Initial Advising and Workshops

Prior to the start of Autumn Quarter, the cohort of incoming students will meet as a group with a faculty/student advising committee during Orientation to discuss their course options for the upcoming year. A schedule of recommended classes will also be provided. Prior to this meeting, students should review course requirements and prepare a tentative plan. Registration for classes should be completed prior to the first day of classes. Courses may be added or dropped until the end of the second week of the quarter without a tuition penalty. A Change of Registration fee will be charged to the student for all registration changes made on a single day during this period. Tuition forfeiture period begins at the start of Week 2.

Graded Course Requirements

A total of 18 graded credits with a minimum 2.7 grade in each course is required before scheduling the General Exam. Students are required to take the following courses in bacteriology, virology, and biostatistics: 

Bacteriology (3 credits)

• MICROM 553 (Spring 2026; Autumn 2027; Autumn, odd years thereafter, 3 credits), Molecular Interactions of Bacteria with their Hosts

Virology (3 credits)

• MICROM 540 (Autumn, even years, 3 credits), Virology

Biostatistics (minimum 2 credits, choose one)

• UCONJ 510 (Summer, 2 credits), Introductory Laboratory Based Biostatistics
• BIOSTAT 511 (Autumn, 4 credits), Introduction to Statistics in Health Sciences

The remaining credits (for a total of 18 graded credits) can come from taking departmentally approved 400- and 500-level courses listed in Appendix 1. Program policy limits students to no more than 6 graded credits per quarter. If students are interested in a class that is not listed, please petition the GPAC by contacting the chair (microgpc@uw.edu) for permission to have it count towards the degree before taking the class. Note that courses change, so verify all course details online. Also investigate the anticipated workload, which varies considerably among graduate classes. 

Non-graded Academic Requirements

1. Attending MICROM 520 (seminar) and MICROM 522 (“Work in Progress” or WIP) is mandatory. Both courses are graded Credit/No-Credit. Departmental seminars are crucial for contributing to the breadth of student knowledge, and students must register for and attend seminar each year of graduate school. WIP serves to develop oral presentation skills. Students must register for and attend WIP through year 5 and will be scheduled and must present in WIP every year of graduate school. The requirement for a grade of “Credit” and the manner in which this requirement will be assessed will be conveyed to students at the beginning of the academic year. A grade of “No-Credit” will result in a Notification, which may escalate to Academic Alert, Final Academic Alert, and Academic Drop (see https://grad.uw.edu/policies/3-7-academic-performance-and-progress/) should the deficiency not be addressed satisfactorily. Failure to register for WIP will immediately escalate to Academic Alert. The only exception is that students may register for a graded class that meets at the same time as WIP. In this case, please notify the GPA of the scheduling conflict and the reason for not attending WIP. For conjoints that conflict with WIP, students are expected to attend WIP for the half of the quarter in which the conjoint does not meet. 
2. Every year, students must maintain full-time status by registering for enough MICROM 500, 600, or 800 credits to bring their total credits to 10-18 per quarter in Autumn, Winter, and Spring. Register for MICROM 500 for each of the three lab-rotation quarters. Once students join a thesis lab, they must register for MICROM 600 prior to completing the General Exam and for MICROM 800 after passing the General Exam for a total of 10-18 credits (graded and non-graded credits) per quarter during the academic year. Registering for less than 10 credits is considered part-time and for more than 18 credits incurs additional tuition costs and should be avoided. Register for exactly 2 credits in Summer, which is either UCONJ 510 (to fulfill the biostatistics requirement) or MICROM 600/800. 
3. Bioethics: Students must complete either 8 hours of Biomedical Research Integrity: Responsible Conduct of Research training (register at https://www.washington.edu/research/required-training/biomedical-research-integrity-program-nih-required-responsible-conduct-of-research-rcr-training/) or Bioethics 101 taught by the Biochemistry Department (register for the Winter Quarter BIOC 533), by the end of Summer quarter of the second year.
4. TA one laboratory course in Microbiology. Developing good teaching skills is an important part of graduate training. Students will be assigned to TA a specific course by the Microbiology Teaching Faculty. Generally, students teach in their second year, and the teaching requirement must be met by the end of the second year. This is an academic requirement and does not constitute a change in ASE duties as outlined in the annual appointment letter. Note that for students who entered the program prior to Autumn 2024, two TAships are required.
5. Creditable passage of the Topic Exam in the second year.
6. Present one lecture in an undergraduate Microbiology course, preferably in the fourth or fifth years. Arrangements for giving these lectures can be made by contacting individual course directors. For example, this requirement can be fulfilled by presenting lectures in the undergraduate methods course (MICROM 431). At the conclusion of the lecture, students must complete the Undergraduate Lecture Self-Assessment (available on the website under Graduate Student Resources) and review their answers with the course instructor(s) within 2 weeks of the lecture. The completed self-assessment must be sent to the GPA (microgpa@uw.edu) as evidence of completion of the lecture requirement. Note that for students who entered the program prior to Autumn 2021, two lectures are required.
7. Be first author on at least one paper related to thesis research, which is published or accepted for publication in referred journals prior to the Final Exam (Thesis Defense).

