1. technology and computing
2. computer reviews

The Research Paper:
Writing a Manuscript and Getting it Published
Kathryn Stockbauer, Ph.D.
Manager, Office of Academic Development
Department of Pathology and Genomic Medicine
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
GETTING STARTED
Choosing a Journal
• Target audience, readership
(translational, clinicians, basic science, cancer?)
• Likelihood of publication
• Impact Factor
GETTING STARTED
Instructions to Authors
Found on the home page of each journal
Will tell you how to format the manuscript:
• Length, section titles and order
• Format figures, tables, and references
• Figure resolution and layout
• Nomenclature, abbreviations
Not suggestions or guidelines, but instructions.
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
THE MANUSCRIPT
“Science is a story. Tell it.”
Wells, J Cell Biol., 165:757
THE MANUSCRIPT
Like any good narrative, your
manuscript will answer:
1. Why?
Introduction
2. How?
Materials and Methods
3. What happened?
4. What does it mean?
Results
Discussion
INTRODUCTION
The “why” of the paper.
Three main components:
• What is known in the field (background)
• What gap does your study fill (hypothesis)
• End by stating what you will show (overview of results)
MATERIALS AND METHODS
The “how” of the paper.
Provide enough detail so that someone
can replicate your results
• Concentrations, incubation times, primer
sequences, where your kits were
purchased, etc.
• If it is a common procedure that has been
done many times, put “as described in
reference X” and reference it
DISCUSSION
The “what does it mean?”
(Typically the most difficult section to write)
• Not a rehashing of the results
• Puts your findings in the context of the field
• What did you contribute?
First paragraph: State what you have shown
directly, declaratively, succinctly
DISCUSSION
Inducible NOS Inhibition Reverses Tobacco-Smoke-Induced
Emphysema and Pulmonary Hypertension in Mice, Seimetz et al
Discussion
We sought to determine whether the vascular pathology is linked to
emphysema development and identified iNOS as a key molecular
player in the underlying processes. Our data showed that
alterations in lung vascular structure and function induced by
tobacco smoke preceded emphysema in mice and were
independent of hypoxia. We also showed that emphysema and PH
occurred independently and are essentially associated with iNOS in
different cell types. Finally, our data indicate that targeting iNOS by
pharmacological inhibition can improve the functional and
structural destruction caused by tobacco smoke.
Cell 147:293-305
DISCUSSION
Include:
•
•
•
•
•
•
The major findings
Their meaning and importance
Relate the findings to the field
Consider alternative explanations
Acknowledge the study’s limitations
Clinical importance/relevance
Hess, Resp Care, 49:1238
DISCUSSION
Avoid:
•
•
•
•
•
Overinterpretation of the results
Unwarranted speculation
Inflating the importance of your findings
Criticizing other studies
Overly broad interpretation – stick to your hypothesis
Remember two things:
• What scientific contribution have you made?
• Why is it relevant?
Hess, Resp Care, 49:1238
ABSTRACT
If your abstract is not interesting or usefulThey will not read the rest of your paper
Four components to an abstract:
1.
2.
3.
4.
Clearly stated hypothesis
Methods used to test hypothesis
Summary of what you found
Conclusions, and how the study contributes to the
unknown (mechanism/pathology of disease)
ABSTRACT
PIK3R1 (p85a) Is Somatically Mutated at High Frequency in
2. Methods
Cancer
1.Primary
ClearlyEndometrial
stated
used to test
hypothesis
hypothesis
3. Summary of
findings
4. Conclusions, and
how study
contributes to the
field
ABSTRACT
Also:
• Limited to no abbreviations
• No references
• Usually 150-250 words, depending on
journal/article type
• Use present tense to tell what is known in the
field and past tense to describe what you show
GETTING STARTED
1. Start with an outline of your figures
Figure 1: Gene schematic
Main Points: 1) Show gene order/arrangement
2) Show transcription start sights
Figure 2: Western Blot, WT verses KO
Main Points: 1) Gene expressed in WT
2) Gene not expressed in KO
GETTING STARTED
2. Write Results first
• You know what you did – often the easiest to
write and good for getting words on paper
• What you show in Results will determine what
you put in M&M, and what you have to
Introduce and Discuss
3. After results I go to M&M, then Introduction,
Discussion, and Abstract
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
SUBMITTING
You are ready to submit
The Manuscript:
1.
2.
3.
4.
