I would not recommend including details about prior rejections from other journals in your cover letter. The editors will not have access to those previous reviews, so it does not provide useful context. Focus instead on clearly explaining the significance and novelty of your findings for the specific readership of the journal you are submitting to.

1. Before writing
Select/develop a project that excites you!
Always keep publication in mind!
• Define the question your research is addressing: try to think of the
“story”
• Think about the figures when doing the experiments!!!
• Gels: arrange marker, control and experimental samples in the
right order.
• Image data: think about magnification, orientation, background etc
• Archive your data in an organized way
• Statistical analysis: do enough repeats and choose an
experimental design that will allow you to derive conclusions.

2. • Organize your data in a compelling way: try to think of the “story”
• What key experiments are needed to justify your conclusions?
• What makes your study unique?
• The paper doesn’t have to be written in the same order as you did the
experiments!
• Give a practice talk to colleagues before starting to write the paper. You
will see if the outline of experiments and flow of manuscript works.
Preparing a manuscript

3. • Start out by assembling and laying out the Figures and writing their
legend (very boring but the whole story is in there!).
• The Result section can be the next step.
• Finish each sub-section with a concluding sentence.
• Keep in mind the flow of the paper: cite the figures in the right order and
present the results as successive steps of a logical demonstration.
How to begin

4. • Submit minimally processed images.
• Retain unprocessed data and metadata files.
• Exercise prudence during data acquisition.
• List all image acquisition tools and image processing software
• Images gathered at different times or from different locations should not be
combined into a single image.
• If juxtaposing images is essential, the borders should be clearly demarcated
in the figure and described in the legend.
• The use of touch-up tools, such as cloning and healing tools is to be avoided.
• Changing brightness and contrast is appropriate only when it is applied
equally across the entire image.
• Contrast should not be adjusted so that data disappear.
Preparing figures

5. • Consult with statistician when appropriate.
• Figure legends should contain a description of the statistical tests applied and of
the error bars.
• Verify that the data conform to the assumptions of the statistical test (eg normal
distribution).
• Correct for multiple testing.
• The number of both technical and biological replicates should be clearly stated.
• Biological replicates: independent biological samples.
• Technical replicates: repeated measurements on the same sample.
• Error bars only for cases where more than two biological replicates analyzed.
• Error bars should not be shown for technical replicates.
• When n is small (n < 5) individual data from each experiment should be plotted
alongside an error bar.
Graphs & stats guidelines

6. structures
sequences
functional
genomics
proteomics
genotype
phenotype
Deposit your data
metabolomics
models JWSBioModels

7. • Background necessary to understand your study
• Should not be a comprehensive review but don’t hide critical citations
• Cite primary literature instead of reviews.
• What are the most recent related discoveries.
• Are there controversies?
• What are the open questions and which one do you address?
• Last paragraph of the introduction: outline of your study:
• What question do you address
• Outline of the experimental strategy
• Outline of the conclusions.
Writing the Introduction

8. • Keep the sentences short and simple
• Be clear, concise and specific
• Avoid jargon or big and complicated words
Clarity
DON’T: Our research, designed to test the fatal effects of X on parasites, was carried
out by intravenously introducing the drug. In the experiments, a relatively small
quantity was administrated in each animal. In each case, X proved fatal; all 10 parasites
expired before a lapse of 5 minutes after the injection.
DO: Intraveneous injection of X into animals killed parasites (n=10) within 5 minutes.
DON’T: It seems to us that it is not unconceivable to suggest that the result of this
study may indicate a possible role for X in killing the parasites.
DO: We suggest that X kills parasites.

