How to Write a Biophysics Article Worthy of Publication: Part 3- From Submission to Acceptance

William O. Hancock
Pennsylvania State University
Member, Biophysical Society Publications Committee

The first part of this series covered writing a first draft of a manuscript, and the second part covered the honing and polishing needed to bring the manuscript to the point where it is ready to submit to a journal.  The topic of this final article is navigating the process of submitting, revising, and getting your manuscript accepted for publication.

Choosing a journal

Because this piece is written with the Biophysical Journal in mind, your manuscript has hopefully developed into an appropriate submission to that journal.  From the journal website:

The mission of Biophysical Journal (BJ) is to publish the highest quality work that elucidates important biological, chemical, or physical mechanisms and provides quantitative insight into fundamental problems at the molecular, cellular, and systems, and whole-organism levels. Articles published in the Journal should be of general interest to quantitative biologists, regardless of their research specialty.

If your manuscript has evolved away from this definition, then you may want to choose another journal.  A good guide is to consider what journals are commonly read by colleagues in your field and fields relevant to your work.  Don’t be overly swayed by impact factors, and avoid predatory journals.  Consider the makeup of the Editorial Board who will be deciding on whether your manuscript is sent to review, and consider the business model of the journal.  Society-based journals (such as Biophysical Journal) carry the weight of the Society, usually have a history, and are generally run by scientists for scientists.

Before submitting your manuscript (and during the process of writing drafts and polishing your figures), consult the Guide for Authors and follow formatting, word count, and figure guidelines.  This will speed the submission and review of your manuscript, it increases the chance of acceptance, and it will save you time during later revision steps.

Most journals accept pre-submission inquiries to assess the suitability of the manuscript for the journal (and some journals require them).  This process involves sending your title and abstract together with a short letter to the editor, and it saves time for everyone involved.

Navigating the review process
picture-3The process of submitting a manuscript involves a number of decision points that are shown in the figure at right.  Upon initial submission, an editor will decide if the manuscript should be reviewed or be rejected (triaged) at this initial submission stage.  Considerations include suitability of the topic for the journal, novelty of the work, completeness of the work, and perceived impact.  Although it can be discouraging, this initial triage is another important time saver for everyone involved.  Avoiding rejection at this juncture can be helped by a pre-submission inquiry to determine suitability, and by a convincing cover letter.

Cover letter

One element that is sometimes underappreciated by authors is the cover letter, which provides the author a platform to persuade the editor of the importance of the work and its suitability for the journal.  The editor will generally be asking two questions:  (1) Is this work significant?  (2) Do the results justify the conclusions?  In the letter, it is important to distill the key findings into a few sentences.  However, more importantly, you want to place the work in the larger context of your field, and of the larger field of biophysics, cell biology, structural biology, or whatever your specialty may be.  This larger perspective is what the editor is thinking about — what is the impact of this manuscript, and will publishing it advance the mission of the journal?  Therefore, it can help to point out important recently published work by yourself and others that relates to the manuscript.  It is also good to remind the editor of the larger impact of the work on medicine, basic science, or technology.  Some of this persuasion means plucking text from the Introduction or Discussion of the manuscript, but it also requires stepping out to more of a 30,000 foot perspective and persuading the editor in a way not unlike a grant application.  Be specific and persuasive without being grandiose.

What makes an effective review?

Now that your manuscript has made it to peer review, it will be read by two or more reviewers who are considered experts in the subject of your manuscript.  The primary goal of the reviewers is to ask:  Do the results justify the conclusions?  A good review should provide substantive feedback that enables the editor to make an informed decision on the manuscript and the authors to revise and improve the manuscript.  Reviews generally begin with a brief summary of the findings and their relevance to the field, and may include the following:

  • A critical evaluation of the experiments, highlighting any flaws in experimental design, questionable interpretation of data, and any internal consistencies.
  • Highlighting previously published work (with references) that either contradict the work or may make the current experiments redundant.
  • Reasonable requests for further experiments, particularly control experiments but also obvious (important) experiments that the authors may have neglected.
  • Request for further analysis, reanalysis, or alternative presentation of experimental data, including adding or clarifying statistics.
  • A critique of the text and figures highlighting areas of confusion, excessive verbosity, or flawed logic.

A good review will be civil, will avoid vague complaints, and will not harp unnecessarily on small details that may not be related to the principal point of the manuscript.  The authors and editor are helped most by specificity and forthrightness in the evaluation of the manuscript.

