Our faculty span a broad range of research interests from structural biology to developmental biology. We emphasize the value of using interdisciplinary approaches to attack important biological problems. Our department provides a friendly, interactive environment where students and faculty exchange ideas easily and get to know each other well. You will have the opportunity to become acquainted with diverse areas of biochemistry through coursework and seminars, while still concentrating on areas that are especially important for thesis research. A series of three month research projects in each of three different laboratories (“rotations”) will help you choose a thesis advisor, usually in June of your first year. A thesis committee of your choice will meet with you regularly, provide advice, and assure rapid progress toward your degree. Although we encourage you to apply for externally funded graduate fellowships, the department guarantees five years of support for all graduate students in good standing.

THE FIRST YEAR

Coursework. Four to five courses are taken in each quarter of the first year. Some of these are core courses, others cover specialty topics. The choice depends on interests, past experience, and previous coursework. Course requirements for students who have entered the Department through the Biomolecular Structure and Design Program (BMSD), the Molecular and Cellular Biology Program (MCB), or the M.D./Ph.D. Program may be slightly different; further information can be obtained from the offices of the BMSD, MCB, M.D./Ph.D. Programs.

A typical first year course program would be:

1. Credit is given for attending the weekly departmental seminar program.

2. Small group discussion of key articles and topics in the current literature (2 graded credits).

3. Work in 3 different research groups on potential thesis projects (credit/no credit).

4. Structure of macromolecules; introduction to crystallography, NMR, mass spectroscopy, molecular dynamics, and protein structure prediction (3 graded credits).

5. 10 week courses, or two 5 week modules, on selected topics taught jointly by the University of Washington and the Fred Hutchinson Cancer Research Center (FHCRC). (1.5 graded credits/5 weeks)

Conjoint courses (Conj 53X and 54X) cover a broad range of molecular and cellular concepts. At least 4 Conjoint modules of 5 weeks each must be taken, and 6 are recommended. Other graduate level courses may be substituted for Conjoint courses with the approval of the Graduate Program Advisor. Note that Conjoint 544 overlaps significantly with Biochemistry 530 and cannot be taken to satisfy this requirement. Most such courses are 3 graded credits.

Laboratory Rotations (Bioc 581) are required in each of the first three quarters, and are graded credit/no credit. At least 20 hours/week are normally devoted to the rotation project, although the time commitment may vary depending on the student's course load and the advisor's expectations. Students should also plan on attending their rotation lab group meetings and journal clubs. The three rotations must be in different research groups unless the student is entering with an advanced degree or from another program or institution (see below). Students are encouraged to select lab rotations that involve diverse biochemical perspectives and approaches. At the end of each rotation, students give a brief oral presentation of the rotation project before an audience of faculty, postdoctoral fellows, and graduate students. (To help students select laboratory rotations, and ultimately choose a thesis advisor, faculty present overviews of ongoing research at the departmental retreat, which is held before the start of Autumn Quarter. The retreat provides a relaxed and informal atmosphere for discussing potential rotation and thesis projects with the faculty.)

The Literature Review Series (Bioc 540, 541, and 542) emphasizes critical evaluation of the current literature. The fall quarter focuses on topics in protein biochemistry; students submit short essays addressing specific portions of journal articles and are guided in the preparation of fellowship and grant applications. Bioc 541 focuses on DNA replication, gene structure and regulation, and Bioc 542 focuses on biochemical aspects of cell and developmental biology. Both of these quarters emphasize student presentation of journal articles. Several faculty members are in charge of the course each quarter, attend each session, and also meet with students individually.

The Weekly Departmental Seminar Program (Biochemistry 520) features outside speakers in prominent research areas, and assures that faculty and students alike are up to date. Students are required to attend all regular departmental seminars in the first year, and expected to attend in subsequent years of graduate study.

The Biomedical Research Integrity (BRI) Series consists of lectures and discussions dealing with the responsible conduct of science, and is organized by the School of Medicine each summer quarter. Students in the first and second year are expected to attend. First year students must also attend a 6 session, ungraded, discussion course in the Responsible Conduct of Science given during the Winter Quarter. The sessions will be led by departmental faculty with special expertise in areas such as research and laboratory management; interpersonal relations, minority issues, and harassment; manuscript review and publication; animal and human research protocols; and intellectual ownership, patents, and industrial/academic conflicts.

The Graduate Program Advisor (GPA) advises all first year students, and meets with them at the beginning of each quarter to assess goals and progress. The GPA also continues to serve as an advisor and student advocate after the thesis advisor and Thesis Committee have been chosen. Any exceptions to departmental rules and practices require approval by the GPA. At the conclusion of Spring Quarter, a faculty meeting is devoted to evaluating student performance in rotations, the 530 and 540 series, Conjoint modules, and specialty courses.

