mendeley
Papers
RefWords
Zotero
ReadCube
TIP: When using a reference manager, make sure you have the
correct style file for your target journal. The reference style
used by the journal can usually be found in the Instructions for
Authors on their website. Formatting references using a
reference manager with a style file is very simple.

Types of journal articles

It is helpful to familiarise yourself with the different types of
articles published by journals. Although it may appear there are
a large number of types of articles published due to the wide
variety of names they are published under, most articles
published are one of the following types; Original Research,
Review Articles, Short reports or Letters, Case Studies,
Methodologies.

Original Research:

This is the most common type of journal manuscript used to

publish full reports of data from research. It may be called
an Original Article, Research Article, Research, or
just Article, depending on the journal. The Original Research
format is suitable for many different fields and different types of
studies. It includes full Introduction, Methods, Results, and
Discussion sections.
Short reports or Letters:
These papers communicate brief reports of data from original
research that editors believe will be interesting to many
researchers, and that will likely stimulate further research in the
field. As they are relatively short the format is useful for
scientists with results that are time sensitive (for example, those
in highly competitive or quickly-changing disciplines). This
format often has strict length limits, so some experimental
details may not be published until the authors write a
full Original Researchmanuscript. These papers are also
sometimes called Brief communications.
Review Articles:
Review Articles provide a comprehensive summary of research
on a certain topic, and a perspective on the state of the field and
where it is heading. They are often written by leaders in a
particular discipline after invitation from the editors of a
journal. Reviews are often widely read (for example, by
researchers looking for a full introduction to a field) and highly
cited. Reviews commonly cite approximately 100 primary
research articles.
TIP: If you would like to write a Review but have not been
invited by a journal, be sure to check the journal website as
some journals do not consider unsolicited Reviews. If the
website does not mention whether Reviews are commissioned it
is wise to send a pre-submission enquiry letter to the journal
editor to propose your Review manuscript before you spend time
writing it.  
Case Studies:
These articles report specific instances of interesting
phenomena. A goal of Case Studies is to make other researchers
aware of the possibility that a specific phenomenon might occur.
This type of study is often used in medicine to report the
occurrence of previously unknown or emerging pathologies.
Methodologies or Methods
These articles present a new experimental method, test or
procedure. The method described may either be completely new,
or may offer a better version of an existing method. The article
should describe a demonstrable advance on what is currently
available.

Structuring your manuscript

Once you have completed your experiments it is time write it up
into a coherent and concise paper which tells the story of your
research. Researchers are busy people and so it is imperative
that research articles are quick and easy to read. For this reason
papers generally follow a standard structure which allows
readers to easily find the information they are looking for. In the
next part of the course we will discuss the standard structure and
what to include in each section.
 Overview of IMRaD structure
IMRaD refers to the standard structure of the body of research
manuscripts (after the Title and Abstract):
 Introduction
 Materials and Methods
 Results
 Discussion and Conclusions
Not all journals use these section titles in this order, but most
published articles have a structure similar to IMRaD. This
standard structure:
 Gives a logical flow to the content
 Makes journal manuscripts consistent and easy to read
 Provides a “map” so that readers can quickly find content of
interest in any manuscript
 Reminds authors what content should be included in an article
Provides all content needed for the work to be replicated and
reproduced
Although the sections of the journal manuscript are published in
the order: Title, Abstract, Introduction, Materials and Methods,
Results, Discussion, and Conclusion, this is not the best order
for writing the sections of a manuscript. One recommended
strategy is to write your manuscript in the following order:
1. Materials and Methods
2. Results
These can be written first, as you are doing your experiments
and collecting the results.
3. Introduction
4. Discussion
5. Conclusion
Write these sections next, once you have had a chance to
analyse your results, have a sense of their impact and have
decided on the journal you think best suits the work
 6. Title
7. Abstract
Write your Title and Abstract last as these are based on all the
other sections.
Following this order will help you write a logical and consistent
manuscript.
Use the different sections of a manuscript to ‘tell a story’
about your research and its implications.

