Ph.D. in in Biochemistry & Biophysics

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Requirements

The Biochemistry & Biophysics Core courses are to be completed during the first two years of the program. The three required Core courses are:

  • BCH 581: Physical Biochemistry (3 cr)
  • BCH 582: Proteins and Enzymes (3 cr)
  • BCH 584: Nucleic Acids (3 cr)

All students are also expected to complete a research ethics course during the spring semester of their first year:

  • BMED 605: Biomedical Research Ethics

All students will do rotations in two different laboratories, one in the fall semester and one in the spring semester of their first year. It is expected that the rotations will aid the student in choosing a research advisor. Rotations are an opportunity for graduate students to test out laboratories without a firm commitment on the part of either the student or the advisor that dissertation research will be carried out in that lab. During the week before classes in the fall, students will have an opportunity to become acquainted with the research of Biochemistry Program faculty and are expected to choose a rotation advisor by the end of the first week of the Autumn Semester. During the rotation, all students must register for 1 credit hour of BCH 570: Introduction to Research. The fall and spring rotations must last at least 8 weeks, but can last the whole semester, if such an arrangement is agreeable to both the advisor and the student. At the end of each semester, a report will be submitted to the rotation advisor. A public talk based on the rotations will be presented to Biochemistry Program faculty and students (this is typically done as part of BCH 547).

Course work for Biochemistry & Biophysics graduate students is determined by the Advisory Committee. The minimum coursework requirement is the three Core courses and one 3 credit hour elective. A list of approved electives is provided below. Other electives may be substituted, if appropriate, with the approval of the student’s Advisory Committee. All course work will normally be completed during the first two years of graduate study.

Approved electives:

  • BCH 486: Biochemistry Lab (3 cr.)
  • BCH/CHMY 595: Biophotonics (3 cr.)
  • BCH 595: NMR Spectroscopy (3 cr.)
  • BCH 600: Cell Organization & Mechanisms (3 cr)
  • CSCI 558: Introduction to Bioinformatics (3 cr.)
  • CHMY 562: Organic Structure and Mechanism (3 cr.)
  • CHMY 569/BMED 621: Medicinal Chemistry (3 cr.)
  • BMED 615: Molecular Pharmacology (3 cr.)
  • BMED 661: Neuroscience I (4 cr.).
  • BMED 667: Neurobiology and Biophysics (3 cr.)

Other courses that may be useful but do not count for the elective requirement are:

  • BCH 561: RNA Structure and Function (1 cr.)
  • CHMY 580: Fluorescence Spectroscopy (1 cr.)
  • BIOB 596: Topics in Virology (1 cr.)

All students are expected to register for Seminar (BCH 694) every semester that they are in residence. Participation in Data Club (BCH 547) is also expected.

The Graduate School requires that all graduate students supported as Teaching Assistants or Research Assistants register for a minimum of 6 credit hours. The Teaching Assistantship tuition waiver covers up to 9 credit hours. In the first year, students take courses, seminar, data club and rotations to reach this limit. In subsequent years, courses, seminar, data club and research are used to reach the 6 credit hour minimum. PhD students must complete a total of 60 credit hours.

All students are expected to choose a Research Advisor and form an Advisory Committee by the end of the spring semester of the first year in residence. The students should formalize their arrangements by submitting a completed Advisory Committee form, available on the Biochemistry program website, to the administrative associate/program coordinator (Andrew Ranck). The administrative associate will deposit the form in the student’s permanent file and submit the committee composition to the Graduate School.

For the PhD, the Advisory Committee will have 4 faculty members in addition to the Research Advisor. At least one member should not be in the home department of the Research Advisor. At the first meeting of the Advisory Committee, a Committee Chair will be selected. The Research Advisor cannot be the Committee Chair.

Each year by the first day of the spring semester, a student will submit a report to their committee members and to the administrative associate/program coordinator (Andrew Ranck). The administrative associate will deposit the report in the student’s permanent file.  The report should be prepared using the current template on the Biochemistry program web site.

A student will also schedule at least one committee meeting every 12 months. Following the meeting, the Committee Chair will write a brief memo summarizing the student’s progress and indicating whether or not the student is in Good Standing. The Committee Chair will forward a copy of the memo to the student and to the administrative associate/program coordinator (Andrew Ranck), who will deposit the report in the student’s permanent file. In the first year before the student selects a research advisor, the GEC will serve as the student’s committee, and the Chair of the GEC will act as the Committee Chair.

The Biochemistry & Biophysics GEC will annually review each student’s progress on the basis of the documentation in the student’s file. The GEC will write a brief memo regarding the student’s progress and their standing in the program and send it to the student, the committee members and the administrative associate/program coordinator (Andrew Ranck), who will add this memo to the student’s file.