Minimum grade requirements. The examinations in Biochemistry 530, Conjoint modules, and Minicourses must be taken, and a grade of 3.0 or above (out of 4.0) obtained in each of these courses as well as in the Biochemistry 540 Literature Review series. Students with grades below 3.0 may be required to retake all or part of a course. Students whose cumulative grade point average falls below 3.0 are automatically placed on probation by the Graduate School (see Graduate School Home Page). Students are required to earn at least 18 graded credits at the level of 3.0 or above in their first year.

The thesis advisor is selected in two steps. Students are encouraged to discuss potential thesis projects with faculty throughout the first year, but no formal commitment can be made directly between faculty and students. Instead, no later than June 1 of the first year, students submit one or two choices of thesis advisor, in order of preference, to the Graduate Program Advisor. The Graduate Program Advisor consults with all involved before formally assigning a thesis advisor. In those rare instances where faculty cannot accept all interested students, students may explore other research possibilities through summer rotations.

THE THESIS COMMITTEE

1. The Supervisory Committee must have a minimum of four (five recommended) members constitutes as follows:

One Chair, e.g., the student’s PI

Two Biochemistry faculty members

One non-Biochemistry member (or another Biochemistry faculty member)

One Graduate School Representative (GSR). The student chooses the GSR. The GSR cannot (a) be in the same department as the chair, (b) have an adjunct appointment in the same department as the chair or (c ) be an affiliate faculty member.

The GSR is a voting member of the committee. The GSR must attest to the validity of examinations (General Exam and Final Exam), indicating approval of the process by which examinations were conducted. This is done by signing the warrant and by submitting a standardized report on the examination process to the Dean of the Graduate School. The Graduate School will provide the required forms.

How to determine if a faculty member can be a GSR
The Graduate Faculty Locator identifies the appointments that each faculty member has. This will help determine who can be on your committee and who can serve as the GSR.

The Graduate Faculty Locator can be found on the Graduate School home page: http://www.grad.washington.edu/ Once you are at the Graduate School home page, you will go to the Resources for Faculty, Staff and Departments. From that list, you can link to the Graduate Faculty Locator. At this point choose the first link: Find Graduate Faculty by Name. You will then type in the name of the faculty member. The results of the search will appear and give you detailed information about the faculty member’s appointment status.

Remember the GSR cannot be in the same department as the Supervisory Committee Chair, have an adjunct appointment in the same department as the Chair, nor be an affiliate faculty member. Once the members of the Supervisory Committee have been chosen, email Kelley Pankow (kelleyp@u.washington.edu) the names of the committee members including: name, department and email address. Be sure to identify the Chair and the GSR of your Supervisory Committee. These names will be submitted to the Graduate School by Kelley.

THE SECOND YEAR

Students are welcome to consider additional graduate level coursework (normally numbered 500 or above) especially if required as preparation for the thesis project. Such courses should be chosen in consultation with the thesis advisor and Thesis Committee, and require the approval of the Graduate Program Advisor. Students typically complete the Minicourse requirements during their second year.

Teaching experience is an integral part of graduate education. Students serve as Teaching Assistants in 2 to 3 quarters of a lecture course and 1 quarter of a laboratory course, although the nature of the participation will vary according to the interests of the student and the needs of the course. To avoid inequities, each course is evaluated annually, and assigned either 1/2 or 1 teaching credit. A normal teaching load is 2 1/2 credits over the course of a graduate career.

The first meeting of the Thesis Committee is scheduled before Thanksgiving Recess in the Fall Quarter of the second year. The Graduate School Representative (GSR) should be invited to attend the first and all subsequent meetings of the Thesis Committee, but the committee may meet without the GSR if the GSR's schedule precludes timely meetings.

One week before the first meeting of the Thesis Committee, the student provides committee members with a thesis proposal (6 to 8 single-spaced pages, but no more than 10, excluding figures) describing the background, specific aims, experimental plans, and any preliminary data for the project. The purposes of this document are to define the scope of the thesis project, to review the relevant literature, and to provide a written basis for discussion with the Thesis Committee. The proposals are not expected to contain extensive data, as students will have spent relatively little time at the bench before the first meeting of the committee; however, the data should begin to indicate the feasibility of the project and/or focus attention on what types of feasibility studies still need to be performed.

The faculty understands that the nature and amount of experimental data will vary considerably from one proposal to another. Some students may spend their initial time at the bench doing a wide range of exploratory experiments; others may focus immediately on a specific project, or mastery of techniques; and yet other students may concentrate primarily on assimilating the essential background literature. The faculty also understand that thesis projects often change as graduate work progresses, so neither the initial written proposal nor subsequent meetings of the Thesis Committee should be viewed as locking the student into a specific project.