Additional Requirements

See also Graduate School Policy 1.1.

1. A minimum cumulative grade point average of 3.00. The GPA for graduate students is calculated entirely on the basis of numeric grades in 400- and 500-level courses.
2. Completion of a total of 60 credits prior to taking the General Exam.
3. Creditable passage of the General Examination. Registration and completion of credits as a graduate student is required the quarter the exam is taken and candidacy is conferred.
4. Completion of 90 credits prior to the Final Exam. With the approval of the graduate program and the Graduate School, a master’s degree in a relevant field of study from an accredited institution may substitute for up to 30 of the required 90 credits.
5. Satisfactorily completion of a minimum of 27 credits of dissertation (800) over a period of at least three quarters, with at least one quarter occurring after the General Exam. With the exception of summer, when students take 2 credits, students are limited to a maximum of 10 credits per quarter of dissertation (MICROM 800).
6. Preparation of and acceptance by the Dean of the Graduate School of a dissertation that is a significant contribution to knowledge and clearly indicates training in research.
7. Creditable passage of a Final Examination, which is usually devoted to the defense of the dissertation in the field with which it is concerned. The General and Final Examinations cannot be scheduled during the same quarter. Registration and completion of credit as a graduate student is required the quarter the Final Examination is taken.

Topic Exam

Purpose 

The objectives of the Topic Exam are for the student to: (i) gain an understanding of a topic area distinct from his or her thesis research, (ii) present a critical written review of previous work and devise a logical plan for future research directions in the topic area, and (iii) effectively present the topic and respond to questions in an oral setting. Additional benefits include an introduction to the student of how the Ph.D. Supervisory Committee functions as a group and a chance for the Committee to identify areas of concern that can be improved for the General Exam.

Procedures 

In preparation for the Topic Exam, second year students must form their Ph.D. Supervisory Committee. Once the Committee is formed, the student is encouraged to contact the members to schedule a date and time for the Topic Exam. If the exam is to take place in Autumn Quarter, scheduling should begin immediately after forming the Ph.D. Supervisory Committee. For Winter Quarter exams, please schedule the exam at least 3 months in advance of your target exam date. For all students, scheduling must be complete by January 31, and the exam must take place by the last day of Spring Quarter. Exceptions to this deadline are dependent upon petitioning the GPAC jointly by the student and advisor no later than January 31 and are at the discretion of the committee.