Title, Abstract and Keywords

The Importance of Titles
The title of your manuscript is usually the first introduction
readers (and reviewers) have to your work. Therefore, you must
select a title that grabs attention, accurately describes the
contents of your manuscript, and makes people want to read
further.

An effective title should:

 Convey the main topics of the study

 Highlight the importance of the research
 Be concise
 Attract readers
Writing a good title for your manuscript can be challenging.
First, list the topics covered by the manuscript. Try to put all of
the topics together in the title using as few words as possible. A
title that is too long will seem clumsy, annoy readers, and
probably not meet journal requirements.

Example:
 Does Vaccinating Children and Adolescents with Inactivated
Influenza Virus Inhibit the Spread of Influenza in Unimmunized
Residents of Rural Communities?
This title has too many unnecessary words.

Influenza Vaccination of Children: A Randomized Trial

This title doesn’t give enough information about what makes
the manuscript interesting.
Effect of Child Influenza Vaccination on Infection Rates in
Rural Communities: A Randomized Trial
This is an effective title. It is short, easy to understand, and
conveys the important aspects of the research.

Think about why your research will be of interest to other

scientists. This should be related to the reason you decided to
study the topic. If your title makes this clear, it will likely attract
more readers to your manuscript.
TIP: Write down a few possible titles, and then select the best to
refine further. Ask your colleagues their opinion. Spending the
time needed to do this will result in a better title.

Abstract and Keywords

The Abstract is:
 A summary of the content of the journal manuscript
 A time-saving shortcut for busy researchers
 A guide to the most important parts of your manuscript’s
written content
Many readers will only read the Abstract of your manuscript.
Therefore, it has to be able to stand alone. In most cases the
abstract is the only part of your article that appears in indexing
databases such as Web of Science or PubMed and so will be the
most accessed part of your article; making a good impression
will encourage researchers to read your full paper.
 A well written abstract can also help speed up the peer-review
process. During peer review, referees are usually only sent the
abstract when invited to review the paper. Therefore, the
abstract needs to contain enough information about the paper to
allow referees to make a judgment as to whether they have
enough expertise to review the paper and be engaging enough
for them to want to review it.
Your Abstract should answer these questions about your
manuscript:
 What was done?
 Why did you do it?
 What did you find?
 Why are these findings useful and important?
Answering these questions lets readers know the most important
points about your study, and helps them decide whether they
want to read the rest of the paper. Make sure you follow the
proper journal manuscript formatting guidelines when preparing
your abstract.
TIP: Journals often set a maximum word count for Abstracts,
often 250 words, and no citations. This is to ensure that the full
Abstract appears in indexing services.

Keywords are a tool to help indexers and search engines find

relevant papers. If database search engines can find your journal
manuscript, readers will be able to find it too. This will increase
the number of people reading your manuscript, and likely lead
to more citations.
However, to be effective, Keywords must be chosen carefully.
They should:
 Represent the content of your manuscript
 Be specific to your field or sub-field

Examples:
 Manuscript title: Direct observation of nonlinear optics in an
isolated carbon nanotube
Poor keywords: molecule, optics, lasers, energy lifetime
Better keywords: single-molecule interaction, Kerr effect,
carbon nanotubes, energy level structure

Manuscript title: Region-specific neuronal degeneration after

okadaic acid administration
Poor keywords: neuron, brain, OA (an abbreviation), regional-
specific neuronal degeneration, signaling
Better keywords: neurodegenerative diseases; CA1 region,
hippocampal; okadaic acid; neurotoxins; MAP kinase signaling
system; cell death

Manuscript title: Increases in levels of sediment transport at

former glacial-interglacial transitions
Poor keywords: climate change, erosion, plant effects
Better keywords: quaternary climate change, soil erosion,
bioturbation

