University of Michigan Chemical Biology Doctoral Program
Chemical Biology Doctoral Program Student Handbook
Summary of Contents
Doctoral Degree Program
Program requirements for the Ph.D. degree are administered by the Operating Committee, which consists of the Program Director, Associate Director and several Program faculty. The Program Director, in consultation with this Committee, has the authority to set and interpret rules and requirements and, when circumstances warrant, grant exceptions upon formal appeal. Upon entry, each student will discuss the following topics with a member of the Operating Committee: his/her background, objectives and any questions related to progress to the Ph.D. degree. The Operating Committee provides advice to the student until a Research Advisor has been formally selected, at which time the Research Advisor will undertake these advisory duties. However, throughout the tenure of the Program, students are encouraged and welcomed to consult with the Program Director, Operating Committee and Dissertation Committee for additional advice and guidance. If questions, concerns or conflict arise at any point in the Program prior to selection of a Research Advisor, students should contact the Program Director or their designate. After selection of a mentor, students should work closely with their Research Advisor to resolve any questions or concerns. If an issue cannot be addressed at this level, students and faculty should contact the Program Director or their designate.
Course elections for each term must be approved either by the Operating Committee or the Research Advisor. Each student's status is reviewed by the Operating Committee after each term and an appropriate report is provided to the student when needed. NOTE: Failure to follow the approved registration can jeopardize a student's standing in the Ph.D. program, which could result in suspension of stipend and benefits. Students should not make unapproved changes to their schedules.
Class periods begin ten minutes after the hour (or half-hour), although classes are listed as beginning on the hour or half-hour. Note: The words “semester” and “term” possess identical meanings at UM and are used interchangeably.
Requirements for the Ph.D. Degree
A student is expected to remain in good standing during his/her term of study by complying with the rules, regulations, and requirements set forth by the Rackham Graduate School, the Program in Chemical Biology and completing the duties of his/her Graduate Student Research Assistantship (GSRA) appointment or Graduate Student Instructorship (GSI) appointment if appropriate.
Graduate School Requirements
Credits and Rackham Requirements
A student is considered full-time with registration of eight credit hours per term. Pre-candidate students may register for one to eight credit hours of CHEMBIO 990 (pre-candidate research) per term as approved by the advisor in additional to any electives.
The current Rackham requirement for candidacy provides for a minimum of 18 credit hours of graded (including the grade of S – Satisfactory) graduate coursework registered as a Rackham student while in residence on the Ann Arbor campus. All required Chemical Biology graduate courses as well as electives may be used to fulfill this requirement. CHEMBIO 990 (pre-candidate research) as well as courses elected as visit (audit) do not meet this requirement.
After admission to candidacy students register for eight units of CHEMBIO 995 (dissertation research) for every term including the defense term. After passing candidacy, a candidate may take either one course per term, or to take more than one course for a total of no more than 4 credits, in addition to CHEMBIO 995 without an additional fee with the approval of the research advisor. Additionally, a candidate who does not take any courses during a term may either register for courses totaling up to 8 credits in the following term, or take no more than two courses that total more than 8 credits. "Unused" credits not taken do not roll over beyond the term immediately following it.
The Operating Committee and the student's Dissertation Committee both are charged with the responsibility to see that the individual student has a program of course work that is both broadly supportive of his/her specialized field of study and also indicative of the breadth and range of interest.
One of the requirements of the Program is for a student to be "in good standing," which requires the student to maintain a grade point average (GPA) of 3.0 or better, on a 4.0 scale. This average must be achieved by the end of the second term. Research and seminar courses are not included in calculation of the GPA.
An "I" (incomplete) grade may be assigned to a student only if the unfinished part of the student's work is small, the work is unfinished for reasons acceptable to the instructor, and the student's standing in the course is a "B" grade or higher. Incomplete grades can be changed to letter grades only if the incomplete work is made up by the end of the fourth full term beyond the term for which the "I" was assigned. The grade of "I" is permanently retained on the student's record next to the actual grade. For example, if a student submits the completed work after receiving an "I" and has earned a B+ for the course, the grade will appear on the transcript as "IB+." "I" grades are not accepted for thesis research courses (CHEMBIO 990 and 995).
