Ph.D. Thesis - Content & Organization

Although obtaining a Ph.D. in the Department is not dependent on obtaining publications, it is a strong expectation that any Ph.D. graduate will obtain first-author publications during their thesis studies. In practice, almost 90% of our Ph.D. students obtain at least one first-author publication and more than 55% obtain at least two.

The thesis should be written in the first person (use of the pronoun “I”), as it describes the student’s individual work: experiments, rationale, hypotheses and conclusions.


  • Should provide the relevant background to the thesis work.
  • Should not be a general survey of every topic touched upon by the work.
  • Should clearly outline the state of knowledge in the field of research and emphasize the outstanding questions in the field, especially those that are specifically addressed by the thesis research.
  • An excellent Introduction will be interesting to read, and will propose a hypotheses (possibly novel) to explain data in the literature. This is the student’s chance to demonstrate mastery of the subject matter of the thesis studies. Students should not be afraid to express their opinions. This is the student’s thesis, and their opportunity to write their own story. The Introduction should end with a brief outline and rationale for the thesis research. The Introduction should not generally exceed 25-30 pages.

Data Chapters

  • Students should aspire to have two data chapters in their thesis.  Note that the data chapters do not have to be published papers. A data chapter should contain enough data to reach a significant conclusion that could be published in a high-quality journal for the field in question.
  • The data chapters should describe the experiments performed by the student.
  • Work of collaborators may be included when this work is crucial for the understanding of the student’s own data. When work by collaborators is included, those experiments done by collaborators should be clearly indicated. There must be a general explanation on the cover page of each data chapter outlining the contributions from each person.
  • In the body of the chapter, use “I” to describe the student’s experiments, and the name of the collaborator(s) (or “we”, if appropriate) to describe others’ experiments/data. The chapter must be written to emphasize the student’s own work.
  • The introduction to a data chapter should not repeat material already presented in the general introduction of the thesis.
  • Figures and tables not exceeding three pages in length (-see the note below for instructions on how to present very large data sets) should be placed in the body of the chapter, on the page following its first introduction, and not in a separate section at the end of the chapter. Where possible, the legend should be on the same page as the display item.
  • Aside from very large data sets or movies (see below), there should be no reference to supplemental materials/figures/tables; all relevant data should be presented in the results section of the data chapter.
  • Sometimes, figures that have been copied into a thesis are of inadequate resolution. Students must ensure that all figures within a thesis are at least 300 dpi.
  • It is never permissible for a published or unpublished manuscript to be used as a data chapter without some alteration. Even in the case of a single author paper by the student, the introduction must be modified to avoid repetition with the thesis introductory chapter, and all supplementary materials will be incorporated into the results section of the chapter as described above.
  • If a study involves Human Subjects, a section in the materials section should be included that indicates that the study was approved by an Institutional Review Board (specify which), and that informed consent was obtained from all human subjects. If a study involves vertebrate subjects, a section in the materials section should be included that indicates that all related protocols that were used were reviewed by the appropriate animal care board (specify which).
  • Finally, the term ‘data not shown’ does not belong in a thesis. Arguments that rely on casual observation because no data was collected should not be present in a data chapter because this provides evidence of poor scientific method. Speculation based on casual observation is permissible within a concluding chapter, so long as it is clearly stated that the argument relies on casual observation and not on real data.

Concluding Chapter

  • Should begin with an overall summary of the work that explains how it has advanced the field. Students should refer to questions and hypotheses raised in the Introduction and explain how the research has solved (or maybe not solved) these problems. This chapter can propose hypotheses and models, and should emphasize the student’s own view of the field. The thesis should finish by suggesting several future investigations that would further address the key issues in the field.

A Note on the Inclusion of Very Large Data sets, Movies, and References to Published Supplemental Materials within the Thesis see here.

Thesis Formatting - In addition to the SGS format rules for the Ph.D. theses, we highly recommend using 12 point un-condensed Times New Roman font for clarity.