The Research Paper: Writing a Manuscript and Getting it Published

Kathryn Stockbauer, Ph.D.Manager, Office of Academic DevelopmentDepartment of Pathology and Genomic Medicine

OVERVIEW

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

OVERVIEW

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

GETTING STARTED

Choosing a Journal

• Target audience, readership (translational, clinicians, basic science, cancer?)

• Likelihood of publication

• Impact Factor

Instructions to Authors

GETTING STARTED

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

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

OVERVIEW

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

THE MANUSCRIPT

“Science is a story. Tell it.”Wells, J Cell Biol., 165:757

THE MANUSCRIPT

Discussion

Introduction

Materials and Methods

Results

Like any good narrative, your manuscript will answer:

1. Why?

2. How?

3. What happened?

4. What does it mean?

INTRODUCTION

The “why” of the paper.

• What is known in the field (background)• What gap does your study fill (hypothesis)• End by stating what you will show (overview of results)

Three main components:

The “how” of the paper.

MATERIALS AND METHODS

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?”

• 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 showndirectly, declaratively, succinctly

(Typically the most difficult section to write)

DISCUSSION

DiscussionWe 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.

Inducible NOS Inhibition Reverses Tobacco-Smoke-Induced Emphysema and Pulmonary Hypertension in Mice, Seimetz et al

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

Hess, Resp Care, 49:1238

Remember two things:• What scientific contribution have you made?• Why is it relevant?

ABSTRACT

If your abstract is not interesting or useful- They will not read the rest of your paper

Four components to an abstract:

1. Clearly stated hypothesis2. Methods used to test hypothesis3. Summary of what you found4. Conclusions, and how the study contributes to the

unknown (mechanism/pathology of disease)

ABSTRACT

PIK3R1 (p85a) Is Somatically Mutated at High Frequency inPrimary Endometrial Cancer1. Clearly stated

hypothesis

2. Methods used to test 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 schematicMain Points: 1) Show gene order/arrangement

2) Show transcription start sights

Figure 2: Western Blot, WT verses KOMain 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

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

OVERVIEW

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

SUBMITTING

You are ready to submit

The Manuscript:

1. Has been read and signed off on by all co-authors2. Has been proofed for GSP and syntax3. References reviewed for accuracy4. Instructions to Authors have been followed

SUBMITTING

The Cover Letter

• The cover letter is the first thing the editor will read, after the title, before the abstract

U. Neill, JCI 117:3599

• It is your first chance to present your work, its implications and how it fits in to the field

• Do NOT discount the importance of a good cover letter

SUBMITTING

The cover letter should:

U. Neill, JCI 117:3599

• 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.)

REVIEW

Top Reasons an Article is Rejected:

Adapted from G. Bordage, Acad Med, 76:889

1. Inappropriate or incomplete statistics2. Overinterpretation of results3. Sample size is too small4. Incomplete or outdated literature review5. Sloppy writing, or “poor” manuscripts

REVIEW

Accepted manuscripts had the following in common:

Adapted from G. Bordage, Acad Med, 76:889

1. The relevance and importance of the subject2. Excellence in writing and data presentation3. Quality of the study design

REVIEW

• 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 textOption to resubmit with major revisions

Could involve additional experimentsOutright rejection

Not appropriate for the readership, fatal flaws in design/findings/statistics, etc.

Process

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 ReviewersThere 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 P-values 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

• Always be polite and professional in your response, even if you disagree!

U. Neill, JCI 117:3599

• Thank the editor/reviewers for their helpful suggestions

OVERVIEW

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

OVERVIEW

1. Getting Started2. What goes where (Introduction, Methods,

Results, and Discussion)3. Submitting and Responding to Reviews4. Writing Tips and Resources

Presentation Outline:

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 basisof 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

• Overwhelmed, don’t know where to start

• Harsh internal critic, aiming for perfection

• Wrong environment (distractions, other responsibilities)

“There is no such thing as writer’s block for writers whose standards are low enough.”

GETTING STARTED

Poet William Stafford

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

GETTING STARTED

RESOURCES

• 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.

Even though you’ve may not have written a manuscript before… you’ve read lots of them.

RESOURCES

Links to articles used to create this presentation

Office of Academic Development Website

Thank you!Questions?