23  Manuscript Preparation and Publication

Adapted by UCD-SeRG team from original by Jade Benjamin-Chung

23.1 Publication Process

The typical workflow for manuscript preparation and publication:

1. Planning: Discuss target journals, outline, and timeline with PIs
2. Drafting: Lead author prepares initial draft
3. Internal review: Co-authors review and provide feedback
4. Revision: Lead author incorporates feedback iteratively
5. PI approval: Obtain final approval from PIs before submission
6. Submission: Submit to journal
7. Revisions: Lead author coordinates response to peer reviewers
8. Publication: Celebrate and share!

23.2 Responding to Peer Review

When a journal asks for revisions, you will typically need to provide a point-by-point response to the reviewers’ comments. The key strategy is to use the “yes-and” approach from improvisational theater—building on what reviewers say rather than contradicting them. Try to avoid explicitly disagreeing with reviewers if at all possible.

Standard response format:

The typical response follows this pattern:

“Thank you for raising this important point. We agree, and now state (page ##):

[quote a section of the revised manuscript here]”

Balancing direct response and manuscript content:

There can be some overlap between the direct response to the reviewer (the sentences before “now state”) and what goes into the revised manuscript (the part after “(page ##)”). This is acceptable, but we usually try to put as much of the content into the revised manuscript as possible, and minimize the direct response section. The goal is to make the manuscript self-contained while showing the reviewer that you’ve addressed their concern.

When content already exists:

Sometimes, a reviewer asks for content that was already in the manuscript. In these cases, first see if there’s anything you can elaborate or clarify. Even if you don’t see room for improvement, you can usually respond with:

“We agree, and now state (page ##):

[quote the content that was already there before]”

The reviewer doesn’t need to know that they missed it the last time (see also: implicature.

Additional tips:

• Always thank reviewers for their time and feedback
• Quote page numbers from the revised manuscript
• Use direct quotes from your revised text when possible
• Maintain a respectful and collaborative tone throughout
• If you make changes beyond what the reviewer requested, mention them briefly

23.3 Preprints and Open Access

• We encourage posting preprints prior to or during peer review on platforms like medRxiv or bioRxiv
• Preprints allow rapid dissemination of findings and can be cited in grant applications
• We support publishing in open access journals when possible to maximize accessibility
• Many funders, including NIH, have public access policies that require making publications freely available

A preprint is a scientific manuscript that has not been peer reviewed. Preprint servers create digital object identifiers (DOIs) and can be cited in other articles and in grant applications. Because the peer review process can take many months, publishing preprints prior to or during peer review enables other scientists to immediately learn from and build on your work. Importantly, NIH allows applicants to include preprint citations in their biosketches. In most cases, we publish preprints on medRxiv.

23.4 Reporting Checklists

Using reporting checklists ensures that publications contain information needed for readers to assess validity and reproducibility. We use checklists appropriate to study design:

• CONSORT for randomized trials
• STROBE for observational studies
• PRISMA for systematic reviews
• Others as appropriate (see EQUATOR Network)

23.5 Manuscript Checklist

Before submitting a manuscript:

• Completed relevant reporting checklist
• Results are reproducible (rerunning code replicates tables/figures exactly)
• Target journal selected
• Title is declarative and states findings clearly
• Word count meets journal requirements
• Manuscript follows journal formatting guidelines
• Consistent voice throughout (typically active voice)
• All figures and tables referenced in main text
• Captions for all figures and tables
• Tables/figures numbered by order of appearance
• Abbreviations defined at first use and used sparingly
• Avoid subjective wording (e.g., “interesting”, “dramatic”)
• Avoid directionless statements (specify direction of associations)
• Causal language only when supported by study design
• Avoid “significant” (easily confused with statistical significance)
• Author contributions drafted using CRediT Taxonomy

23.6 Scientific Writing: Claims and Evidence

All factual claims in scientific writing should be supported by appropriate evidence.

Citation requirements:

• Cite primary sources for factual statements about established knowledge, methods, or findings
• Cite official documentation when describing how software, tools, or systems work
• Link to authoritative sources like peer-reviewed publications, official repositories, or technical specifications
• Avoid citing secondary sources when primary sources are available

When you can’t find a citation:

• Demonstrate directly: Show the behavior through experiments, data, or explicit examples
• Acknowledge uncertainty: Use appropriate hedging language (“may”, “appears to”, “in our experience”) when evidence is limited
• Remove the claim: If you cannot substantiate a claim with either citations or direct evidence, consider whether it needs to be included

Why this matters:

• Builds reader trust and credibility
• Enables readers to verify information independently
• Maintains scientific rigor in all communications
• Prevents propagation of misinformation

This principle applies to all lab writing, including: manuscripts, documentation, grant applications, and technical reports.

Using AI tools for writing:

When using AI tools to help develop manuscripts or other academic writing, follow the special guidance in Section 18.4 to ensure transparency, maintain intellectual ownership, and avoid plagiarism.