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.

• 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

• 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

• 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

• 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

structures

sequences

functional

genomics

proteomics

genotype

phenotype

Deposit your data

metabolomics

models JWSBioModels

Reproducibility: figures as packages

descriptive

metadata

RDF

experimental

data

CSV

figure

JPEG

manifest

XML

caption

HTML

code

PY

Reproducibility: figures as packages

• 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

• 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.

Clarity: use visual

explanations

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

Title and abstract are important as most people will come across your

work from Pubmed - Make it Count!

Title:

• should grab the reader’s attention

• 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

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

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

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

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

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

"The manuscript has been rejected already by Natureand 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...