FAQs - Writing a Thesis With Publications

The following document is based on questions and concerns raised in a number of recent workshops on theses with publications (TWPs). There is no one right answer to any question. You can access examples of theses including publications online at:

The theses referenced in this document range across many disciplines, so are quite representative. Where possible, reference to a thesis which illustrates the answer to a question is given.

1. What are the advantages and disadvantages of TWPs


  • Publishing in peer-reviewed journals creates a de facto standard
  • It allows candidates to engage with broader scientific community
  • Being open to a process of continual review and criticism outside the domain of their direct supervisors instils a high level of discipline in a student’s research conduct
  • The process of serial publication allows the student to learn the importance of ‘self-permission to make mistakes’
  • Doctoral candidates learn how to take an authoritative stance in the field of expert others and to assert their contribution to that field before they feel authoritative.
  • The multiple project format allows for a closer relationship with practice than is often possible with the traditional monolithic thesis
  • It involves working within a team framework
  • It validates and confirms candidates’ work in process
  • It teaches ability to accept critical comment
  • It teaches ability to disseminate findings within constraints of science
  • Much tighter constraint leads to more conciseness
  • TWP contrasts favourably with the demonstrably low publication rates from traditional theses. The traditional thesis needs a significant rewrite, which is often never done


  • The thesis often includes co-authored articles and therefore is not entirely the student’s work as in a traditional thesis;
  • There may be difficulty in conveying coherence between what is in effect a series of independent published papers;
  • Avoiding repetition when giving context for all papers may be a challenge
  • The cumulative argument can be lost
  • There is a time delay while waiting for journal editors or co-writing supervisors
  • An article may be published before later significant research has appeared and, if the candidate must or wishes to bind the article in journal format, it will have to stand as it is
  • Candidates may rely on what calls ‘safe spaces’ for publication, and approach the same non-refereed journals again and again

2. What does a TWP look like?

There are 4 basic formats:

  • All chapters of the body are in journal format (JF). This means that all have been published. For an example of a thesis with all chapters of the body in JF, see Ashlie Hartigan.
  • The body is a combination of JF and manuscript form (MS), it means that some are still in press or submitted. For an example of this mixed type, see Robyn Keall’s thesis.
  • All chapters of the body are in MS and chapters in the body are identical to the articles published in journals. You can’t tell unless you look at the articles. In some cases, the article (s) is/are added in JF as an appendix. For an example of this type see Simon Firestone.
  • The entire thesis is in MS but published chapters in the body are changed somewhat from the published article. Sometimes the Literature Review (LR) is omitted in the non-JF article. For an example of this type, see Emily Don, p. 48ff, cf p. 225ff
    Ashlie Hartigan.
  • For an example of the mixed type, see Sarah McIntyre’s thesis.
  • All chapters are in MS but chapters in the body are identical to the articles published in journals. In some of these cases, the article (s) is/are added in JF as an appendix.
  • The entire thesis is in MS but published chapters in the body are changed somewhat from the published article. Sometimes the Literature Review (LR) is omitted in the thesis introduction.

3. Do all papers have to be published?

In most faculties, you can include papers regardless of the stage of publication; that is, they can be published, accepted (in press), or submitted (under review). The University Policy "Thesis and examination of higher degrees by research procedures 2015" states: 'Students must clearly indicate their role and the extent of their contribution to the paper either in the introduction to the thesis or the introduction to the chapter. Provided that this is done, where more than one of the authors of a work is a higher degree by research student, each student may include the work as part of their thesis.' p. 16

Therefore, a List of Publications is essential. This List is found either before or after the Table of Contents. In the List, some writers link the publications to the specific chapter in which they are found. For examples of this, see Simon Firestone, pp. x-xi, and Ashlie Hartigan, p. 9. Many theses record the bibliographical details of the article on the title page of each chapter, as well. See Simon Firestone, p. 107.

4. Where do you place the co-author contribution statements for each paper? Do you put them in the appendix?

Not every thesis has such a statement. When it is included, it usually is put with the List of Publications or before each chapter. See, for examples of each, Paul Stoodley, p. xvii, and Sarah McIntyre, p. 162ff and Shauna Downs p. 45 for a statement before each chapter.

