Additional Details of Procedures and Requirements

Each first-year student will be assigned a faculty advisor for the first year, based on the student’s expressed interests (if possible). This will be done by the Graduate Studies Coordinator in consultation with the Education Chair. Students should meet with the advisor frequently (monthly is desirable) and should consult with him/her about research rotation choices, coursework, and any other questions or problems that they encounter. The faculty advisor will be formally responsible for advising the student until s/he has selected a Thesis Advisor.

All first-year students are required to complete three laboratory rotations during the first year. Laboratory rotations in three different laboratories are required but additional rotations can be taken. Additional rotations will take place either in the summer prior to entering the program or in the summer following the first academic year. Prior to the completion of three different rotations, two consecutive rotations in the same laboratory will not be allowed.

At the beginning of the academic year, faculty members will present short (20-30 min) informal lectures to the incoming students to describe their research activities. The goals of this series are to acquaint students with ongoing research in the BSCB Program and to alert them to opportunities for their laboratory rotations and future Ph.D. research. Attendance at these lectures is strongly encouraged. At the end of this series of presentations, students are expected to sign up for laboratory rotations by submitting a list of three choices to the Graduate Studies Coordinator. Before selecting laboratory choices for any rotation, a student must meet with his or her advisor to discuss choices for laboratory rotations and the advisor must sign off on the student's list. At a minimum, one rotation must be in the laboratory of a faculty member who is a member of the BSCB Program. Near the end of the first and second rotations, students should submit their three choices for the subsequent  rotation to the Graduate Studies Coordinator. Again, the rotation choices must be approved by the acting advisor. Subsequent rotations may be conducted in any active research laboratory in the Program (including laboratories in the Chemistry or Biology departments), or in other  laboratories in the Medical Center. Every effort will be made to accommodate the students' choices. Students are expected to satisfactorily complete three projects in three different laboratories representing more than one area of interest before requesting assignment to a laboratory in which their Ph.D. research project will be completed.

Students will be evaluated at the end of each rotation period. The written evaluations will be kept in the Department’s files and a copy will be sent  to the dean’s office. These evaluations will also be used to fulfill the progress report requirement in the first year (see below).

PLEASE NOTE: Graduate students are expected to be in residence, working in laboratory rotations, during semester, fall and spring “breaks” listed on the University (undergraduate) academic calendar. The Graduate School calendar is included in the Appendix.

All students must pass Health Physics Radiation Safety tests 1 and 2 by December 1 of their first year in order to qualify as an Authorized User of Radioisotopes. A lecture and information regarding these tests will be presented at Orientation. Radiation certification does not count toward the 30 hours of course credit necessary for the Ph.D.

The objectives of the Biophysics seminar series are multifold. These include: gaining experience in the organization of research data, the interpretation of data, synthesis of information from diverse sources into a testable model or hypothesis, and presentation of original information to a broad audience of scientific colleagues with diverse experimental and theoretical backgrounds. Such seminars are intended to provide valuable preparation for a scientific career in academic or industrial settings. Therefore, BSCB students will be required to present a yearly seminar in the student series beginning in the second year of study. Thesis Committee meetings should be conducted immediately after the student’s seminar (pending committee member availability). Otherwise, the meeting must take place within one month of the student’s seminar date or before June 1, whichever comes first.

All students will register for the student seminar series each semester: BPH 571 (Fall) and BPH 572 (Spring). Each student is expected to ask at least two questions per semester. Credit will be awarded for presentation of a seminar in the series (once a year, beginning in the second year) and for attendance at ≥75% of the seminars in each semester (every year). Students are required to demonstrate their attendance by signing the list of attendees prior to the commencement of class; this record of attendance will be checked weekly throughout the semester. If a student fails to attend 75% of the student seminars in a given semester, s/he must write a 750-word summary for every missed student seminar that places him or her below the mandatory attendance level. The seminar assigned as the subject of the 750-word summary will be that from Departmental seminar series held Wednesday at 2 pm. Other seminars can be substituted with approval from the BPH 571/2 course directors (Prof. Paul Boutz & Eric Phizicky).

During the course of their studies, students will be required to make at least six seminar and/or poster presentations. Presentations at the Student Seminar Series or in another approved seminar course will fulfill this requirement. University poster sessions and other scientific  meetings may also fulfill the requirement with the approval of the Education Chair. An abstract or outline of each presentation is required for the  file in the Department Office.