Has been read and signed off on by all co-authors
Has been proofed for GSP and syntax
References reviewed for accuracy
Instructions to Authors have been followed
SUBMITTING
The Cover Letter
• Do NOT discount the importance of a good cover letter
• The cover letter is the first thing the editor will read,
after the title, before the abstract
• It is your first chance to present your work, its
implications and how it fits in to the field
U. Neill, JCI 117:3599
SUBMITTING
The cover letter should:
• Be 3-4 paragraphs in length
• Introduce the study
• Briefly explain the premise, why it is important,
and what your findings contribute
• Suggest referees and any exclusions (and why,
e.g. direct competitor, known bias, etc.)
U. Neill, JCI 117:3599
REVIEW
Top Reasons an Article is Rejected:
1.
2.
3.
4.
5.
Inappropriate or incomplete statistics
Overinterpretation of results
Sample size is too small
Incomplete or outdated literature review
Sloppy writing, or “poor” manuscripts
Adapted from G. Bordage, Acad Med, 76:889
REVIEW
Accepted manuscripts had the
following in common:
1. The relevance and importance of the subject
2. Excellence in writing and data presentation
3. Quality of the study design
Adapted from G. Bordage, Acad Med, 76:889
REVIEW
Process
• Your paper is sent to 2-3 peers for review
• Turn around time is typically 1-2 months
What types of reviews are you likely to see?
Accepted with minor revisions
Usually involves clarification to the text
Option to resubmit with major revisions
Could involve additional experiments
Outright rejection
Not appropriate for the readership, fatal
flaws in design/findings/statistics, etc.
RESPONSE
Important: Use the editor’s and reviewers’
responses to improve your manuscript
Address all editor/review comments with:
• New experimental data
• Revised text
• Convincing, POLITE rebuttal as to why the
reviewer/editor is not entirely correct
RESPONSE
Response to Reviewers
There is a correct way to present a point-by-point response:
Reviewer 1
Comment 1: Materials and Methods section: The authors say that Hardy-Weinberg tests were
performed, but no results are shown. It would be useful to have an individual list of polymorphisms
not in HWE in each ethnic group, or an indication in the tables, or the proportion markers out of
HWE overall should be shown.
Response: A supplemental table with each SNP and the corresponding Fisher exact test Pvalues for each ethnic group has been added.
Comment 2: Results section: It is not clear how and why a cut-off of <3% was used to define “rare”
NSPs. This needs to be explained.
Response: The cut-off lines for rare and common are usually 1% to 5%. In this study, we used
3% as cut-off line because the sample sizes in our adult case control study ranged from 110 to
375 in different ethnic groups of cases and controls. If an SNP had an allele frequency of 3% in
one ethnic group, it will be have at least 6.6 alleles in the smallest group of having 110
individuals (e.g. Caucasian controls). It is statistically feasible for 2X2 Chi square test.
RESPONSE
Response to Reviewers
• The point-by-point response is included in
the cover letter of the resubmission
• Thank the editor/reviewers for their
helpful suggestions
• Always be polite and professional in your
response, even if you disagree!
U. Neill, JCI 117:3599
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
OVERVIEW
Presentation Outline:
1. Getting Started
2. What goes where (Introduction, Methods,
Results, and Discussion)
3. Submitting and Responding to Reviews
4. Writing Tips and Resources
WRITING
WRITING TIPS
Think back to freshman composition…
•
•
•
•
•
Use short, declarative sentences
Say what you need to say as simply as possible
Be exact and concise
Each paragraph has a topic sentence
Each paragraph conveys one thought/theme
WRITING
Genetic basis
of virulence
Pathogenesis and
gene expression
SNPs and RopB
GETTING STARTED
Overcoming Writer’s Block
Reasons for Writer’s Block:
• Too busy, low on the priority list
• Harsh internal critic, aiming for perfection
• Overwhelmed, don’t know where to start
• Wrong environment (distractions, other responsibilities)
GETTING STARTED
“There is no such thing as writer’s
block for writers whose standards
are low enough.”
Poet William Stafford
GETTING STARTED
TIPS:
• Sit your butt in the chair and write
• Set aside a certain time every day, every week
• The first draft is just that – a first draft
• You will (and should) go through multiple iterations
RESOURCES
Even though you’ve may not have written a
manuscript before… you’ve read lots of them.
• There are 10s of 1000s of articles in PubMed
and/or journal homepages
• Find ones you thought were well written, the data
was well presented, and emulate them.
RESOURCES
Office of Academic Development Website
Links to articles used to create this presentation
Thank you!
Questions?