5. Are there any copyright issues to consider?

If your thesis includes material that you have published elsewhere (e.g. journal articles) you will need to get written permission from your publisher to do so.

The University Library will only accept a digital copy as its definitive version.
See http://sydney.edu.au/graduate_studies_office/students/thesis.shtml

6. Do I have to be first author of all papers?

No, but most theses have at least one paper in which the doctoral candidate is first author.

7. How do you paginate the PDF pages of journal articles which have their own numbering system, so that the pages of the thesis are consecutive?

Both paginations are on each page, in most theses; sometimes these are superimposed on each other. If the journal page numbers are in bottom right hand corner, for example, perhaps you can put yours at the top, or vice versa. See Emily Don, p. 10. Other theses have a footer underneath the journal article. Yet other writers, Sarah McIntyre for example, omit thesis-wide pagination in the journal articles.

8. How many papers should a TWP include?

The total number of published papers examined for this document in any one thesis ranged from 12 to 1. The average number of publications was 3.5. Many theses also contain papers that are in press or under review. In some theses, related published journal articles and/or conference papers are added in an appendix.

9. Do the list of tables and list of figures for the thesis include those in the published articles, and how are tables and figures numbered?

Usually a thesis does not include published tables/figures in the List of Tables/Figures. Sarah McIntyre and Ashlie Hartigan, for example, do not do so. McIntyre includes additional tables after the published paper, but in MS. The tables are almost always numbered according to chapters: so 4.5 is the fifth table in ch 4.

10. How do I tie the thesis together?

Cohesion is the most important issue facing the writer of a TWP. It is possible to have a number of publications and still be unsuccessful. To quote the University of Sydney policy "Thesis and examination of higher degree by research 2015"

A collection of disparate publications, no matter what their quality, must not be approved for the award of a higher degree by research if they do not meet the criteria for the award.

The List of Publications can note which publication corresponds to which chapter. For an example, see Michael Bowen's thesis p. xiv at http://ses.library.usyd.edu.au/handle/2123/11943

The introductory chapter may have a final section entitled 'Summary/Synopsis/Structure' which does not merely catalogue what each chapter is about, but uses language to tie them together; e.g., 'Ch 3 continues this theme'; 'Ch 4 builds on the findings in ch 3'. For example, see Simon Firestone pp. 2-4 and Fereshteh Pourkazemi, pp. 34-35.

A concept map or a flowchart (perhaps in colour) showing the connections can be placed at the end of the introductory chapter. Even if you do not include it in the final version, it may be useful to draw it up just for your own benefit. For examples, see Natalie Allen, p. xix, Sarah McIntyre, p. 29, and Vanessa Allom pp. 4 and 179. Paul Stoodley (p. 4) has a diagram which distinguishes published from non-published work.

In the LR, you might refer to what chapter fills in what gap identified in the literature. For example, after the relevant section of the LR, the writer might explain: "To date no trials have been completely randomized. Chapter 2 presents the protocol of a randomized trial, and Chapter 3 describes the results of that trial."

You may include a page or half page introduction or 'bridging section' before each chapter of the body or at the end of each chapter; this tells the reader how what comes next connects with what has gone before. Here are some examples:

Sarah McIntyre (p. 108) has a 'Synopsis' at the end of each chapter signaling the connection with what is to come. Paul Stoodley (p. 67) has a bridging section entitled ‘Preamble’, at the beginning of the chapter, which signposts the connection between two chapters.

In the Discussion section, you will of course refer back to the various papers. Cohesion, however, is better obtained by looking at the thesis as a whole (see below Q 15 on broadening the discussion for more detail).

You might like to draw up your Table of Contents early and use numerical ordering to establish the hierarchy of major and minor sections.

Some theses have a flowchart which shows the cohesion between the findings of the studies.

For an excellent example, see Jennifer McArthur’s thesis, p. 188.

N.B. No one thesis has all these features, and some of them might not be feasible for you, but the more links you can establish between the various parts of your thesis, the more coherent it will be. In any case, it is a courtesy to your examiners to make your thesis story as clear as possible.