Inform the GPA (microgpa@uw.edu) of your exam date. The GPA will coordinate the following deadlines relative to the actual exam date for each student:

1. Six weeks prior to the exam date: Deadline to submit two topic proposals to the GPA. For each proposed topic provide: 1) a title, 2) a paragraph briefly outlining the subject of the proposed topic and the gap in knowledge that you propose to address, 3) a hypothesis statement and the methodology that you will use to test the hypothesis, 4) two or three recent references that serve as the basis for the topic to be explored. In addition, please describe your thesis project in a short paragraph, so that the GPAC can judge how different your proposal will be both in subject and approach from your thesis work.
   1. What constitutes an acceptable Topic? Since one of the goals of this exercise is for you to explore and learn about an “off topic” area outside of the expertise of your lab and the focus of your thesis project, you should consider other areas of microbiology that you find intriguing. But “off topic” need not be completely far afield. Virology students can still write proposals on viruses, and bacteriology students can still write proposals on bacteria. However, pick a different organism and a different aspect of the biology of the organism than is the focus of your thesis research. The proposal should not be derived from papers that you have used (or plan to use) in a class that includes proposal writing or from prior research experience (either in rotations or before entering graduate school). By venturing into a related but distinct area of microbiology, you can expand your knowledge, gain new skills, and potentially discover synergies between your thesis research and the topic you choose to explore in this exercise. The key is to find a balance between staying within the broad field of microbiology while still branching out from your immediate research focus.
   2. How long should you spend looking for Topics? You can be thinking about ideas for this exercise throughout your rotations and coursework in your first year and in the beginning of your second year. A significant amount of time dedicated exclusively to looking for topics is generally unwarranted.
   3. How much help can you receive for the exam? Although the goal is for you to come up with the proposal topic yourself, seek advice from your thesis advisor and peers when vetting topics to make sure that the area is distinct from your thesis work and that what you learn is likely to be of use to your general knowledge and development as a microbiologist. Review the Topic and General Exam Rubric (available on the website under Graduate Student Resources) to see how you will be evaluated. We encourage your advisors to talk to you about best practices in grant writing. They are welcome to provide you with an example of what a grant application looks like, although you must adhere to the length and formatting limitations of this exam. If your advisor reads a draft, at most once during the process, they can comment on areas that are unclear or in an illogical order but not how to fix them. They should not edit the text or point out gaps in logic or missing elements.
2. Four weeks prior to the exam date: If there is a question about the suitability of the proposed topics, the GPAC may request clarifications, modifications, or revisions. Once they reach a decision, the GPAC will inform the GPA. Four weeks prior to the exam, the GPA will inform the student that one or both topics are approved. This feedback will also be provided to the Thesis Advisor, who has the option to share it with the Ph.D. Supervisory Committee. If both topics are approved, the student can choose which one to work on.
   1. How long should you spend preparing for the exam? For the first two weeks after your topic is approved, think about hypotheses and Aims. Read a little bit more, mull over some ideas, and outline the proposal. At this point, you should still be 100% engaged in lab activities, and any writing should not impact time in the lab. Devoting almost full-time effort to the proposal is only acceptable in the last two weeks before the exam. Inform your advisor of your plans, as he/she may want at least partial effort in the lab even at this point.
3. Three business days prior to the exam date: The student will distribute to all members of the Ph.D. Supervisory Committee:
   1. A copy of their most recent IDP.
   2. The Topic and General Exam Rubric (available on the website under Graduate Student Resources).
   3. The written component of the exam. The document must be written in 11-point font or larger, single-spaced, with half inch margins on all sides on standard letter paper. Recommended fonts are Arial, Helvetica, Palatino Linotype, or Georgia. Include page numbers on the bottom and a header with your name and the date of the exam. The document consists of 3 sections totaling no more than 4 pages. Up to one additional page of figures (with figure legends) as well as an unlimited number of pages of references may be included that do not count against the 4-page limit. The format is:

Section 1 (1 page): Briefly describe current knowledge about the subject of your proposal and the gap in knowledge that your proposal will address. State the objective of the proposal and how it will address the gap in knowledge. State the central hypothesis and provide a brief description of two or three specific aims to address the hypothesis. End with expected outcomes and how your proposal will impact the field. This is equivalent to the “Specific Aims” page of an NIH grant application. Aim for a scope of work that could be completed in approximately 2 or 3 years. Refer to online guidance for tips on writing an effective NIH “Specific Aims” page.