The Program is concerned that the student has an adequate undergraduate background in chemistry, biology and mathematics and that the Program’s core courses adequately prepare students to branch into more specialized fields in chemical biology and to begin independent research. During Year One, students are required to complete four core courses in Chemical Biology: CHEMBIO 501, 601, 502 and 602. Also in Year One, students are required to complete PIBS 503 (research responsibility and ethics) and two terms of CHEMBIO 599 (Chemical Biology Research Rotation). In Year Two, students are required to present their research, usually at the annual Program in Chemical Biology Fall Retreat prior to the beginning of the Fall Term. In addition to the core courses, four other graduate level courses (minimum of 2 credits) are required. Students are expected to take a suite of electives that cover the breadth of Chemical Biology. Students entering with relevant previous graduate credit from other universities may be excused from some of the preceding course requirements by petitioning the Program Director and Operating Committee.
In many cases, students will elect a Research Advisor from one of the labs in which they have rotated; however, there is no compulsion for the students to join the research groups in which they rotate. Fall laboratory rotation projects must be selected by the second week of classes; Winter lab rotation projects are selected in the first week of December. Faculty are not permitted to make rotation commitments to students prior to the Fall Retreat. For the Winter term, that date is the 4th week of November.
In general, 20 hours per week of time spent conducting research in the lab is considered the minimum requirement, although each lab will differ. Additionally, students are encouraged to spend as much of their study time in the laboratory as possible, as this provides students with the greatest exposure to the laboratory culture.
Once a research rotation is complete, students are required to prepare a one-page report that consists of the following sections: introduction, results, discussion, conclusion and references (references are not to be included in the one-page requirement). This report must be prepared independently by the student and submitted to the Program Office by the last day of classes.
1. Completion of the research rotation course (CHEMBIO 599) in two separate labs over the Fall and Winter terms.
The student and the Research Advisor are jointly responsible for following the Program and Graduate School requirements for the Ph.D. degree. The Advisor’s responsibilities begin at the time of his/her agreement to accept the student into his/her group. In addition to supervising the research, the Research Advisor is expected to advise the student on course elections, examinations, independent study pertinent to his/her general development as a scientist and any other matters affecting his/her general progress toward a degree. Faculty are not permitted to make Research Advisor commitments to students prior to the first Monday in April each year.
Students are expected to find a Research Advisor by the beginning of the Spring term of their first year. Under special circumstances the student may choose to rotate during the spring term with the expectation that they will find a Research Advisor by the beginning of the Summer term.
Formation and Function of the Dissertation Committee
The Program requires that a student meet with their Dissertation Committee before being admitted to candidacy. The Dissertation Committee may consult with the student about concerns of his/her development as indicated by his/her course work, seminar participation and performance during examinations and in conducting research.
After being admitted to candidacy, the Dissertation Committee will meet at least once per year in order to assess the progress being made towards completion of the thesis. It is the responsibility of the student to arrange this meeting. Meeting dates should be forwarded to the Program Office so they may be recorded in the student’s permanent file.
Advancing to Candidacy
The Candidacy Examination
The Dissertation Committee will elect a Chair (other than the Research Advisor) before the examination meeting and that Chair will be responsible for the conduct of the exam and to consult with the student’s Research Advisor prior to the exam if needed. The Research Advisor is not a member of the examining committee and does not attend the oral examination.