That is why the introduction and conclusion are especially important in tying the thesis together. But coherence can be made explicit throughout the thesis.

11. How long should a literature review be?

This depends on whether you include your literature review in your introductory chapter or have it as a separate (second) chapter. In the first option, the chapter tends to be longer because it needs to include more. If you have a separate literature review chapter, the Introduction can be much shorter.

12. How do I make my literature reviews different?

There are 4 strategies which writers use to deal with the need to give the context of their research each time they write a paper. Only the first two strategies use replication. The third alternative is becoming more common.

(1) Paraphrasing. See Simon Firestone (p. 1 compared with p. 67).

(2) Synthesising. Writers take the longer discussion in the introductory chapter and synthesise it in the article (where there is less space). Even if the article is written first, as normally would be the case, the literature review in the article will no doubt be cut down from an initial comprehensive literature review. For an example of synthesis, see Melissa Nott (pp. 28-29 compared with p. 121, first paragraph).

In any case, it is always useful to look at each of the literature reviews you write from the point of view of the different readership: a thesis needs to cover all bases whereas a journal article aims to cater for busy readers who probably need less background.

(3) Making the literature reviews quite different. For example, see Sarah McIntyre (p. 5 compared with p. 11).

(4) Removing the literature review (but only if the published chapter is presented in MS).

13. What happens if more relevant literature comes to light after publication?

Some writers just put the new literature into the introductory literature review, and let the original article stand, as in Melissa Nott above (note the reference to Lequerica et al on p. 29). Others add an addendum to the literature review chapter with an update on recent work on the topic. Emily Don adds an update to her published literature review p. 28. Paul Stoodley has two literature reviews, Part A and Part B, and he explains why in a 'Preamble' to Part B:

'As 3 years have elapsed since the publication of the original review, Part B provides greater detail and additional recent information that was unavailable when part A was published… While the arrangement of this section is purposely similar to part A, there is very little overlap of content in the two chapters; thus part B completes the literature review’ (p. 47).

14. How can I reference myself?

Here are some examples of how writers reference their own work:

In more recent work [2 refs], our group has described …. [Bowen, p. 66.]

In a recent comprehensive systematic review, we found that none of these factors has been investigated prospectively … (ref) [Pourkazemi p.105.]

Previously, we reported…(ref); our aim in this study was to investigate [Stoodley, p. 89]

15. How many reference lists do I need?

  • When all articles are in JF, their individual reference lists are included and so the Reference List at the end of the thesis contains only references from the Introduction/Literature Review and Discussion/Conclusion (often numbered)
  • When all articles are in MS, there is often no Reference List attached to individual articles; every reference is put together in one big Reference List at the end of the thesis (alphabetical)
  • Some theses have a separate Reference List at the end of each chapter (including Introduction/Conclusion)

16. How do I broaden the discussion in the Discussion Section?

Many writers discuss their results chapter by chapter, aim by aim, or hypothesis by hypothesis; however, that seems not quite in accordance with the guidelines (former University of Sydney policy document, as well as other university guidelines for HDR students) which state:

"The thesis must contain an overarching discussion of the main features of the thesis including, inter alia, the principal significance of the findings, problems encountered and future directions of the work. The discussion should not include a detailed reworking of the discussions from individual papers within the thesis."

  • It would seem best therefore to avoid discussion chapter by chapter, or aim by aim. If you do so in an opening summary, you should widen it out
  • A way of doing this is to use singular terms such as ‘this study’ or ‘this thesis’.

Here are some example phrases:

A common theme running through this thesis
Our work highlights the importance of …
The series of 3 studies that comprises this thesis
Another key contribution of this study was …

Many thanks to Emily Don, Simon Firestone, Ashlie Hartigan, Sarah McIntyre, Melissa Nott, Paul Stoodley, Vanessa Allom, Michael Bowen, Shauna Downs, Robyn Keall, Fereshteh Pourkazemi, Jennifer McArthur and Natalie Allen for permission to cite their theses.

Many thanks to Dr Marie McInnes, a retired Learning Centre staff member, who developed these FAQs.