To be in Good Standing, a graduate student must:

  • Maintain a GPA of 3.0 or higher. If the GPA falls below 3.0 at the end of a semester, the student will meet with the Advisory Committee (GEC in the first year) before the beginning of the next semester. The Committee Chair (Chair of the GEC in the first year) will write a memo to the student defining the strategy and timeline for raising the GPA to 3.0. A copy of this memo will be placed in the student’s permanent file. If a student’s GPA remains below 3.0 for more than one semester, the program will recommend to the Graduate School that the student be dismissed from the program.
  • Exhibit competency in their role as a Teaching Assistant. Quality of teaching will be assessed by student evaluations and input from the professor in charge of the course.
  • Identify a research advisor by the end of the spring semester of their first academic year. Failure to have an advisor will affect the student’s financial support and may lead to dismissal from the program.
  • Pass the Out-of-Field Proposal examination by the end of the autumn semester of their third year and defend the Dissertation Proposal by the end of the spring semester of their third year.
  • Make clear and substantive progress in their dissertation research, as judged by their Research Advisor and Advisory Committee at the time of their annual meeting. If research progress is insufficient, the Committee Chair will outline in the memo following the annual meeting the corrective measures the student must take to show substantive progress in their research. This memo will be placed in the student’s permanent file and a copy will be forwarded to the Graduate School by the administrative associate/program coordinator (Andrew Ranck). Students not making substantive research progress will meet with their committee six months after the annual meeting. If there is not adequate improvement in research progress, as judged by their Research Advisor and Advisory Committee, the GEC will recommend to the Graduate School that the student be dismissed from the program.

The Out-of-Field Proposal examination will typically be completed no later than the autumn semester of the third year. Students will prepare an original research proposal following NIH format (Specific Aims, Significance, Innovation, Approach, References). The proposed research must not be directly related to the student’s thesis project. In particular:

  1. The research system must be distinct from the system the student is using in their dissertation research.
  2. The approach used to study the system cannot be the same as the approach being used in the dissertation research.
  3. The body of literature necessary to design the research must be different from that of the dissertation research.

Students will present a concise outline of one possible research proposal to the Advisory Committee (no more than 500 words). If the proposal grows out of a mini-proposal done in a graduate course, the student must provide the mini-proposal to the committee and in the outline explain in detail how the current proposal will extend the aims of the mini-proposal. The topic for the out-of-field proposal will be finalized at a meeting with the Advisory Committee. It is expected that the Advisory Committee will give the student pertinent advice regarding their expectations at this meeting. The student will provide a written proposal to the Chair of the Advisory Committee no more than eight weeks after the meeting where the topic is finalized.

The written proposal will be no more than 12 pages single-spaced (NIH margins and font style, excluding references). The student should also provide a half page single-spaced Project Summary that concisely outlines the biological importance of the work, the important scientific hypotheses to be tested and the specific aims that will address the hypotheses. An NIH style Biographical Sketch should also be included. The committee members will provide written feedback to the student, within ten days, in the format of an NIH review. The Committee Chair will include a cover memo for the committee reviews, which indicates the outcome of the written portion of the exam. Copies of this memo and the committee critiques will be placed in the student’s permanent file. If the committee judges that the written proposal is satisfactory, the student has passed the written portion of the comprehensive exam and proceeds to the oral component of the exam. If the committee consensus is that the written proposal is unsatisfactory, the student fails the comprehensive exam. If the written proposal is found to be potentially defensible, but contains significant flaws, the oral part of the exam will be postponed and the student may be permitted one revision of the written proposal, which must be provided to the committee within 4 weeks.

The oral part of the exam will take place no later than two weeks after the student passes the written part of the exam and has received the committee reviews. The first part of the oral exam will be a concise (15 – 20 min.) presentation to the committee which will include responses to the written critiques. In the second part of the oral exam, the student will be questioned by the committee. Students can expect:

  1. Questions on the feasibility of proposed work and questions assessing their understanding of the content of the proposal and methods used to carry out the proposed work.
  2. Questions that test the student’s working knowledge in their field, which may include material derived from the Core and elective courses, may also be expected.