Section 2 (1 page): The current state of the field based on selected results from 2 or 3 key recent papers. Think of this as your preliminary data.

Section 3 (1-2 pages): A research plan for each Aim. Include a brief rationale, experimental approaches, alternative approaches, and expected outcomes. You should provide sufficient information to convey the logic behind the approach and its feasibility without going into experimental detail.

4. The Oral Component of the Exam: The exam is administered by the student’s Ph.D. Supervisory Committee and must take place in-person by the last day of Spring Quarter. The advisor and at least three additional members of the committee must be present. The GSR is not required to attend though should be invited. The advisor does not participate in the exam, which is conducted by a temporary chair who is selected by the faculty at the start of the meeting. The oral presentation should last approximately 30 minutes, with allowances for clarifying questions, followed by questions. It should be an expanded version of the written document, which will allow a more in-depth discussion of key elements of the proposal. This is a “closed-book” exam and notes should be kept to a minimum. Questions from the committee generally originate with the material in the proposal; however, a line of questioning may delve into basic knowledge from course work. The entire exam, including the presentation and questions, should not exceed 90 minutes.

Evaluation

Immediately following the exam, the student will be evaluated by the Ph.D. Supervisory Committee in the absence of the advisor, using the criteria listed in the Topic and General Exam Rubric. The outcome of the exam and feedback will then be provided first to the advisor and then to the student. The Committee will complete the Topic Exam Report (available on the website under Graduate Student Resources), which will be submitted to the GPA. The temporary chair will provide a written evaluation that will be distributed to the student and other members of the Committee and submitted to the GPA within 2 weeks of the exam.

Guidelines for the outcome of the exam based on the number of “does not meet expectations” categories are provided on the Topic and General Exam Rubric. While a highly developed and innovative research plan is desirable, it is recognized that this is still a formative area for a second-year student. If both the written and oral components of the exam are satisfactory, then the determination should be “Pass”. If moderate weaknesses are identified that can be addressed by revising or elaborating a portion of the proposal, by taking a class to bolster basic knowledge, or by some other remedial work, then the determination should be “Conditional Pass”. The conditions and deadline for the conditions to be met should be clearly conveyed to the student and recorded on the Topic Exam Report. The temporary chair of the Topic Exam committee is responsible for ensuring that conditions are met, with the consent of the examining committee. If the performance is unsatisfactory, the Committee may reach a determination of “Re-examine” and require the student to repeat some or all aspects of the examination. The student will be placed on Academic Alert in the quarter following the examination and will remain on Academic Alert until successful re-examination. The timing of the re-examination is at the discretion of the committee. Note that only one re-examination is allowed. Alternatively, the Committee may reach a determination of “Fail” and recommend that the student be dropped from the program. Successful completion of the Topic exam is a prerequisite for the General Exam.

General Exam

Purpose 

The objectives of the General Examination are for the student to (i) demonstrate mastery of the field in which they intend to conduct their thesis work, (ii) demonstrate general knowledge of microbiology and other disciplines (e.g., immunology, biochemistry, genetics) relevant to their thesis project, (iii) present a written plan for future research directions in the form of an R21 grant application, and (iv) effectively present their research proposal and respond to questions in an oral setting.

Scheduling 

The oral component of the General Examination must occur by the last day of Winter Quarter (mid-March). Accordingly, the meeting must be scheduled by the last day of Autumn Quarter (mid-December). When2meet (www.when2meet.com) polls or similar services facilitate scheduling. The student's advisor, the GSR, and at least two additional members of the Ph.D. Supervisory Committee must be present. The student must enter the date, time, and location of the exam on MyGrad (https://grad.uw.edu/for-students-and-post-docs/mygrad-program/) under “Schedule a doctoral general or final exam”. Once this is completed, inform the GPA so that the Department can officially approve the date. The date must be officially approved in advance to obtain credit for the exam from the Graduate School. Exceptions to this deadline are dependent upon petitioning the Ph.D. Supervisory Committee and the GPAC jointly by the student and advisor no later than the last day of Autumn Quarter (mid-December). The Ph.D. Supervisory Committee will advise GPAC of their willingness to grant an extension, with GPAC making the final determination.

