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

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

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

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?

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

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

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

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

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

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

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?

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

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

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

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

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?

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

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!

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

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

STAR Methods: Key Resources Table The Lamprey Pallium Provides a Blueprint of the Mammalian Layered Cortex Suryanarayana et al. Current Biology 27:3264-77, 6 Nov. 2017

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