The Committee Chair will moderate the oral exam and keep the exam to three hours or less. Passing the Out-of-Field Proposal Exam constitutes advancement to PhD candidacy. Thus, a student’s research progress will also be considered at this  time. At the completion of the oral part of the exam, the student’s Advisory Committee can Pass, Fail, or ask that a student do additional work and repeat the oral part of the exam at a later date (no sooner than one month and no later than two months after the original exam date). If a student fails the Out-of-Field Proposal exam at either the written or oral stage the program may recommend to the Graduate School that the student be dismissed from the program. At the discretion of the Advisory Committee, the program may also recommend to the Graduate School that the student be transferred to the MS program. The Committee Chair will write a memo to the student indicating the outcome of the Oral part of the exam. A copy of this memo will be placed in the student’s permanent file. Students who pass the Out-of-Field Exam will be advanced to PhD candidacy. The Committee Chair will file the appropriate paperwork with the Graduate School.

The PhD student must write and defend a doctoral dissertation, which describes original scientific research performed by the student and developed by the student with input from the Research Advisor or Research Director. The Research Advisor or Academic Advisor along with the Advisory Committee determine the length and content of the dissertation. The PhD requires demonstrating proficiency in the scientific method, mastery of the current state of knowledge in the field of study, and a substantive new contribution to the body of either knowledge or methodology in the field of study. The student must demonstrate a rigorous comprehension of the principles and current techniques in the field of study, a thorough understanding of  scientific data and error analyses, an appreciation of academic and scientific ethics, and a competence in scientific writing and presentation. These elements should be embedded in the written Dissertation Proposal required for the Dissertation Proposal Exam.

The Dissertation Proposal Exam should be completed no later than the spring semester of the third year. Students will prepare both a written document and an oral presentation on their proposed dissertation project. The written document must be provided to the Advisory Committee one week before the oral presentation. Students will be expected to provide background on the project that explains the current state of the field. In explaining the rationale for their research project, they will be expected to explain where there are weaknesses or gaps in the current state of knowledge in their field. The remainder of the Dissertation Proposal (10 to 25 pages including references) will focus on preliminary results obtained by the student to this point, and experimental design and implementation for planned experiments. In particular, an outline of the specific questions the proposal will address, the methods and experiments to be used to achieve these goals and a discussion of the likely outcome of the experiments should be presented. The Dissertation Proposal should define the expected scope of the Dissertation research. The scope of the project defined in the Dissertation Proposal should be such that the PhD degree can be completed in approximately 5 years. The Advisory Committee will expect the student to be fluent in the science surrounding the Dissertation Proposal. The Advisory Committee may Pass the student. The Advisory Committee may ask for written revisions followed by a second oral discussion of the Dissertation Proposal (within four weeks). If the Advisory Committee judges that the student’s Dissertation Proposal and their fluency in the science surrounding the Dissertation Proposal are beyond remediation, the program will recommend to the Graduate School that the student be dismissed from the program. After the oral presentation of the Dissertation Proposal, the Committee Chair will write a memo to the student indicating the outcome of the Dissertation Proposal. A copy of this memo will be placed in the student’s permanent file.

First Year

Core Courses
Autumn Semester (odd years)
  • BCH 584: Nucleic Acids (3 cr)

  • BCH 570: Intro to Research (1 cr)
Autumn Semester (even years)

  • BCH 582: Proteins and Enzymes (4 cr)

  • BCH 570: Intro to Research (1 cr)
Spring Semester (even years)

No core courses offered

Spring Semester (odd years)

BCH 581: Physical Biochemistry (3 cr)

Other Requirements
  • Seminar (BCH 694, 1 cr) both semesters
  • Data Club (BCH 547, 1 cr) both semesters
  • Other coursework as appropriate. Research Assistants and Teaching Assistants must enroll for at least 6 cr, but no more than 9 cr each semester

Second Year

Core Courses
Autumn Semester (even years)

BCH 582: Proteins and Enzymes (3 cr)

Autumn Semester (odd years)

BCH 584: Nucleic Acids (3 cr)

Spring Semester (odd years)

BCH 581: Physical Biochemistry (3 cr)

Spring Semester (even years)

No core courses offered

Other Requirements
Elective courses as appropriate
  • Seminar (BCH 694,1 cr) both semesters
  • Data Club (BCH 547, 1 cr) both semesters
  • Research (BCH 597) both semesters to reach at least 6 cr, but no more than 9 cr each semester

Third Year

  • Elective courses as appropriate
  • Seminar (BCH 694, 1 cr) both semesters
  • Data Club (BCH 547, 1 cr) both semesters
  • Research (BCH 597) both semesters to reach at least 6 cr but no more than 9 cr each semester
  • Out-of-field and Dissertation proposals must be completed

From this point until Dissertation Defense

  • Seminar (BCH 694, 1 cr) both semesters
  • Data Club (BCH 547, 1 cr) both semesters
  • Research (BCH 597) both semesters to reach at least 6 cr but no more than 9 cr each semester

Forms