Introduction, Methods and Results

Introduction
The Introduction should provide readers with the background
information needed to understand your study, and the reasons
why you conducted your experiments. The Introduction should
answer the question: what question/problem was studied?
While writing the background, make sure your citations are:
 Well balanced: If experiments have found conflicting results on
a question, have you cited studies with both kinds of results?
 Current: Every field is different, but you should aim to cite
references that are not more than 10 years old if possible.
 Although be sure to cite the first discovery or mention in the
literature even if it older than 10 years.
 Relevant: This is the most important requirement. The studies
you cite should be strongly related to your research question.
TIP: Do not write a literature review in your Introduction,
but do cite reviews where readers can find more information if
they want it.
Once you have provided background material and stated the
problem or question for your study, tell the reader the purpose of
your study. Usually the reason is to fill a gap in the knowledge
or to answer a previously unanswered question. For example, if
a drug is known to work well in one population, but has never
been tested in a different population, the purpose of a study
could be to test the efficacy and safety of the drug in the second
population.
The final thing to include at the end of your Introduction is a
clear and exact statement of your study aims. You might also
explain in a sentence or two how you conducted the study.

Materials and Methods

This section provides the reader with all the details of how you
conducted your study. You should:
 Use subheadings to separate different methodologies
 Describe what you did in the past tense
 Describe new methods in enough detail that another researcher
can reproduce your experiment
 Describe established methods briefly, and simply cite a
reference where readers can find more detail
 State all statistical tests and parameters
TIP: Check the ‘Instructions for Authors’ for your target
journal to see how manuscripts should present the Materials
and Methods. Also, as another guide, look at previously
published papers in the journal or sample reports on the journal
website.
 Results
In the Results section, simply state what you found, but do
not interpret the results or discuss their implications.
 As in the Materials and Methods section, use subheadings to
separate the results of different experiments.
 Results should be presented in a logical order. In general, this
will be in order of importance, not necessarily the order in
which the experiments were performed. Use the past tense to
describe your results; however, refer to figures and tables in the
present tense.
 Do not duplicate data among figures, tables, and text. A
common mistake is to re-state much of the data from a table in
the text of the manuscript. Instead, use the text to summarize
what the reader will find in the table, or mention one or two of
the most important data points. It is usually much easier to read
data in a table than in the text.
 Include the results of statistical analyses in the text, usually by
providing p values wherever statistically significant differences
are described.
TIP: There is a famous saying in English: “A picture is worth a
thousand words.” This means that, sometimes, an image can
explain your findings far better than text could. So make good
use of figures and tables in your manuscript! However, avoid
including redundant figures and tables (e.g. two showing the
same thing in a different format), or using figures and tables
where it would be better to just include the information in the
text (e.g. where there is not enough data for a table or figure).

Discussion and Conclusions

Your Discussion and Conclusions sections should answer the
question: What do your results mean?

In other words, the majority of the Discussion and Conclusions

sections should be an interpretation of your results. You should:
 Discuss your conclusions in order of most to least important.
 Compare your results with those from other studies: Are they
consistent? If not, discuss possible reasons for the difference.
 Mention any inconclusive results and explain them as best you
can. You may suggest additional experiments needed to clarify
your results.
 Briefly describe the limitations of your study to show reviewers
and readers that you have considered your experiment’s
weaknesses. Many researchers are hesitant to do this as they feel
it highlights the weaknesses in their research to the editor and
reviewer. However, doing this actually makes a positive
impression of your paper as it makes it clear that you have an in
depth understanding of your topic and can think objectively of
your research.
 Discuss what your results may mean for researchers in the
same field as you, researchers in other fields, and the general
public. How could your findings be applied?
 State how your results extend the findings of previous studies.
 If your findings are preliminary, suggest future studies that
need to be carried out.
 At the end of your Discussion and Conclusions sections, state
your main conclusions once again.

Figures and tables

Figures and tables (display items) are often the quickest way
to communicate large amounts of complex information that
would be complicated to explain in text.

Many readers will only look at your display items without

reading the main text of your manuscript. Therefore, ensure
your display items can stand alone from the text and
communicate clearly your most significant results.