In preparation for the exam, the student must submit a written proposal to each member of his/her Dissertation Committee at least two weeks before the exam. This is a hard deadline. The proposal must be sufficiently detailed so that the nature of the research problem and the direction of the effort are defined and characterized; however, the proposal is not to exceed ten double-spaced typed pages (not including references) and must be written in an NIH-derived format. The proposal should contain:
The purpose of the Candidacy Exam is to determine if the student is ready to lead their thesis project and if there are areas of knowledge or experimental design that need strengthening in order for the student to succeed. Towards that end, at the Exam the student presents a summary of their research project, no more than 15 slides. This is best accomplished by presenting brief background material that illustrates why the object of study is important and places the specific work by the candidate in context followed by the particular project goals; typically this is presented in Specific Aim format similar to an NIH proposal. Results generated thus far should be presented (and are expected) followed by specific future experimental plans for each project goal. Students can expect questions on the background material in addition to specific questions about the choice of experiments, strategies for data analysis and alternative plans if things do not work as outlined. This Exam should not last longer than 2 hours at which time the committee will provide specific feedback to the student. There are several possible outcomes of the Exam: Pass, Pass with additional requirements, Fail. The Pass with additional requirements typically occurs if it is noted that a student needs to shore up knowledge in a specific area or if a specific aspect of the project needs to be more clearly defined. In such cases, the Committee will ask the student to take a course, identify a collaborator and/or re-write an aspect of their candidacy document. A Failing grade reflects more significant issues and the committee will provide specific recommendations on addressing the concerns. Students who do not pass their exam at the initial taking are able to re-take the exam within a 3-6 month time frame.
Annual Dissertation Meeting
Students in their fourth year of study are required to submit to their dissertation committee a draft timeline that outlines the final experiments, analysis, and writing schedule. This timeline is also submitted to the Program Office.
All additional steps and requirements before, during, and after the dissertation defense can be found within the Rackham Doctoral Degree Resources.
The Final Oral Examination Report should be submitted to Rackham within 48 hours of the exam, but no later than the deadline for the final term of enrollment. The student should confirm with the chair of the Dissertation Committee that the report has been submitted. Any disagreement over the acceptability of a dissertation will be resolved by the Dean of the Graduate School, who will act as final arbiter in consultation with the Dissertation Committee members. The Certificate of Dissertation Committee Approval must be submitted no later than the deadline for the final term of enrollment. As well as completing the pre-defense meeting the candidate must also register with Rackham OARD for a post-defense meeting and complete the final paperwork also before the final deadline for the term. A candidate who fails to submit these materials by the deadline will be required to register for another term and incur tuition charges.
Additional information is available in the Rackham Dissertation Handbook, including defense formatting, what to do if committee members are unable to attend, final submission, and so on.
Before the Defense
After the Defense
Rackham OARD annually publishes the last day to complete and submit all degree requirements without a new registration. If all requirements are not met by the published deadline, a new registration will be required. Candidates must submit final revisions to Rackham OARD.
Please keep in mind that these deadlines are absolute and you will be required to register in the following term if you do not meet them. The deadlines are published on the Rackham website.
Chronology of the Ph.D. Degree
Year One: Fall Term (September - December)
Year One: Winter Term (January - April)
Year One: Spring Term (May - June)
Year One: Summer Term (July - August)
Year Two: Fall Term (September - December)
Year Two: Winter Term (January - April)
Years Three - Five
Students may also receive fellowship support in the form of a Research Fellowship awarded directly to the student by a national agency (e.g., NSF), a research foundation, or the University, awarded on a competitive basis.
Research Assistantships (GSRAs). These appointments are provided by a Research Director from grant funds under their supervision. Specific duties and schedules should be discussed with the Research Advisor.
NSF Fellowships. Applications for nationally awarded NSF Fellowships are submitted electronically using the NSF's Fast-Lane system. Information about these fellowships can be found on the NSF website. All applicants for NSF or other highly competitive national fellowships should notify the Program Director before preparing their application in order to obtain assistance in making the application as competitive as possible.
Rackham Predoctoral Fellowship. These fellowships are available only to students who have achieved candidacy. Recipients must have been formally admitted to candidacy before the Fellowship is to begin. Selection of nominees for the University-wide competition is made by the Chemical Biology Operating Committee . These fellowships are relatively unrestricted and are awarded on the basis of scholastic record and the student's research achievements. For more information on this fellowship, see Rackham's website. Each year, candidate students may request that their Research Advisor nominate them for this fellowship. Final nomination decisions are be made by the Operating Committee.
