How to Write A Paper
Iris Lindberg 3/05
What Is a Paper?
• Communicates a linked series of
observations in a logical fashion
• Interprets data neither too much nor
too little
• Provides historical and biological
context
• Tells a story
• Moves the field forward
Assemble Your Data
• Most often present in the order it
was obtained
• Re-order if this makes a more logical
presentation
• First step: get a list of figures ready
with the conclusions from each figure
– Figure 1. Compound X lowers the amount
of compound Y in HEK cells.
When to Write Up?
• After you think you have a good story
• All critical experiments are finished
• Before you finish tying up all of the
loose ends
– Writing up will show you clearly what
controls/additional experiments still
need to be performed
Choose a Journal
• Select before you start so format is
appropriate
• Focus of journal should be appropriate
• Best journal that the work is appropriate
for
– Availability and readership
– Ranking (“impact factor”)
– Time to publication
In What Order Should Paper
Be Written?
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•
•
•
•
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•
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Figures and Legends
Results
Methods (easy part!)
Introduction
Discussion
Abstract
Referencing
Letter to the Editor
Figures
• Easy to read and logically presented,
• Can be reduced severely without loss
of legibility (use the reducing Xerox
machine) with little white space
• Try different types of format: bar
graphs vs. figures- which is easiest to
interpret?
• Figures should not need legends to be
comprehensible if at all possible
Results
• Succinctly describes each major
finding, grouping appropriately in
figures/panels.
• Every statement made in the results
should be supported incontrovertibly
by the data in the paper.
• Make sure results are internally
consistent!
• There is no substitute for beautiful
data (to convince the reader)
Methods
•
•
•
•
•
Easiest part to write if you have kept a
good notebook
Enables the reader to actually repeat the
experiments
Skip methods that can be found in
Current Protocols- just cite
Cite the source of all reagents used and
where QC information is to be found
Cite previous your papers whenever you
can
Introduction
• Orients the reader as to why the
work is important
• Should provide fair and
comprehensive referencing of the
field
• Should cover all required subjects in
a logical order
• Concludes with a brief summary of
what was done (BRIEF!)
Discussion
• Does not repeat the Results but
rather takes each major finding
presented in the results and
discusses it in the context of how it
relates to previous and future work,
with comprehensive and appropriate
literature citation.
• Ends with a brief speculative
statement or idea for future work
Abstract- write last!
• Summarizes the major findings in
the broad context of the work.
• Consists of two or three sentences of
topic introduction
• Selected results (not all but the most
important)
• Concludes with implications of work
Tips
•
•
•
Save the journal space by writing
concisely and by eliminating
unnecessary or negative figures and
tables
Proof all text carefully for errors-
–
typos, omissions, inconsistencies in the
data, redundancies, or errors in
referencing.
Expect to revise again and again- 10
times ? Until language is perfect
Writing Good Sentences
• Omit all unnecessary words- the
shortest phrasing is usually the best
• Use active voice when possible
• Use the correct tense- present
means it is true while past means it is
true under a specific set of
circumstances
• Do not switch tenses frequently
Common Mistakes
• Data= plural; datum= singular. DATA ARE!!
• Effect vs Affect (both are nouns and
verbs. But you will seldom use “affect” as a
noun unless you are a psychologist)
– We studied the effect of different
concentrations of X on Y
– Compound Z effected a large change in Y
– The inclusion of compound Z affected the pH
of Y.
Common Mistakes
• Dependent, not dependant; ensure, not
insure, principle vs principal
– The principal of the school had 3 principle
reasons for not allowing gum in class
• Dangling participle:
– Running for the bus, a package fell out of my
arms
• Use of commas instead of semi-colons:
– “however” is almost always preceded by a semicolon
Common Mistakes
• Inconsistent use of abbreviations
• Colloquial language: contractions, “some”;
“done” vs “performed”; “spun” vs
“centrifuged”
• Redundant language (e.g. use of “excellent”
twice in two neighboring sentences)
Rebuttal Letter
• Thank the reviewers for their time. They
did not have to spend it on your work!
• Address each criticism in numbered order
• Repeat or include the criticism in your
answer
• You are allowed to argue one or two items
but most items should be addressed
precisely the way the referee indicates
• Conclude by saying that you feel the paper
is improved and you hope it is now
acceptable for publication
Reviewing the Work of
Others
• You cannot review a paper if you are
simultaneously engaged in identical work
• You cannot review a paper if you have
strong feelings (hate or love) for the
authors; or have recently
collaborated/mentored/been mentored
• Golden Rule applies- apply the standard you
would apply to your own work (neither be
too critical nor too soft)
• Be helpful rather than pejorative; soften
criticisms with an initial positive statement
Reviewing- General
• Read the manuscript with a pencil in
hand, making notes on the margins
• Is the English used up to par?
(suggest editorial revision by a native
speaker; do not edit for them)
• Is it sloppily done? (referencing
wrong, many typos etc)
• Is the content appropriate for the
particular journal audience?
Reviewing, continued
• Set down your thoughts in a
numbered order – cite figure and/or
page for each
• Introduction
– Is it sufficiently comprehensive and
fair?
– Does it provide a good rationale for the
work?
– Are all abbreviations clear or is there
jargon?
Reviewing Methods
• Are the methods neither too detailed
(common methods not described) nor
insufficiently described? (primers)
• Could the work be repeated by an
outside group? (amounts of starting
material given etc)
• Are the methods clearly written?
Reviewing Results
• Are the figures cited in order?
• Is the rationale for each experiment
given?
• Do the text conclusions agree with
the result you see in each figure?
– Watch for over interpretation
• Are all of the figures really
necessary?
Reviewing Figures
• Accuracy
– are stated results really present and
really significant?
– Does the figure number correspond to
the correct figure?
• Presentation
– is there a minimum of white space?
– are figures sharp and clear? Are legends
readable?
• Is the legend neither too long nor too
short?
Reviewing Discussions
• Does it simply repeat the introduction?
• Does it provide alternative explanations
for the data/ introduce necessary
complexities?
• Is it about the same length as the results?
• Does it put the work in context and
suggest further lines of experimentation?
• Most importantly: does it go too far?
Review Format
• State ms. number, title, authors
• Review the major findings of the
authors
• Give major problems in numbered
order
• Give minor problems in numbered
order
• Do not state whether paper is
acceptable- this is not your decision