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Writing and submitting a thesis

Use this guide to find resources to help in the writing process. This guide also includes guidelines for the submission of your thesis.

Reproducing your own published articles in your thesis

Versions of work

If the copyright of a publication in which you are an author has been or will be, assigned to a publisher through a Copyright Transfer Agreement (see a sample here), the Agreement may contain a clause granting you, as the primary author, the right to reproduce the Accepted version in your thesis. Without this clause you will need to gain a licence via the RightsLink service as described on the Managing Copyright page of this guide.

Publishers have different policies on the versions of papers they will allow you to self-archive and make openly accessible. If the work is about to be or has been, published by a traditional publisher you may have transferred your copyright as part of the publication agreement.

It is important to understand these terms as they often define the rights/permissions you have as an author.

  • The Submitted version is the Preprint of the manuscript before peer review. This is the author/s' original version of the article that was sent to a journal for consideration. The author/s hold the copyright of this version.
  • The Accepted version is the Postprint of the manuscript after peer-review. This is the version of an article that has been amended in order to reflect any peer review revisions in the publication process. The publisher holds copyright over this version.
  • The Published version is the final version as it appears in the publication. The publisher holds copyright over this version of the work.

The Submitted Version of an article is permitted to be open and uploaded into an institutional repository. 

The Accepted Version of a publication is also permitted to be open and uploaded into an institutional repository under a publisher licence, but often under restrictive embargo periods, ranging from 12 to 24 months.

The Published version can be included if it is an Open Access article and carries a Creative Commons licence.

Publishing in an Open Access journal

If you are intending to publish in an Open Access journal you will be paying an Article Processing Charge (APC) and generally be making your article available under a Creative Commons (CC) licence which makes the work free for the reader to download and use according to the terms of the licence.

As most publishers provide a limited choice of CC licences it is best to become familiar with the six available licences so you are aware of the benefits and limitations of each licence.  See the Creative Commons Licences page in this guide.


HDR students can apply for Article Processing Charge (APC) assessment and approval for publication of a research article in a peer reviewed Gold Open Access (OA) Journal to be paid from their Project Budget funds.

See the APC Support page for HDR students.

Citing your published work

Accepted version permission citation:

If the Accepted version of an article is to be included in a thesis the publisher's permission statement, as provided in the licence, should appear before the article. 

Citation example: 

Author, Title, Journal Title, Volume/Issue, DOI, Copyright ©, [year], Link to the published article on the publisher's website.
Reproduced with permission from [Publisher].

Copyright permission licences received from publishers should not be reproduced in the thesis itself.  Compile all permissions into one Copyright pdf file to accompany your thesis submission in WorkFlowGen.


Open Access article with a Creative Commons (CC) Licence:

If you have published an article with a CC licence you may reproduce it in full in your thesis in the format in which it was published, or you may change the format to match your thesis.  The full citation of the published article should appear in the chapter where it is reproduced and the CC licence should be stated with a hyperlink to the licence at the end of the citation.

Citation example:

Pickard A, Calverley BC, Chang J, Garva R, Gago S, Lu Y, et al. (2021) Discovery of re-purposed drugs that slow SARS-CoV-2 replication in human cells. PLoS Pathog 17(9): e1009840. Made available under a Creative Commons Attribution Licence (CC BY 4.0).


Pickard A, Calverley BC, Chang J, Garva R, Gago S, Lu Y, et al. (2021) Discovery of re-purposed drugs that slow SARS-CoV-2 replication in human cells. PLoS Pathog 17(9): e1009840. Made available under a CC BY 4.0 licence.


Refer to the HDR Handbook for further information on the treatment of published works in a thesis. 

Examples of Bond Doctoral theses with publications