Shapiro/Malik Awards. These awards were established by Harold T. Shapiro, former President of the University of Michigan and Vivian Shapiro, former faculty member at the University of Michigan, to assist with interest payments on the unsubsidized educational loans that students are obliged to pay while still in graduate school. Dr. John Malik, a devoted Rackham alumnus in Physics, established an endowment for the same purpose. Both awards are made through a single competition. Students who have unsubsidized educational loans in excess of $10,000 are given priority. For more information on this fellowship, see Rackham's website.
Travel Grant. The Rackham Graduate School provides up to $600 for travel to present a poster or a lecture at domestic professional conferences and meetings ($700 - $1,100 for international conferences). Students may only receive one travel grant per fiscal year (July 1 - June 30). Due to strict deadlines and the rapidity with which travel grant funds are depleted, students are encouraged to apply for this funding several months in advance. For more information on travel grants, please see Rackham's website.
Graduate Student Instructorships (GSIs). Students who are interested in teaching in a given semester may request teaching assignments in the various departments that have undergraduate courses; however, positions are not guaranteed for Chemical Biology students. This appointment is made to qualified Chemical Biology graduate students who have an aptitude and interest in teaching. The conditions of this appointment are governed by the agreement which exists between the Graduate Employees Organization (GEO) and the University. The standard half-time appointment calls for an average of eight contact hours per week and up to 20 hours per week for all teaching-related activities. This time commitment includes, in addition to classroom contact hours, preparation, grading, attendance at staff meetings, office hours and other similar duties. All Graduate Student Instructors who teach chemistry courses are required to attend a Chemistry Department GSI training program, which occurs once per year in August. All international students who wish to teach chemistry courses are required to complete a 3-week acculturation training course given in August (or May for eligible students) in addition to attending the chemistry GSI training. GSIs who teach courses in other departments must meet the specific training requirements of that department. Students will receive the same stipend amount per term regardless of whether or not they decide to teach. Students are only allowed to hold a GSI position in their fifth year with the approval of the Operating Committee.
The university maintains a system of certifying the percentage of effort to demonstrate to the university's sponsoring partners that the sponsor did in fact receive the level of effort committed through the award process.
Effort certification is completed in Wolverine Access. Students who are unable to complete the process on-line should contact the program for paper certification.
Stipend Payment Schedules
Income Tax Liability
The Chemistry Department has a number of technical services, including shops for the fabrication and repair of electronic instruments, glassblowing, and computer support. NMR, mass spectrometry, EPR, elemental analysis, small-molecule X-ray crystallography and other analytical instruments are available for either hands-on use (after training) or as a service. Extensive descriptions can be found on the Chemistry Department website.
The Medical School maintains a number of core facilities that offer important analytical services. The Biomedical Research Core Facilities include separate facilities devoted to DNA sequencing, flow cytometry, transgenic animals, NMR and protein analyses (mass spectroscopy, sequencing, amino acid analysis, etc.). For details, see the Core Facilities website. The Comprehensive Cancer Center maintains an Affymetrix and cDNA Microarray Core Facility. The Department of Pharmacology has established a Biomedical Mass Spectrometry Facility.
The Life Sciences Institute (LSI) operates the Center for Structural Biology, which has facilities for the determination of the structures of macromolecules by X-ray diffraction. The LSI also operates the Center for Chemical Genomics, which has facilities for high-throughput screening of small molecule libraries, protein production, automated cloning and protein expression and high-throughput macromolecular crystallization. For more information on these, see the LSI's website.
A number of departments and research groups maintain their own computer resources. Beyond these, campus-wide computing facilities and resources are available.
The University library system has a very large collection of scientific journals (both print and on-line), books and databases to support research in Chemical biology.
Emergency and Safety Regulations/Emergency Telephone Numbers