Senior Thesis

A senior thesis gives you a chance to dive deeper into a research topic of interest. It is the culmination of your undergraduate research career at one of the best biochemistry departments in the country. The thesis experience will help you develop your reading, research, and writing skills, and many students find this a rewarding experience in which to develop new skills through independent work. Senior theses are two-semester commitments, and senior honors theses are often required by Honors programs here at UW–Madison. Senior Thesis (691-692) and Senior Honors Thesis (681-682) are two-semester course sequences for students in the lab of a Biochemistry department faculty member. You must be a senior and you cannot take the two semesters concurrently.

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Getting permission to enroll

Work with your thesis advisor (the faculty member who is the PI of your lab) to complete

  • Your Senior Thesis Proposal Form (download here), signed by your thesis advisor
  • Your Research Proposal

Turn in your completed Research Proposal Form and Research Proposal to the Biochemistry/Microbiology Undergraduate Advising Hub ( by the end of the third week of class.

Thesis proposal guidelines

Your senior thesis or senior honors thesis proposal should be two to five double-spaced pages with 1-inch margins and 11-12 pt font. The abstract and references are included in the 5-page limit and the proposal should follow disciplinary guidelines and use headers appropriate to the field. If you are uncertain about how to format your proposal, talk to your thesis advisor. All proposals should contain the following:

  • An abstract of the proposed research (200 words or less, may be single-spaced)
  • Introduction and literature review, detailing the originality and significance of the proposed project
  • Methods section, describing plans for data collection and analysis
  • Timeline for completion of project
  • Conclusion/future directions
  • References (may be single-spaced)

These guidelines are adapted from the Hilldale/Holstrom Application with permission from the Office of Undergraduate Academic Awards. Your thesis advisor may have additional requirements or recommendations.

Thesis guidelines

Overall, your senior thesis should follow a similar format as a Masters or Doctoral thesis. Consult with your thesis advisor for guidance.

  • Title Page: Cover Page (download here) signed by your thesis advisor
  • Introduction and Literature Review: Provide a short introduction to the questions addressed in the thesis, including a review of the relevant literature. The literature review need not be extensive, but it should summarize the status of the field at the time the project was undertaken. This section should conclude with a clear, concise statement of the hypothesis to be tested or the questions to be answered.
  • Materials and Methods: In this section, you should report the materials (usually biological and/or chemical) used in the experiments and describe all techniques. If a technique has been used essentially as reported in the literature, it can be referenced without further description. You should note any significant modifications of the original report. Methods should be reported in enough detail to allow an interested colleague to reproduce the experiments.
  • Results: You should describe the major experimental findings, which are usually summarized in the form of tables or figures. Tables and figures should be numbered consecutively, with each on a separate page. They may be inserted into the text as needed (usually as the page immediately following the text page on which a given table or figure is first mentioned) or collected together at the end of the thesis.
  • Discussion and Conclusions: You should provide a discussion, interpretation, and summary of the thesis findings. The conclusions that can be drawn from the data should be stated clearly and defended concisely. It is often appropriate to discuss the results in relation to the findings of other investigators, particularly if the conclusions appear to be in conflict with those of others.
  • References: You should collect all references cited in the text together in a bibliographic listing at the end of the thesis. Use a consistent format for all references. References may be cited in the text by number (in parentheses or as superscripts) and listed in the Reference section in order of citation. Alternatively, references may be cited by name and listed alphabetically in the References section. In the latter case, papers with one or two authors are usually cited in the text by name(s) and year (i.e., Smith and Barnish, 1999), whereas papers with three or more authors are usually cited as the first author et al. with the year (i.e., Barnish et al., 1999).
  • Other Sections: It is helpful to include a short (≤1 page) abstract or summary and a table of contents at the beginning of the thesis. The thesis may also include a page of acknowledgments to express appreciation to those who were especially helpful in the work.
  • Appendices: Experimental details or findings that are only tangentially relevant to the thesis may be included as appendices, if it seems desirable to preserve a record of the information.

Additional resources:

Final thesis submission

We recommend that you give a completed copy of your thesis to your thesis advisor three weeks before the semester ends, so they have enough time to review your work and assign a grade.

You also need to turn in your thesis with a signed Cover Sheet to the Biochemistry / Microbiology Undergraduate Advising Hub (​​​ by the last day of class of your second Senior Thesis semester. If you are in an honors program, check with them to see if they have an earlier deadline.

If you anticipate needing additional time to complete your work, you must discuss this with your thesis advisor and have the advisor inform Biochemistry/Microbiology Undergraduate Advising Hub (​. You will receive a grade of incomplete and you will not officially graduate until the thesis is reviewed and the incomplete grade is changed to a letter grade.


The grade for the thesis will be given by your thesis advisor. During the first semester, your thesis advisor will give you a grade of “P” for progress or “F” for non-attendance/non-contact. Your thesis advisor will assign the letter grade at the end of your second semester, and it will serve as both the first and second semester grade. The thesis advisor will assign the grade through MyUW.

Student checklist for Biochemistry Theses

Semester before thesis work begins:

  • Speak with a professor about doing a thesis in their lab.
  • Begin work on the research proposal, which includes an experimental plan, methods and procedures, expected results, and the significance of the work (2-5 pages).
  • Get authorized to enroll! Turn your Research Proposal Form and your Research Proposal in to the Biochemistry/Microbiology Undergraduate Advising Hub ( this semester or by the end of the third week of class of your first semester of thesis work.
  • Enroll in BIOCHEM 681 or 691

Start of first semester of thesis work:

  • Turn in your Research Proposal Form and your Research Proposal to the Biochemistry/Microbiology Undergraduate Advising Hub ( by the end of the third week of class.
  • Enroll in BIOCHEM 681 or 691 by the end of the third week of class, if you haven’t already.
  • Work on your thesis!

End of first semester and beginning of second semester of thesis work:

  • Enroll in the second semester of your Senior Thesis course (BIOCHEM 682 or 692). If you are not authorized to enroll, then contact the Biochemistry / Microbiology Undergraduate Advising Hub (​​​​
  • Your thesis advisor will issue you a “P” grade for “progress” for the first semester of thesis work. This is normal. The grade received for the second semester will automatically also apply to the first semester once it is issued.
  • Work on your thesis!

Three weeks before end of second semester of thesis work:

  • Complete your thesis!
  • Have thesis advisor read your final thesis and sign your thesis cover sheet — the thesis advisor will then assign a grade electronically.
  • Submit one copy of the finished thesis with the signed cover sheet to the Biochemistry/Microbiology Undergraduate Advising Hub ( before the end of the last week of class.
  • Note: Students in Honors programs may require earlier thesis submission and additional paperwork, depending on the program requirements and deadlines.