Format of the written research proposal

The written research proposal on the student’s thesis work should follow the format specified for an NIH R21 grant application. There is a single “Specific Aims” page. The “Research Strategy” includes the “Significance, Innovation, and Approach” subsections and can be no more than 6 pages in length. References are not included in the 6-page limit; however, unlike for the Topic Exam, figures must be embedded in the text and count towards the page limit.  The document must be written in 11-point font or larger, single-spaced, with half inch margins on all sides on standard letter paper. Recommended fonts are Arial, Helvetica, Palatino Linotype, or Georgia. Include page numbers on the bottom and a header with your name and the date of the exam. 

The student should present a draft of the proposal to her/his advisor at least three weeks prior to the oral exam. The advisor may give the student feedback on the overall organization and format of the proposal but should not edit the scientific content or participate in a substantive way in the writing process. The written proposal must be sent to the committee at least one week prior to the oral exam.

Format for the oral exam

1. The student should bring the Graduate School Committee Signature Form (obtained from the GPA), the Microbiology General Exam Checklist, and the Topic and General Exam Rubric. The last two forms are available on the website under Graduate Student Resources.
2. Prior to beginning the oral exam and in the absence of the student, the advisor will review the student’s academic record and give the Supervisory Committee members a written evaluation of the student's research performance and potential (see Appendix 2 below). The advisor should have discussed the evaluation with the student prior to the exam. The evaluation should include an overall assessment of the student's effort level, creativity, independence, lab techniques, ability to design and execute experiments, and ability to communicate. This evaluation will be sent to the GPA (microgpa@uw.edu) for inclusion in the student’s file.
3. The oral exam is chaired by a member of the Ph.D. Supervisory Committee other than the advisor or the GSR. The advisor will not examine the student but will be present and available for comment or clarification when needed.
4. The exam begins with a 30-minute oral presentation of the research proposal by the student summarizing his/her research progress and indicating future directions of the research in relation to the proposed Specific Aims. Although the length of the presentation is limited to a maximum of 30 minutes, an allowance will be made for interruptions by committee members who ask clarifying questions. Following the oral presentation, members of the Ph.D. Supervisory Committee other than the advisor will examine the student. Although the research proposal will provide the starting point for the oral exam, questioning can extend into related topics including experimental techniques. The meeting may last up to three hours in total.

Final evaluation

At the end of the oral exam, both the student and the student's advisor will leave the room. The outcome of the General Exam will be determined solely by the committee members in the absence of the advisor. At the end of the deliberations, the student's advisor is apprised of the outcome in the absence of the student. Finally, the student will be called back into the room and members of the committee will provide feedback to the student on his/her performance.

The decision made at the end of the oral exam is a cumulative one, taking into account the student's performance in all areas since entering graduate school. These include, in the order of relative importance:

1. the performance on the oral exam
2. the quality of the written research proposal
3. the performance on the Topic Exam and improvement in areas of deficiency from the Topic Exam

The final decision must be one of the following: Pass, Fail, or Re-examine. If the committee feels deficiencies exist that need to be corrected, the “Re-examine” option must be chosen rather than awarding a “Pass” with stipulations concerning the deficiencies. Timing of the re-examination is at the discretion of the committee. A "Fail" means the student must leave the Ph.D. program, generally with the option to obtain a non-thesis master's degree (see Appendix 3). A written summary of the Committee’s decision prepared by the member of the committee who chairs the exam will be placed in the student’s file.

Final Exam and Format for the Ph.D. Thesis

To graduate, students are required to submit an Electronic Thesis/Dissertation (ETD) and a Committee Approval Form to the Graduate School through the UW ETD Administrator Site. ETDs are distributed by ProQuest/UMI Dissertation Publishing and made available on an open access basis through UW Libraries ResearchWorks Service.