The second Thesis Committee meeting is scheduled before the Memorial Day Recess in the Spring Quarter of the second year. One week before this meeting, students should provide committee members with a brief summary indicating how their thesis proposal and experimental data have progressed since the previous committee meeting. Additional meetings of the Thesis Committee can be scheduled by the student or the committee if either feels this would be useful.

THE THIRD YEAR AND AFTER

The General Examination is scheduled before or during Fall Quarter of the third year. The following steps are required: (a) By October 1, the student chooses an examination date and schedules their general exams online using the MyGrad - Student View. (b) Four weeks before the exam, the Thesis Committee should receive a detailed thesis proposal (8 to 10 single-spaced pages excluding figures and tables). The Thesis Proposal normally includes an abstract, background, objectives, key experiments and techniques, anticipated problems, alternative approaches, significance, and future directions. The Thesis Committee may accept the initial proposal as a basis for the oral examination, request modest modification, or require major modification followed by resubmission. (c) One week before the examination, the Thesis Committee should receive a short hypothetical proposal (1000 word maximum, not including references) drawn from an area of biochemical research distinctly different from the thesis topic and clearly outside of the advisor's areas of investigation. The student must verify, before writing the hypothetical proposal, that committee members agree the topic area is indeed sufficiently different from the thesis topic and the advisor's research areas. Note that the General Examination may not be scheduled until all required courses in Biochemistry (with the possible exception of 1 Minicourse credit) have been successfully completed and the Graduate School requirement of 18 graded credits has been satisfied (or formally petitioned).

General Examinations typically last about 2 hours and consist of the student presenting and discussing the thesis proposal and hypothetical proposal with the committee. The Thesis Advisor attends the General Examination, and can ask questions or provide clarification, but one of the other Biochemistry Department faculty members chairs the exam. Students may pass the General Examination outright or conditionally. Conditions may include revision or expansion of the proposals, or additional coursework. A student who fails the General Examination may be allowed to retake the exam, or be asked to withdraw from the Ph.D. pathway. Upon successful completion of the General Examination, the student is admitted to candidacy for the Ph.D. as soon as a total of 60 credits (including at least 18 graded credits) have been amassed as required by the Graduate School Doctoral Degree requirements. The additional 42 credits required to reach a total of 60 usually reflect 6 to 7 quarters of thesis research, not additional academic coursework. Thesis research is formally considered a course, designated Bioc 600 before the General Examinations and Bioc 800 afterwards, for which 6 to 8 credits are awarded each quarter depending on whether other academic courses are being taken concurrently.

The Thesis Committee meets with the student at least annually, and usually twice a year, to provide advice and counsel. It is the joint responsibility of the student and thesis advisor to schedule these meetings, but the Graduate Program Advisor will keep track of the meetings and alert the student if meetings did not take place. Well before each Thesis Committee meeting, the student should provide all members of the committee and the GPA with a Progress Report outlining accomplishments, complications, and plans for the coming year.

Preparation of the DOCTORAL Thesis

Graduate School rules and regulations for the preparation of the thesis must be followed (see Style And Policy Manual For Theses And Dissertations).

The student chooses a Reading Committee and informs the Graduate Program Assistant who will notify the Graduate School. The Reading Committee is composed of three members of the Thesis Committee, at least two of whom must be Biochemistry faculty members. The student provides the Reading Committee (and all other members of the Thesis Committee) with copies of the thesis, allowing adequate time for them to read the thesis. Doctoral candidates are to schedule their final exam online using the MyGrad - Student View.

Manuscripts, preprints, and reprints may be included as an integral part of the thesis, or as an appendix, with permission from the Reading Committee. These articles cannot take the place of comprehensive Introductory and Discussion sections; however, the amount of additional material to be included under Materials and Methods, and Results, as well as all questions of style, are left to the discretion of the student, thesis advisor and Reading Committee.

The candidate schedules the thesis seminar ("Thesis Defense") for a time when all members of the Thesis Committee and the Graduate School Representative can attend. The seminar is open to department, University, and general public; it is followed immediately by the Final Examination (a brief discussion with the Thesis Committee) and very soon thereafter by celebration.

The M.A. or M.S. degree

In the unusual event that a student is unable to complete their PhD studies, a student who has successfully completed at least 36 credits (usually the first 5 quarters of the graduate program), may be eligible for a non-thesis M.A. degree as described in Graduate School Memorandum No. 28. A student who has completed at least 36 credits and has performed significant rotation or thesis research, but chooses not to continue toward the Ph.D., may be eligible for the M.S. degree. Research required for the M.S. degree need not be conclusive, or publishable; however, a formal M.S. thesis must be written in consultation with the Thesis Advisor and Thesis Committee and a formal thesis presentation must be made to the Thesis Committee as required by the Graduate School's Summary of Requirements. M.S. candidates may also request to present their thesis work in a seminar open to the entire department.