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Curriculum

Courses

The curriculum consists of several components: the core course requirements, the general seminar requirements, and elective courses.  The goal is to provide a curriculum that is balanced in breadth and depth. The breadth is provided by the core course requirements. The depth is provided by elective courses chosen by the student in consultation with his/her advisor. Some elective courses are listed below; however, the list is by no means exhaustive.  The School requires an academic load of 16 hours per semester.

Core Curriculum

Fall Semester 2018

  • IND 408 - Advanced Biochemistry - 5 credits
  • IND 431 - Foundations in Modern Biology I - 5 Credits
  • BPH 592 - Special Topics in Molecular Biology1 - 1 Credit
  • IND 501 - Ethics & Professional Integrity in Research - 1 Credit
  • BPH 571 - Biophysics Seminar - 1 Credit
  • BPH 595 - Ph.D. Research (Rotation)2

Total - 16 Credits

Spring Semester 2019

  • IND 432 - Foundations in Modern Biology II - 5 Credits
  • BPH 509 - Molecular Biophysics - 5 Credits
  • BPH 572 - Biophysics Seminar - 1 Credit
  • BPH 595 - Ph.D. Research (Rotations) - 5 Credits

Total - 16 Credits

1. Offered for students requiring remedial training in molecular biology in preparation for IND 410 (Spring)

2. Credit hours will be determined based on other courses taken in this semester.

Subsequent Semesters

  • BPH 411 - Methods in Structural Biology - 5 credits
  • BPH 567 - Writing Proposals in BPH - 1 credit
  • BPH 571, 572 Biophysics Seminars [each semester] -  1 credit
  •  Elective course(s) – consult with advisor

Elective Courses

A total of at least 24 graduate course credit hours must be accumulated before taking the Qualifying Examination.  These credits are fulfilled by the required courses of the program (IND 408, 431, 432, BPH 411, 509, 567).  Additional elective courses may be taken at your discretion with the consent of the advisor. Any graduate course offered by the University of Rochester may be used as an elective provided it is appropriate to your area of research.  Some of the courses listed below provide the fundamental background that is commonly needed for biophysics students; however, this list is by no means exhaustive and the student is advised to check the availability of courses in any given year or years because course offerings may change.  See the Appendix for course descriptions.

Partial list of electives

Fall Semester Courses (credit hours)
  • BIO 402 - Molecular Biology (4)                                                          
  • BPH 592 - Special Topics in Biophysics – Math for Molecular Biophysics (credit to be arranged)
  • CHM 423 - NMR Spectroscopy (2)
  • CHM 451 - Quantum Chemistry I (4)
  • CHM 469 - Computational Chemistry (4)
  • MBI 473 - Immunology (3)                                                                    
  • NSC 512 - Cellular Neuroscience (5)                                                     
  • PHP 403          Human Cell Physiology (4)
Spring Semester Courses (credit hours)
  • BCH 412         Advanced Topics in Biological Macromolecules (5)           
  • BME 442        Microbiomechanics (2)
  • CHM 414        Biological Inorganic Chemistry (4)
  • CHM 416        X-ray Crystallography (2)
  • CHM 440        Bioorganic Chemistry (4) (even numbered years)
  • IND 443          Eukaryotic Gene Regulation (4)
  • IND 447          Signal Transduction (4)

Suggested Progress Toward the Ph.D. in Biophysics

First Year

  • Fall Semester:  Course work as indicated, one laboratory rotation
  • Spring Semester:  Course work as indicated, two laboratory rotations
  • End of May:  Choose paper for first year exam
  • Beginning of June: Take first year preliminary exam
  • Middle of June:  Choose laboratory and begin Ph.D. research

Second Year

Fall Semester

  • No later than September 30th, submit a list of proposed members of Thesis Advisory Committee to the Department Office for approval
  • Write thesis proposal outline and meet with Thesis Advisor to discuss it
  • Take required course(s), elective(s), plus research credit

Spring Semester

  • Take BPH 567, Proposal Writing
  • Complete course work and finish required courses (BPH 411 or BPH 509) 
  • Present first Student Seminar
  • Meet with Thesis Advisory Committee for first Research Review
  • Prepare for Qualifying Examination

Note:  Students generally complete the Teaching Assistantship (TA) assignment in the second year of studies (see Section III F).