Display items are also important for attracting readers to your

work. Well designed and attractive display items will hold the
 interest of readers, compel them to take time to understand a
figure and can even entice them to read your full manuscript.
Finally, high-quality display items give your work
a professional appearance. Readers will assume that a
professional-looking manuscript contains good quality science.
Thus readers may be more likely to trust your results and your
interpretation of those results.
When deciding which of your results to present as display items
consider the following questions:
 Are there any data that readers might rather see as a display item
rather than text?
 Do your figures supplement the text and not just repeat what
you have already stated?
 Have you put data into a table that could easily be explained in
the text such as simple statistics or p values?

Tables
Tables are a concise and effective way to present large amounts
of data. You should design them carefully so that you clearly
communicate your results to busy researchers.
The following is an example of a well-designed table:
 Clear and concise legend/caption
 Data divided into categories for clarity
 Sufficient spacing between columns and rows
 Units are provided
 Font type and size are legible
 Source: Environmental Earth Sciences (2009) 59:529–536

Figures
Figures are ideal for presenting:
 Images
 Data plots
 Maps
 Schematics
Just like tables all figures need to have a clear and concise
legend caption to accompany them.
Images
Images help readers visualize the information you are trying to
convey. Often, it is difficult to be sufficiently descriptive using
words. Images can help in achieving the accuracy needed for a
scientific manuscript. For example, it may not be enough to say,
“The surface had nanometer scale features.” In this case, it
would be ideal to provide a microscope image.
For images, be sure to:
 Include scale bars
 Consider labeling important items
 Indicate the meaning of different colours and symbols used
Data plots
 Data plots convey large quantities of data quickly. The goal is
often to show a functional or statistical relationship between two
or more items. However, details about the individual data points
are often omitted to place emphasis on the relationship that is
shown by the collection of points. Here, we have examples of
figures combining images and a plots in multiple panels.
For data plots, be sure to:
 Label all axes
 Specify units for quantities
 Label all curves and data sets
 Use a legible font size

Source: Nano Research (2010) 3:843–851

Source: Borrego et al. Cancer & Metabolism 2016 4:9
Source: Borrego et al. Cancer & Metabolism 2016 4:9

Maps
Maps are important for putting field work in the context of the
location where it was performed. A good map will help your
reader understand how the site affects your study. Moreover, it
will help other researchers reproduce your work or find other
locations with similar properties. Here, we have a map used in a
study about salmon.
 For maps, be sure to:
 Include latitude and longitude
 Include scale bars
 Label important items
 Consider adding a map legend

Source: Environmental Biology of Fishes (2011) DOI:

10.1007/s10641-011-9783-5

Schematics
Schematics help identify the key parts to a system or process.
They should highlight only the key elements because adding
unimportant items may clutter the image. A schematic only
includes the drawings the author chooses, offering a degree of
flexibility not offered by images. They can also be used in
situations where it is difficult or impossible to capture an image.
Below is a schematic explaining how nanotubes could be used
to harvest energy from a fluid.
For schematics, be sure to:
 Label key items
 Provide complementary explanations in the caption and main
text
 Source: Nano Research (2011) 4:284–289

TIP: it’s important to consider how your figures will look in

print as well as online. A resolution of 72 ppi is sufficient for
online publication whilst in print 100 ppi is recommended. You
can adjust the resolution of your figure within the original
program you used to create it at the time you save the file.
TIP: There are two main colour models; RGB which stands for
red, green, blue and CMYK or cyan, magenta, yellow and black.
Most microscopes will take images using the RGB however
CMYK is the standard used for printing so it is important to
check that your figures will display well in this format.

Avoiding image manipulation

You should never knowingly manipulate your images to change
or improve you results. To avoid inadvertent manipulation, you
should only minimally process your figures before submitting
them to the journal, your submitted images should faithfully
represent the original image files.
 Adjusting the brightness or contrast of an image, in fluorescent
microscopy for example, is only acceptable if applied equally
across all images including the controls
 The cropping of images in the creation of figures should be
avoided unless it significantly improves the clarity of
conciseness of presentation. Be sure that the cropping does not
 exclude any necessary information for the understanding of the
figure, such as molecular markers in electrophoresis gels.
 Any adjustments or processing software used should be stated.
TIP: keep copies of the original images, files and metadata used
to create your figures as these can be requested by the journal
during the review process.

