anis.karimpour-fard@ucdenver.eduhttp://compbio.ucdenver.edu/Hunter October 18,2011

Preparing research manuscripts

Anis Karimpour-Fard

Can I publish this?

• Have you done something new and interesting?• Have you provided solutions to a problem?• Have you checked the latest results in the field?• Is the result interesting or useful for others in the field?• Is the hypothesis straightforward?• Did the experiments test the hypothesis?• Can you describe the study in 1 or 2 minutes?• Do your findings tell a nice story?

If all answers are “yes”, then start preparing yourmanuscript.

Starting out

Give an informal ORAL presentation of the work before you start to write the paper

This way you will clarify the story you want to tell and can anticipate objections or misunderstandings that must be addressedin the text.

Types of scientific papers

• Research articlesFull articlesBrief communicationsShort communicationsLettersApplication note

• Non-research articles Book chapters Review articles Letter to editors

Self-evaluate your work: Is it sufficient for a full article?

Which conference/workshop/journal?

Choose journal

Look at your references –these will help you narrow your choices

•Is the journal peer-reviewed?•Who is this journal’s audience?•What is the average time to print?•What is the journal’s Impact Factor?

A measure of how frequently its articles are cited in other journals

Choose journal: A Few Suggestions

• Study “instructions to authors”• Think about possible reviewers• Each journal has its own style; Review recent publications in each candidate journal. Find out the hot topics, the accepted types of articles, etc.• Know the journal, and why you submitted the

paper there

Instructions to authors

Follow the Instructions!• Every conference/journal provides “Instructions to Authors” or “Submission instructions” which detail

Paper types Paper length Length of abstract Paper format (LaTeX, Word template) Paper sections Reference format Spelling/capitalization/formatting conventions Deadlines

It is best to know the limits in advance than have to go back and change the paper later

Authors

• Identify co-authors Contributions to the work Often listed largely from greatest contributions to least

• Discuss author order• Make sure your co-authors agree about the message• Discuss target publication venue

Writing the manuscript

The hardest part is getting started

Parts of a manuscript

Title• Abstract• Introduction: What was the question?• Methods: How did you try to answer it?• Results: What did you find?• Discussion: What does it mean?• Acknowledgements• References

Write in what order?

TitleAbstractIntroductionMethodsResultsDiscussionAcknowledgementsReferencesFigures Tables

Start by drafting whatever part of the paper you find easiest to prepare

Title

• The TITLE is critical- it must be short and give the big-picture

• Should be specific enough but not overly narrow

• The fewest possible words that adequately indicate the contents of the paper

• Important in literature searching

Methods• Purposes: to allow others to replicate and to evaluate

what you did• Should describe the study design• Begin writing when experiments still in progress• Reference published methods where appropriate

• Should identify (if applicable)Statistical methodsMethods previously described but not well knownMethods that you yourself devisedCite and briefly describe the well-known methods

Results

• The core of the paper• Briefly repeating method can be effective• Decide on the elements of the story you wish to tell • Choose the subset of text, figures, and tables that most

effectively and concisely coveys your message• Do not speculate or over discuss results• Rather than telling the reader that a result is interesting

or significant, show them how it is interesting or significant

Introduction

• why the current study is of scientific interest Build case for why study is important/necessary Provide brief background to understand the paper and appreciate its

importance to set the stage for the present research, indicating gaps in

knowledge and presenting the research question to introduce present research, stating its purpose and outlining its

design

• State hypothesis / central question • Give a one sentence summary of findings • Emphasize your specific contribution to the topic• Typically should be funnel-shaped, moving from general to

specific

• First paragraph of introductionIs crucial for catching the attention of the audiencewhy the current study is of scientific interest

• Last paragraph of the Introduction Short summary of what you set out to do What you have achieved

Introduction: A Few Suggestions

Discussion• Often should begin with a brief summary of the main

findings• Should answer the question stated in the introduction• Some other items commonly addressed

Limitations of the studyRelationship to findings of other research (show how it

agrees or disagrees with previous models)Include suggestions for improving your techniques or

design, or clarify areas of doubt for further research• Discuss weaknesses and discrepancies Typically

should move from specific to general (opposite of introduction)

References• Functions

To give credit To add credibility To help readers find further information Will help in choosing journalBetter insight into possible reviewers

• Importance of accuracy• Existence of various reference formats• Availability of citation management software

(examples: EndNote, Reference Manager)

References A Few Suggestions

•Make sure references are comprehensive, accurate, relevant and recent

Seemingly relevant paper not cited

• Be highly selective

• Do not misquote

Abstract• The quality of an abstract will strongly influence the editor’s decision

• Use the abstract to “sell” your article•The major goal in reading the abstract is to understand the research question, how is done, what did the research find, and what do the findings mean.

