Papers and manuscripts can be used largely as-is as chapters in a thesis or dissertation in the CS graduate program. This approach to formatting encourages the preparation of publishable work in a publishable form and reduces the effort required to meet thesis or dissertation formatting requirements. To maintain consistently, the University requires a specific format for the title page and other front matter and also required pdfs to contain embedded fonts. Theses and dissertations generated by CS students should satisfy all University requirements.

The difference between a paper and a manuscript is that a paper has been published (or accepted for publication) and a manuscript has not. For clarity in the following details, the term "thesis" to refer to a dissertation or a thesis unless the difference is significant. Similarly, the term "paper" refers to a paper or a manuscript.

These requirements specify how theses should be formatted. They do not specify the content that should appear in a paper or thesis. Content is determined by the student and thesis committee working together.

We have created an Overleaf project containing an example thesis prepared using these formatting requirements. The example thesis contains an introductory chapter in the traditional chapter format, a chapter containing a published paper, a chapter containing a manuscript (in the example, for illustration purposes it's a manuscript for the published paper. This would likely not occur in an actual thesis.), and a concluding chapter in the traditional style. The manuscript chapter is formatted to allow it to be shared between two students both of whom included the same manuscript in their theses.

Title Page, Front Matter and Fonts

University guidelines specify the format of the title page, abstract page, acknowledgments page, and signature page (bound copies only).

All fonts in the final thesis pdf must be embedded.

Three Kinds of Chapters

All chapters must be in one of the following three formats. A single thesis may include any combination of these formats. Details about each format are given in the sections that follow. An example of a thesis that contains each of these kinds of chapters is available as a sharelatex project.

  • A chapter containing the camera-ready accepted paper with the student as a primary author. Minor modifications, such as to fix a last minute typo for example, are allowed. The bibliography should be included as part of the paper as it would normally appear in a paper. Also, the student and advisor may choose to include supplemental material in an appendix to the thesis. Details below.
  • A chapter containing a manuscript that has been or could be submitted for publication with the student as a primary author. The student should remove elements (such as line numbers) included only for peer review, should de-anonymize the manuscript and remove all references to the venue. The bibliography should be included as part of the manuscript as it would normally appear in the manuscript. Supplemental material can be added to an appendix. See details below.
  • A traditional thesis chapter in the old format, but with single line spacing rather than double line spacing. This could be useful, for example, as an introductory chapter for dissertation that contains several papers. Many committees may require such an introductory chapter, but a student, advisor or committee may choose to include a chapter in this format for other reasons. Bibliographies for traditional chapters should be included at the end of that chapter or at the end of the thesis. Note that works cited in several chapters will be contained in several bibliographies.

If more than one student is a primary author on a paper or manuscript, it may make sense for more than one student to include the paper or manuscript as a chapter. This kind of collaboration is encouraged but several additional conditions must be met to include a paper or manuscript in two theses. See details below.

Chapter Containing a Paper

An accepted or published paper with the student as the primary author can be used as a chapter in the format it was submitted for publication. The bibliography is included as-is for the original paper. “Accepted” means accepted after a peer review process by a program committee or journal editorial board. The final camera ready pdf of the paper can be included as-is (with minor modifications) in the thesis. A chapter containing an accepted paper must include

  1. a complete citation to the paper
  2. the statement "I hereby confirm that the use of this article is compliant with all publishing agreements."
  3. a chapter title with is same title as the paper itself

Formatting additional material: Some students may choose to include additional material in the thesis beyond what was included in the paper. In that case, the student should add the additional material in an addendum or appendix at the end of the paper in the same format as the paper or in the traditional BYU CS thesis style. The addendum or appendix should indicate that this material does not appear in the publication.

Publishing agreements: You can review publishing agreements with the ACM and IEEE. We believe this use of the accepted paper in a thesis is consistent with the most variations of publishing agreements.

Minor changes: Minor formatting and other minor changes to the paper are allowed. For example, the student might not yet have the DOI for the paper when they defend the thesis.

“Accept with revisions” or shepherding: Articles accepted with revisions or in shepherding on the date of the thesis defense should also be included as manuscript chapters.

Pre-prints: Articles published by arXiv or similar pre-print sites do not count as accepted papers and should be included as manuscript chapters.

Chapter Containing a Manuscript

A manuscript with the student as a primary author that has not yet been accepted for publication can be included in a format suitable for submission to peer review---with several modifications listed below. The bibliography is included in the chapter as part of the final manuscript.

  1. Remove elements used only for review. This includes line numbers in the margins and paper/submission identifiers.
  2. Remove anonymization. All author names should be included. The inclusion of references to the author’s prior work, suitable acknowledgments, and other elements are appropriate to include if they would normally be included in the published paper but have been removed or anonymized for double-blind review.
  3. Remove all references to the venue that the manuscript has been (or might be) submitted to for peer review. This avoids creating the appearance that a manuscript has been accepted when it has not been (if the manuscript has been accepted, use the “accepted paper” option above).