Revising and responding to reviews

When the editor receives the reviews back, they then make a decision either to accept the manuscript as is (which is rare), reject the manuscript, or ask for major or minor revisions.  At this point, the author has to make a decision. Rejections can be appealed in select cases, but this avenue should be used sparingly and should have strong justification.  If the appeal is denied, then the authors should incorporate suggestions from reviewers before resubmitting to another journal, because it is likely that other reviewers will have the same complaints.

If minor revisions are requested, the authors can generally address the comments by editing the text, improving the figures, or making other modifications that don’t take much time.  In this case, the authors should attend to these tasks immediately and resubmit the revision.  In the case of major revisions, the authors have other decisions to make.  In some cases, the revisions and additional experiments requested are so extensive that it essentially requires rewriting the manuscript.  Depending on constraints, the best avenue may be to make minor modifications and submit it to a more specialized or lower profile journal.  If the decision is to revise and resubmit, then the authors must make a battle plan that involves some combination of further experiments, reanalysis of data, and revising the text and figures.  Often a limit of 90 or 120 days for resubmission is given (though deadlines can usually be extended by a reasonable request); this timeline provides a scale of the amount of new work that is expected.

When resubmitting a manuscript, the authors should also submit both a marked copy that highlights changes, and a point-by-point response to the reviewer comments.  It is expected that authors make a good faith effort to make edits and carry out further analysis and experiments.  A letter that tries to simply rebut every suggested experiment will not generate good will with the editor or reviewers.  That being said, it is reasonable to carry out some of the experiments suggested by reviewers and rebut suggested experiments that are onerous or extraneous.  Editors and reviewers will be more inclined to accept an explanation for not doing an experiment if you have followed their directive on other suggested work.  In some cases, data addressing a reviewer concern can be presented in the response to reviewers letter and not included in the text of the revised manuscript.

Upon resubmission, the editor may decide to accept the manuscript, or they may send it back out for review. At this point, the manuscript will be re-evaluated by one or more of the original reviewers.  In some cases, a new reviewer may be added to address a particular aspect of the manuscript.  If a major revision is requested and the authors have not carried out the requested experiments or sufficiently revised the work, the manuscript may be rejected at this point.  If the revisions were extensive and the reviewers still have complaints, then the manuscript may be sent back to the author for another round of revisions.  While this action is necessary in some cases, the extra work and time can be avoided by authors responding fully to critiques on their first revision and by reviewers detailing all of their concerns on their initial review and abstaining from making new critiques of aspects of the manuscript that were not commented on during the first round.

Publishing your paper

Hopefully this process will culminate with your manuscript being accepted for publication.  Congratulations!  But before you can move on to your next paper, there are a number of details to take care of.  First, it is imperative that the final revision that was submitted is error free.  It is worth taking the time now to be sure that the version that the journal has in hand has all figure numbers correct, all references in order, and other small details in place.  This is also the last time you will be able to edit the Supplemental Information, so be sure that document is properly formatted and is complete.  You will be sent page proofs for final checking, but it is best to have everything ironed out before the manuscript goes to proof stage, so that the final stage only involves checking for typesetting errors, figure placement, and related small details.

Over this three-part series, we have gone from data in a lab notebook to a published paper.  This process takes a lot of work, and although it gets easier the more you do it, publishing a paper is always a considerable effort.  However, peer-reviewed publications are the currency of science, and so the effort is necessary and worth it, and reaching this milestone is cause for celebration.  And, after the celebration dies down, then get back to the lab and do it again…


The author thanks Beth Staehle for assistance and advice, Olaf Anderson for many of the ideas that went into this work, and members of the Biophysical Society Publications Committee for many helpful suggestions.  He also thanks his mentors Joe Howard and Al Gordon, as well as his 8th grade grammar teacher, Jim Ernst, for teaching him how to write.  W.O.H. is supported by the NIGMS.

Helpful online resources

In addition to the references presented in Part 2 of this series, there are a number of more general resources online to help improve your scientific communication.

  • An excellent online writing resource with tutorials that focus on science writing fundamentals

  • Helpful eBook on writing scientific papers from Nature Education

  • A useful style guide, particularly for questions on grammar

  1. Gopen and J. Swan. The Science of Scientific Writing. American Scientist, November-December 1990.
  • An in-depth article that focuses on the readers’ perspective and breaks down sentence and paragraph structure for maximum communication


Michael Alley, The Craft of Scientific Writing, 3rd Edition, Springer, 1995.

Michael Jay Katz, From Research to Manuscript:  A Guide to Scientific Writing.  Springer Netherlands, 2009.

Interested in learning more about writing a good biophysics article?  Want a chance to ask questions?  Dr. Hancock will present a webinar on this subject today, March 10, at 1:00 PM ET.  Register at





Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s