9. Clarity: use visual
explanations

10. First paragraph should summarize the key findings of the paper in a clear
and concise way without rewriting the entire Results section.
Include a model figure if helpful.
Use the discussion to discuss what are the implications of your work.
What new have we learned?
Do your results explain previous poorly understood observations?
Does it fit with previous work? If not, discuss reasons for discrepancies.
Some speculation can be interesting, but make a clear distinction between
what is hypothetical and what has been demonstrated.
The last paragraph is used to set the stage for future experiments and
provide a forward look.
Writing the Discussion

11. Title and abstract are important as most people will come across your
work from Pubmed - Make it Count!
Title:
• readers may have a short attention span
• describe contents clearly and accurately
• avoid over generalization or overstatements
• should be short but understandable
• avoid abbreviations when possible
Abstract:
• be short but specific
• state main objectives
• specify key elements of the experimental strategy and of the
biological system investigated
• summarize most important results
• state major conclusions and significance
• make overall conceptual advance clear
Title & Abstract

12. Deleterious sustained inflammation mediated by activated microglia
is common to most of neurologic disorders. Here, we identified
sirtuin 2 (SIRT2), an abundant deacetylase in the brain, as a major
inhibitor of microglia-mediated inflammation and neurotoxicity.
SIRT2-deficient mice (SIRT2−/−) showed morphological changes in
microglia and an increase in pro-inflammatory cytokines upon
intracortical injection of lipopolysaccharide (LPS). This response
was consistent with increased NF-κB-dependent transcription of
inflammatory genes, NF-κB was found hyperacetylated in the
absence of SIRT2, and became hypoacetylated in the presence of
S331A mutant SIRT2. This finding indicates that SIRT2 functions as
a ‘gatekeeper’, preventing excessive microglial activation through
NF-κB deacetylation. Our data uncover a novel role for SIRT2
opening new perspectives for therapeutic intervention in
neuroinflammatory disorders.
Introduction
Results
Conclusions/
Implications
Abstract: example

13. Deleterious sustained inflammation mediated by activated microglia
is common to most of neurologic disorders. Here, we identified
sirtuin 2 (SIRT2), an abundant deacetylase in the brain, as a major
inhibitor of microglia-mediated inflammation and neurotoxicity.
SIRT2-deficient mice (SIRT2−/−) showed morphological changes in
microglia and an increase in pro-inflammatory cytokines upon
intracortical injection of lipopolysaccharide (LPS). This response
was consistent with increased NF-κB-dependent transcription of
inflammatory genes, NF-κB was found hyperacetylated in the
absence of SIRT2, and became hypoacetylated in the presence of
S331A mutant SIRT2. This finding indicates that SIRT2 functions as
a ‘gatekeeper’, preventing excessive microglial activation through
NF-κB deacetylation. Our data uncover a novel role for SIRT2
opening new perspectives for therapeutic intervention in
neuroinflammatory disorders.
Introduction
Results
Conclusions/
Implications
Abstract: example

14. Resolve authorship issues before submitting!!
What constitutes authorship?
• Authorship of a paper is justified when a researcher has contributed
to the work being published.
• If you are adding data to a paper during a revision – clarify with PI
authorship upfront.
• Authorship goes with responsibility: authors are responsible for the
content of a paper.
Authorship

15. Make sure to address the cover letter to the right journal!
Brief summary of your work
Do not repeat the abstract or your introduction
Put the findings into context!
Why this work will be of interest to the journal’s audience
Avoid gross overstatements to impress the editors!
Inform the editors about any important issues:
Conflicts of interest
Competing manuscript
Just have been scooped – mention what you paper adds
Related study (which should be enclosed)
Cover letter

16. Dear Editor
We would like to submit our manuscript “XXX” for publication in The EMBO
Journal.
In the manuscript, we report on the functional characterization of the X.
We show that protein X…
Recently, a manuscript by ZZ et al was published in Journal Y showing that
protein X is required for... Our results do not support these observations.
In contrast, we show that…Furthermore, we present evidence that the antibody
used by ZZ et al. recognizes proteins in addition to protein X.
We believe that the content of our manuscript is novel will be of great interest
for the readers of The EMBO Journal, and we are looking forward to hear your
comments.
Cover letter: example

17. "The manuscript has been rejected already by Nature
and Nature Immunology. So, I guess we may have
misunderstood the policy of Nature for publication.
You may be going to have difficulty to find any
interesting results in our manuscript to wide range of
researchers in cell biology. It is difficult. We would
like, however, to submit this to Nature Cell Biology in
case.”
Don’t...