A manuscript chapter must include the following elements:

  1. The statement “This manuscript has not yet been accepted for publication” Do not include the names of venues to which you have or plan to submit the manuscript for review.
  2. A chapter title with the phrase “In preparation:” prepended in front of the full title of the manuscript.

Traditional Chapter

Other kinds of chapters such as Introductory or Conclusion chapters are optional (and allowed) but should be formatted in the traditional BYU CS thesis style with single line spacing, one inch margins, and a Times font in 11 or 12 pt. These are the same formatting requirements as generated by the CS thesis and dissertation latex class. If the chapter cites other work, the bibliography for that chapter should be included at the end of the chapter or at the end of the thesis. A thesis may consist entirely of traditional chapters.

Sharing a paper across several theses

In collaborative work, more than one student might be a primary author on a paper or manuscript (both are hereafter referred to as a “paper” for clarity). In this case, it might make sense for two or more students to include the exact same paper as a chapter in their thesis (recall that the term "thesis" refers to both a thesis and a dissertation). Our intent is to make this kind of sharing clear and explicit across all theses that might share a paper. And to make that sharing clear before any of the students defend.

Sharing a paper as a chapter among primary authors is encouraged under the following conditions:

  1. The writing and research in each students’ complete thesis stands on its own. There will be references and connections to the other primary authors’ work, but the writing and research claimed by each student, in addition to other chapters that might appear in the thesis, stands on its own. And,
  2. Each chapter in every student thesis that contains a shared paper includes the statement “<Other student names> and I are primary authors of this paper. We have agreed that each of us will include this paper in our thesis (or dissertation).” And,
  3. Each chapter in every student thesis that contains that paper includes identical summary statements that describe each students’ contribution to both the research and the writing.

It would also be wise to involve the thesis committee early in plans for sharing papers as chapters in theses and in plans for presenting the work at the defense. These plans might, for example, include an introductory chapter that clearly defines the research and writing completed by the student.

Frequently Asked Questions

Question: What's the easiest way to include my paper as a chapter in my thesis?

Answer: Find a pdf file containing your paper. In the latex document for your thesis, use the pdfpages package and include the paper with the command


Papers included in the sample chapters of the sample thesis use this command.

Question: I'm working on a dissertation not a thesis, what are the formatting requirements for a dissertation?

Answer: In this document the term "thesis" is used to refer to both a thesis and a dissertation unless the difference is significant. The formatting requirements for a thesis and a dissertation are the same.

Question: What if a student uses a manuscript as a chapter in their thesis, graduates and then the manuscript is rejected after the defense?

Answer: Nothing. The student defended their work as a research contribution, the committee voted to pass the student and the student is done regardless of what a program committee or journal editor decides to do with the work.

Question: What if... Student A uses a manuscript as a chapter in their thesis, defends and graduates. Student A's manuscript is eventually rejected in peer review. Later, Student B continues that same line of work, carries out additional research, and revises (not rewrites, but revises) the original manuscript for resubmission. Can Student B include the revised manuscript in their thesis even though Student A didn't include a statement about sharing the manuscript as per the requirements for sharing a manuscript as listed above?

Answer: Yes, Student B can include the revised manuscript because it is not a verbatim copy of the same manuscript included by Student A. Student B should describe what parts of the work and writing belong to Student B and which parts were generated by Student A. The thesis committee will need to decide whether or not Student B's work (along with any other work included in the thesis) is sufficient as a thesis.

Question: Where does the bibliography go in my thesis?

Answer: Each paper or manuscript chapter includes it's own bibliography. Traditional chapters can include a bibliography after each chapter or the thesis may include a complete bibliography for the traditional chapters (but not the paper or manuscript chapters) at the end of the thesis. In latex, most authors find it easiest to include the bibliography for traditional chapters at the end of the thesis rather than at the end of each chapter. This is what is done in the sample thesis.

Question: If I include the bibliography for each paper at the end of each chapter, I'll end up citing the same paper more than once. Is that ok?

Answer: Yes. Include each paper as-is as a chapter (following the guidelines above) including the bibliography.

Question: I've got a manuscript that's nearly ready for submission for peer review. It just needs some more editing and formatting adjustments. Can I use that as-is right now as a chapter in my thesis?

Answer: No. Manuscript chapters much be in a format suitable for peer review (with some modifications as described above). A manuscript that is not quite ready for peer review and will be included as a chapter in a thesis should be formatted as a traditional chapter.

Question: This document seems to assume I'm going to prepare my thesis in Latex. But I'm going to use Word (or something else). How do I prepare my thesis in the right format using Word instead of Latex?

Answer: You will need to work with your advisor to figure out how to meet formatting requirements. The department has decided to focus it's support on Latex as a tool for formatting theses. You are free to use any tool you want, but you and your advisor will need to figure out how to meet formatting requirements. The Latex skills required to meet the formatting requirements are not advanced. For example, you might use Word to prepare your papers and manuscripts but if you can convert them to a pdf, which you likely will for peer review and publication, then you can include those pdfs in your thesis in Latex with minimal effort.