2.5.1. Writing manuscripts

Journal articles, or manuscripts, are the primary means by which scientific results are disseminated. As a result, your publication record will be one of the major components of your applications for new jobs and promotions. Consequently, it is important to publish your work in popular, well-read journals, and it is important to communicate your ideas clearly to gain acceptance to these journals. Below is an overview of the publication process and how to write, submit, and resubmit manuscripts for publication.

2.5.1.1. The publication process

Below are the typical steps in the publication process.

  1. Complete a scientific project

  2. Select a journal to submit a manuscript about the project to

  3. Optionally, discuss the suitability of the proposed manuscript for publication in the selected journal

  4. Write the manuscript, figures, tables, and supplementary materials, following the journals submission guidelines

  5. Submit the manuscript to the journal via the journal’s online submission system

    • Submit a cover letter to the journal’s editors which introduces the manuscript
    • Submit a list of recommended reviewers
    • Submit the manuscript
  6. The editor will then evaluate the suitability of the manuscript for the journal and either assign the manuscript to ~3 peer reviewers (other scientists in the field) or reject the manuscript

  7. If the manuscript is assigned to reviewers, the reviewers will then review the manuscript and submit their recommendations and concerns to the editor

  8. The editor will then collate the reviewers’ concerns and decide whether to accept, potentially accept, or reject your manuscript

  9. Manuscripts which are potentially accepted must be resubmitted along with responses to the reviewers’ concerns (see below), which leads to another round of reviews by the reviewers and another decision by the editor.

  10. Once a manuscript is accepted, the journal’s production staff will provide you instructions on how to submit production quality files which they will use to format your manuscript for publication.

2.5.1.2. How to write a manuscript

The keys to writing good manuscripts are to describe why your work is significant (i.e. how it solves and important problems), to describe how your work is novel (i.e. how it is different from previous work), and to clearly present your ideas so they can easily be understood with minimal effort.

Often these goals are best accomplished by organizing the body of your manuscript into the following sections

  • Introduction: describe the problem that you’ve tried to solve, why it is important, the prior work that has been done on the problem, how you’ve approached the problem in a novel way, and provide a brief overview of the methods and results of the project
  • Methods: describe how you’ve solved the problem
  • Results: describe the results of your work
  • Discussion: describe the implications of the results of your work
  • Conclusion: re-summarize the manuscript
  • Supplementary materials: Supplementary materials should communicate all of the additional information needed to understand your project that cannot fit in page limit for your manuscript. This should include all of the data, code, and intermediate results needed to understand and reproduce the work described in the manuscript. Supplementary materials can either submitted directly to the journal or they can be submitted to public repositories and linked to the manuscript.

2.5.1.3. How to write an abstract

Abstracts should follow this hour-glass structure

  1. Introduce the broader problem which you have tried to solve and why is significant
  2. Describe what specific problem you have tried to solve
  3. Describe why the problem had not yet been solved
  4. Describe how you innovatively solved the problem
  5. Describe the results of your work
  6. Describe the broader significance of your results

Abstracts are generally limited to 200-250 words.

See Nature’s annotated abstract for more information about how to write an abstract for a manuscript.

2.5.1.4. How to to format a manuscript for submission

Below are general guidelines for formatting manuscripts for submission to journals. Before submitting to a journal, also reviewing the journal’s submission guidelines.

  • Layout

    • Title, authors, and affiliations
    • Abstract
    • Body of the manuscript
    • Acknowledgements
    • References
    • Figure and table captions
    • Figures, 1 per page
    • Tables
    • Supplementary content
  • Citation format: consult the journal’s guidelines

  • Paper size: 8.5 x 11 in

  • Margins: 1 in

  • Font

    • 12pt
    • Serif, Times New Roman (Word) or Computer Modern (LaTeX)
  • Line spacing: doubling

  • Line numbers: display in left margin

  • For resubmissions, use yellow highlighting to mark all major changes

  • Filetype: .docx, .tex, or .pdf

  • Figures:

    • Size: Below are the sizes for Cell. Consult your journal’s guidelines.

      • Full width: 174 mm
      • 1.5 width: 114 mm
      • Half width: 85 mm
    • Font:

      • Subfigure labels: 8pt, bold
      • Other text: 5-7pt
      • Sans-serif, Arial
    • Color: RGB

    • Filetype: .eps, .pdf, or .ai

2.5.1.5. How to write a response to reviewer critiques

  • As much as possible, try to address the manuscript to address the reviewers’ concerns. Clearly explain which concerns you do not agree with and why.

  • Begin the response with a summary of the major changes you have made in response to the reviewers concerns.

    • Thank the reviewers for their suggestions.
    • Discuss how you’ve improved the manuscript based on their suggestions or why you believe their suggestions should not be incorporated into the manuscript.
  • Then provide point-by-point responses to each concern raised by the reviewers

    • Intersperse your responses with the reviewers’ concerns.
    • Thank the reviewers for their suggestions.
    • Discuss how you’ve improved the manuscript based on their suggestions or why you believe their suggestions should not be incorporated into the manuscript.
  • Format

    • Paper size: 8.5 x 11 in
    • Margin: 1 in
    • Font: 12pt, Serif
    • Color the reviewers’ concerns blue so they can easily be differentiated from your responses.
    • Filetype: .docx or .pdf

Below are several examples of responses to reviewer critiques.