Third Year

  • Qualifying Examination should be taken before the start of the fifth semester of studies by October 1st (see Section IV).

Note:  Students entering the program with an M.S. degree are encouraged to accelerate their examination schedule.

Other Educational Opportunities

Departmental Seminars

The Department of Biochemistry & Biophysics, other departments in the School of Medicine & Dentistry and in the College sponsor seminar series with outside speakers.  While not considered formal courses with associated credit, these seminars are an important part of the graduate student experience, which aims to provide a broad and diverse background of biology for those with quantitative backgrounds.  Every effort must be made to attend and participate whenever possible.

BSCB Program Retreat - (Annual) 

The BSCB program holds an annual retreat using a Gordon Conference format.  It is a one-day event that starts with breakfast, includes lunch, and ends before dinner.  Speakers are senior graduate students, postdoctoral fellows, and faculty.  A poster session is also included and students are encouraged to participate.  All graduate students are invited and expected to attend.

Bioinformatics Cluster

For students interested in computational biology, it is strongly encouraged that they attend the monthly Bioinformatics Cluster meeting.  These meetings generally occur on the second Thursday of the month at 11:30 am for seminars by intramural and extramural speakers.

Exemptions from Course Requirements

Entering students who wish exemptions from core courses may request that the Director of Graduate Studies arrange an exemption interview to determine whether an exemption is appropriate. The exemption interview consists of a 30-60 minute discussion with the course director who will ask questions based on the content of the course under consideration. The course director will then advise the student, the student’s advisor(s) and the Graduate Studies Director, whether or not the course needs to be taken.

Requests for exemption for BPH 567 (Proposal Writing) will be reviewed by the Education Committee.  The critique written for the First Year Preliminary Exam, if high enough in quality, is one means of exemption and the final decision rests on the recommendation by the chair of the exam.  If the student has written a research proposal previously, that proposal may be submitted for review by the Education Committee as a basis for exemption.

Minimum Course Performance

If a student in the program receives one grade of “C” or below, s/he will be reviewed by the Program faculty.  A recommendation will be made to the dean that may include termination from the program. Note; two C grades are automatic grounds for expulsion from the Program by the dean’s office.  If the student is allowed to remain in the program with one “C,” the course (or an appropriate substitute) must be re-taken successfully with a final grade of B- or higher.

Students encountering difficulties in coursework should immediately seek the advice of the course director and/or faculty advisor. Personal tutoring by advanced graduate students can be arranged by the Graduate Studies Coordinator.

M.D./Ph.D. Students

Students in the M.D./Ph.D. program who are considering a Ph.D. in Biophysics are encouraged to meet with the Biophysics Program Director and potential thesis mentors as early as possible but no later than the middle of the second year of the M.D. program.

Curriculum

All M.D./Ph.D. students in the Biophysics program must complete the following courses:

  • BPH 411 - Methods in Structural Biology - 5 Credits
  • BPH 509 - Molecular Biophysics - 5 Credits
  • IND 501 - Ethics & Professional Integrity in Research - 1 Credit
  • BPH 571,572  Biophysics Seminar (each semester) - 1 Credit
  • BPH 595 - Ph.D. research (each semester)

Elective Course

At least one elective course must be taken.  The Ph.D. advisor and Program Director must approve this choice. Recommended courses are listed below:

  • IND 408 - Advanced Biochemistry - 5 Credits
  • BCH 412 - Advanced Topics in Biological Macromolecules - 5 Credits
  • IND 431 - Foundations in Modern Biology I - 5
  • IND 432 - Foundations in Modern Biology II - 5

Other Requirements

Two research rotations should be conducted prior to joining a laboratory for dissertation research. Students are encouraged to complete these rotations during the first two years of the M.D. program.

The qualifying examination must be completed by the end of the second year of Ph.D. studies.

The teaching assistant requirement is waived.

At least one meeting per year must be held with the thesis advisory committee (normally held after the student’s Biophysics Seminar presentation).

A satisfactory thesis must be written and successfully defended.  Details of these requirements are given elsewhere in this handbook.