1. Manuscripts and publishing
Scientific Writing Retreat 2018
Stephen Matheson, PhD
Editor, Cell Reports
Laureen Connell, PhD
Senior editor, Genes & Development and Molecular Case Studies

2. Overview of presentation
Writing and submitting a paper – some hints
What happens to a paper after submission
Reviews and decision letters
Miscellaneous!

3. Writing and submitting a paper
Choosing a journal to submit to
Preparing the manuscript
The cover letter

4. Choosing a journal to submit to
Does the paper fit within the journal’s scope? – see the ‘aims and scope’
Does the journal publish broadly similar papers?
Is it widely read by the people you want to see the paper? Do you read it?
If you are unsure, consider sending a pre-submission inquiry
How much do you care about Impact Factor?
Do you want, or need, Open Access?

5. What does open access mean (at Cell Reports)?
Readers have immediate and unrestricted access to your paper
Authors retain full copyright
Authors choose one of two Creative Commons licenses
Authors pay APC (publication fee)
Discuss: Gold OA vs. Green OA

6. Preparing the manuscript
Pay careful attention to the author guidelines for the journal (but please stand by for more)
Present the paper as a logical story, not just chronologically
Include a well-referenced introduction and an insightful discussion
Ask colleagues outside the field to read it
Seek language assistance if necessary

7. Preparing the manuscript
Many requirements might be optional at initial submission
Extras like graphical abstract and highlights not needed
Formatting might not be important
Look for single-file upload option

8. The cover letter
An opportunity to put the paper’s contribution in context and discuss potential implications
Reviewer exclusions are allowed; for Cell Press it should be no more than 3 people
Reviewer suggestions are allowed, but not required, and editors may not use them
Include copies of related work submitted or in press elsewhere

9. What happens to a paper after submission
The initial assessment process
What editors look at

10. Initial assessment Each paper is read carefully by a scientific editor
Editors often discuss papers with each other, and may seek external advice
The editor decides whether to send the paper for in-depth review
If it is sent out, the editor selects expert reviewers, typically 3 people
If it is not sent out, the editor writes to the authors explaining why

11. What editors look at Does the paper fall within the journal’s scope?
Does it address an interesting and important question?
How much do the findings advance the field above the current literature?
Will the findings be of interest to scientists outside the immediate field?
Are the experiments presented appropriate for the conclusions drawn?

12. Reviews and decisions When the reviews come in Decision letters
Revisions and appeals

13. When the reviews come in
The editor reads the reviews carefully
Reviewers often have varied opinions
Editorial decisions are based on the points made overall, not a simple ‘vote’
The editor may discuss the paper again with colleagues and/or the reviewers
The editor sends the authors a letter outlining the overall decision

14. When you receive the decision
Read the decision letter and reviews carefully and digest the points that the reviewers and editor have made
Did the editor invite, or mention, resubmission?
For a revision, address the criticisms raised as well as you can, prepare a point-by-point response letter, and resubmit

15. Appeals
If the editor did not invite or mention resubmission, the paper has been declined
If the reviewers raise substantial valid criticisms, it is often best to submit the paper elsewhere
New data are more effective than arguments alone
Be realistic – only appeal if you really think you have a valid case

16. Accepted! Enjoy the party. The editors are pretty happy too.
Now you have a bunch more work to do: extras, proofs, legal docs, press release, call parents
Image forensics… what?

17. Image forensics Done by production staff
Images are over-enhanced and scanned for:
Splicing (common)
No background (usually too much contrast)
Low quality/resolution
Image modification (erasure, pasting)
NOT scanned for:
Duplication
Fraud

18. Final tips
Editors are there to help, but they are busy, and handle a lot of papers
Be concise in your communications
Focus on scientific points at all times
Wait at least 24 hours before sending any response!

19. STAR Methods Structured,Transparent, Accessible Reporting
Six headings plus a Key Resources Table
No length limit

20. STAR Methods: Headings
Contact for Reagent and Resource Sharing
Experimental Model and Subject Details
Method Details
Quantification and Statistical Analysis
Data and Software Availability
Additional Resources

21. STAR Methods: Key Resources Table
The Lamprey Pallium Provides a Blueprint of the Mammalian Layered Cortex Suryanarayana et al. Current Biology 27: , 6 Nov. 2017

22. bioRxiv and Cell Press Cell Press is so cool with bioRxiv
Direct submission (B2J) to Cell Reports and Structure
Potential pitfalls with media coverage