1. A proposed outline of the thesis must be reviewed and approved by the Ph.D. Supervisory Committee prior to the beginning of writing. Once approved, the student must schedule the final exam. It is strongly recommended that the Final Exam (Thesis Defense) occur no later than two weeks before the end of the quarter.
2. Confirm with your committee the day and time that you would like to defend your thesis.  The GPA can help reserve a room for you. Once the room has been reserved, please schedule a doctoral final exam in MyGrad at least three weeks prior to the Final Exam.
3. Establish a Reading Committee from the members of the Ph.D. Supervisory Committee at least five weeks prior to the Final Exam. When at least three faculty members have agreed to serve, the student will notify the GPA (microgpa@uw.edu) so that the committee can be formed in MyGrad.
4. A draft of the thesis is due to the Reading Committee no later than four weeks prior to the defense. The Committee will inform the student of required revisions to the Thesis no later than the day of the defense. Note that alterations to these deadlines are acceptable at the discretion of the Reading Committee and should be clearly communicated to the student.

Format of the Thesis: A typical Ph.D. thesis is organized into the following chapters: Introduction (overview of the field and rationale for the thesis research), Materials and Methods, one or more Results chapters (each with its own brief Introduction, Results, and Discussion sections), and a Future Directions chapter. If any of the thesis research has been published, the papers can be reformatted as is for inclusion in the thesis. In the event that a published paper contains work carried out by another researcher, only the experiments done by the student should be included in the thesis. For continuity, a summary of related work done by others may be included with proper citations. Whether the Materials and Methods are collected into one chapter or left in each chapter is a matter of personal choice, but often it is desirable to place all the methodological information in one chapter to avoid excess redundancy.  

See the Graduate School Guidelines for the proper format of the Electronic Thesis or Dissertation. Note that only the format of the front matter is specified. The remainder of the thesis should be prepared with one-inch margins using Arial 11 font. Figures should be prepared in the same way as for journal publication and be included in the text near the point where they are cited and with an accompanying figure legend. Figures can be presented singly on a separate page or embedded within the text. If included within the text, the size of the figures should be adjusted so that the data are clearly visible. During preparation of the thesis and prior to final submission, the student's advisor should be consulted concerning overall style and presentation.

5. The Final Exam (Thesis Defense) is a public, in-person seminar on the student’s Ph.D. thesis research.
   1. If you would like a defense flyer prepared, let the GPA know at least two weeks prior to the defense and send a picture if you want something other than your website photo to be used on the flyer.
   2. Committee Signature Form: The GPA will prepare a Committee Signature Form before the exam and send it to you.
   3. The advisor, GSR, and two other committee members are required to attend.
   4. At the end of the seminar, the Ph.D. Supervisory Committee and the public are invited to ask questions. It is the prerogative of the Committee to continue to question the student in private.
   5. The Ph.D. Supervisory Committee members who attend the defense sign the Committee Signature Form. Please return the form to the GPA promptly after the defense so that your degree can be approved by the last day the quarter.
6. Return a revised thesis to the Reading Committee, if needed, so that final approval can be obtained by the deadline for the quarter. The Reading Committee approves the Thesis electronically in MyGrad.
7. Upload your dissertation according to Graduate School instructions (https://grad.uw.edu/current-students/enrollment-through-graduation/thesis-dissertation/).
8. Thesis Copies: You must order at least three copies of your dissertation to be printed. You may obtain worktags to use for payment from the GPA. Deliver one printed copy for the Department to the GPA. Deliver one to your advisor. The third copy is yours. You may wish to obtain additional copies at your own expense.

 

Approved Electives

Appendix 1: Approved Electives

The following courses are approved to count towards the degree.  Note that departmental offerings change from year to year and that the quarter in which courses are offered, especially conjoints (CONJ), can vary.  Note also that categories are based on course titles rather than a thorough review of the syllabus.

 

SECTION UNDER CONSTRUCTION - SEE 2025 HANDBOOK FOR CURRENT APPROVED ELECTIVES