Acknowledgments and References

Acknowledgments
This usually follows the Discussion and Conclusions sections.
Its purpose is to thank all of the people who helped with the
research but did not qualify for authorship (check the target
journal’s Instructions for Authors for authorship guidelines).
Acknowledge anyone who provided intellectual assistance,
technical help (including with writing and editing), or special
equipment or materials.
TIP: The International Committee of Medical Journal Editors
has detailed guidelines on who to list as an author and who to
include in the Acknowledgments that are useful for scientists in
all fields.
Some journals request that you use this section to provide
information about funding by including specific grant numbers
and titles. Check your target journal’s instruction for authors for
specific instructions. If you need to include funding information,
list the name(s) of the funding organization(s) in full, and
identify which authors received funding for what.

References
As references have an important role in many parts of a
manuscript, failure to sufficiently cite other work can reduce
your chances of being published. Every statement of fact or
description of previous findings requires a supporting reference.
 TIP: Be sure to cite publications whose results disagree with
yours. Not citing conflicting work will make readers wonder
whether you are really familiar with the research literature.
Citing conflicting work is also a chance to explain why you
think your results are different.
It is also important to be concise. You need to meet all the above
needs without overwhelming the reader with too many
references—only the most relevant and recent articles need to be
cited. There is no correct number of references for a manuscript,
but be sure to check the journal’s guidelines to see whether it
has limits on numbers of references.
TIP: Never cite a publication based on what you have read in a
different publication (such as a review), or based only on the
publication’s abstract. These may mislead you and readers.
Read the publication itself before you cite it, and then check the
accuracy of the citation again before submitting your
manuscript.
You should reference other work to:
 Establish the origin of ideas
When you refer to an idea or theory, it is important to let your
readers know which researcher(s) came up with the idea. By
citing publications that have influenced your own work, you
give credit to the authors and help others evaluate the
importance of particular publications. Acknowledging others’
contributions is also an important ethical principle.
 Justify claims
In a scientific manuscript, all statements must be supported with
evidence. This evidence can come from the results of the current
research, common knowledge, or from previous publications. A
citation after a claim makes it clear which previous study
supports the claim.
 Provide a context for your work
By highlighting related works, citations help show how a
manuscript fits into the bigger picture of scientific research.
When readers understand what previous studies found and what
 puzzles or controversies your study relates to, they will better
understand the meaning of your work.
 Show there is interest your field of research
Citations show that other researchers are performing work
similar to your own. Having current citations will help journal
editors see that there is a potential audience for your manuscript.

Formatting your manuscript

It is important to format your manuscript according to your
target journal’s requirements, which can be found in the
Instructions for Authors. This will speed up the submission
process because the journal’s editorial team will not have to
send your manuscript back to you for formatting. It can
also increase your chances of success because you will not omit
materials that the journal might require.

TIP: Before writing a complete draft of your manuscript, it is a

good idea to select an initial target journal. Read the formatting
requirements for the journal on its website, then write your
draft. This could save you a lot of time, as you won’t have to
reformat an already-written manuscript after selecting the
journal!

Review all guidelines and ensure that your manuscript meets

them. Have you:
 Obeyed all word and character limits (title, running title,
abstract, manuscript text)?
 Included all required sections?
 Met language requirements (US or UK English)?
 Supplied all requested contact information?
 Inserted figures in the correct location (in text, end of
manuscript, separate files)?
 Correctly formatted references?
 Used the correct file format for your images
(.jpg, .png, .pdf, .ppt)?
 Stated ANY conflicts of interest?
 Included details of any required ethics and
regulatory permissions?
 Obtained consent from ALL authors?
TIP: Some journals provide templates to assist authors. Also
look for template style files for use with your reference
manager.