• A good abstract: State main objective How the study was done Summarize most important results State major conclusions and significance Can stand alone Is brief and specific (Follow word limitations (50‐300 words))

Tips and Tricks

• Write your abstract last: it is a summary• Take phrases from each section and put them in a sequence which summarizes the paper• Then revise to make it cohesive and clear• Include key words• Conclusion: restate message• No new information

Figures : A Few Suggestions

• Intelligible without reference to the text• Avoid including too much information in one figure• Make sure any lettering will be large enough once published• Follow the journal’s instructions

Assemble draft figures

Decide what are the key points that you need to make, and write them out (how and what). Focus on hypotheses that you tested.

Tables: A Few Suggestions

• Design tables to be understandable without the text• If a paper includes a series of tables, use the same

format for each• If your table includes the results of a statistical

analysis, be sure to provide the information necessary for the reader to properly evaluate the analysis

• Be sure to follow the instructions to authors

Acknowledgments

• A place to thank people who helped with the work but did not make contributions deserving authorship

• Anyone who provided technical help

• Anyone who supplied data or computational resources

• State why people have been acknowledged• Sometimes the place where sources of financial

support are stated

Criteria for evaluation

• Relevance• Content & Significance

Results adequately discussed?Reasonable conclusion drawn from data?Clear statement of implications of research?

• Content• Writing

Recommendation: Accept as is /Accept with minor revisions /Accept with major revisions /Reject but encourage re-submission after the work is more developed /Reject

Reviewer Blind Comments to Author:Reviewer Confidential Comments to Editor:COMMENTS TO THE EDITOR:Please rate the manuscript with respect to the following items:(Place an X on the line in front of your rating.)1. TECHNICAL CORRECTNESS__ Excellent __ Good __ Acceptable __ Fair __ Very Poor 2. NOVELTY/ORIGINALITY__ Excellent __ Good __ Acceptable __ Fair __ Very Poor3. REFERENCE TO PRIOR WORKx__ Excellent __ Good __ Acceptable __ Fair __ Very Poor4. QUALITY OF ART__ Excellent __ Good __ Acceptable __ Fair __ Very Poor5. QUALITY OF EXPERIMENTAL RESULTS__ Excellent __ Good __ Acceptable __ Fair __ Very Poor6. APPROPRIATENESS TO JOURNAL__ Excellent __ Good __ Acceptable __ Fair __ Very Poor7. IMPORTANCE TO THE FIELD__ Excellent __ Good __ Acceptable __ Fair __ Very Poor8. ORGANIZATION AND CLARITY__ Excellent __ Good __ Acceptable __ Fair __ Very PoorReviewer Recommendation and Comments for Manuscript

Journal Review Form

• Not novel

• Serious flaws of design, methodology, analysis, or interpretation inadequate review of the literature insufficient methodologyunclear statistical analysis Inappropriate statistical techniquesDiscussion that goes beyond the dataHypothesis not adequately tested

• Inappropriate for journal

• Poorly written

Major reasons for rejection

Summary: Steps in preparing research manuscripts

• Read the Instructions to Authors of the journal chosen• Decide who the authors will be• Draft a working title and abstract• Decide what are the key points that you need to make, and

write them out (Focus on your hypotheses).• Make sure references are comprehensive and accurate• Check the illustrations and tables and make the final versions• Find someone to review your manuscript• Put the manuscript away for a few days • Write a cover letter to the editor• Create the list of poteinial reviewers

Sources of Further Guidance

• How to Write and Publish a Scientific Paper, 6th edition, by Robert A. Day and Barbara Gastel (Greenwood Press, 2006)

• Fundamentals of Writing Biomedical Research Papers, 2nd edition, by Mimi Zeiger (McGraw-Hill, 2000)

• Preparing Scientific Illustrations: A Guide to Better Posters, Presentations, and Publications, 2nd edition, by Mary Helen Briscoe (Springer, 1996)

• Huth EJ. How to Write and Publish Papers in the Medical Sciences, 2nd Edition. Baltimore: Williams & Wilkins, 1990.