In April, the Graduate Studies Director and Education Chair will meet formally with students to discuss the expectations for performance on the examination. Student will be given a list of articles selected by Program faculty and screened by the Education Chair for suitability based on the purpose of the examination, and for variety in subject matter. The student will request to be assigned one of the articles for the examination. Each article may be used by only one student; conflicts arising will be resolved by the Education Chair.

By Friday at noon, the student must indicate in writing to the Department Office which of the articles s/he has chosen to serve as the basis of the examination. Within 14 days following article selection, the student must submit to the Graduate Studies Coordinator, or proxy thereof, a carefully written document, comprising 10-15 double-spaced, typewritten pages (excluding cover page, figures, tables, schemes, references and title page that must include a title, the student’s name, exam date, time and exam location), font 11pt. Arial or 12 pt. Times New Roman with 1” margins on all sides. This document must be sent via email as a PDF with the subject line in the format of Last Name – 1st Year Exam Proposal. The proposal should comprise the following four sections:

0. Cover page (not included in page limitations) with name of student, exam date and time, exam location, and citation of article. Do not exceed one page.
1. Questions addressed by the article, i.e. What questions does the article try to answer and how significant are they? What hypotheses are being tested? This section should be approximately 1-2 pages.
2. Critical appraisal of the article, i.e. How effective is the article in answering the questions posed? Do the results support the conclusions? This section should not exceed 1-2 pages.
3. Proposal for additional research, i.e. What additional work needs to be done (if any), or what interesting questions can be pursued on the basis of what has been learned from this article? This section should be substantial with specific expectations for success or failure, including alternative approaches if the primary experimental plan does not succeed. This should be the longest section.
4. References (not included in page limitations). Any reference style can be used, but it should include the complete reference title and all authors (up to 6).

These sections are to be as specific and as comprehensive as the length restriction allows. Each page should be numbered in the page footer. The student should understand that there will be an opportunity to expand on any aspect of the document during the oral part of the examination. The examination anticipates the application of all information and understanding gained in graduate course work as well as undergraduate background, or other research experience. Note; late submission of an exam will result in the deduction of 1 point per day from the written-exam score, which is rated on a 10 point scale. Here, a day means any day of the week with no special consideration of weekends or holidays; as such, every late day is a 1 point deduction from the committees average score on the written exam. Only the Graduate Studies Coordinator or Program Director can allow extensions. Such requests must be requested in writing at least 24 h prior to the submission deadline.

First Year Examination Rules

Each first-year student will be asked to analyze independently a paper s/he has selected from the set of papers recommended by the faculty. In order to maintain a uniform policy with regard to responding to questions that may be posed by first-year students preparing for the exam, the BSCB Program requires that faculty, graduate students, post-doctoral trainees, and scientific technicians abide by the following pre-exam preparation guidelines:

1. It is appropriate to answer questions that are directed to understanding technique or theory.
2. It is appropriate to suggest additional references if you know of either helpful basic texts or review articles.
3. It is inappropriate to offer an opinion on the quality or defects of the paper chosen by the student or to answer a question such as “What experiment would you do next?”
4. It is inappropriate to read and criticize a draft of the student’s paper before the exam date.

NOTE: Students should be very careful to develop their own analysis of the chosen work and to express it in their own words. Reiterating the analysis of others (without proper citation) either in paraphrase or verbatim from published works is considered plagiarism and is a very serious offense that may lead to dismissal from the University. The policy on plagiarism is detailed in Section VII of this handbook. Also see Section X of this handbook on the use of Artificial Intelligence.

The written document, together with a copy of the selected article, will be distributed to the members of the examining committee. This committee will comprise three members chosen by the Graduate Studies Director or Education Chair: the faculty member submitting the selected article and two other members of the BSCB Program with at least peripheral knowledge of the topic.

Approximately 1-2 weeks after submission of the document, the student will have an oral examination before this committee. The oral examination will start with a 20 min presentation by the student, during which the student presents and explains his/her analysis of the selected article, keeping in mind that the committee consists of experienced and knowledgeable scientists who are not necessarily experts in the research area of the selected article but who have read and evaluated both the selected article as well as the student's written document. The balance of the examination will be devoted mainly to questions raised by the committee.

The examining committee assesses the student's performance with respect to five criteria:

1. the student's ability to evaluate published research critically and fairly.
2. the student's ability to draw upon graduate course work to analyze the research.
3. the student's creativity in suggesting new and justified research to improve and/or extend the study.
4. the strength of the content and the clarity of the writing of the submitted document.
5. the ability of the student to defend, modify or extend their written document during oral questioning.

At the end of this oral examination, the committee meets in a closed session to evaluate the student's performance and to arrive at a consensus about the student's performance. Included in that evaluation will be whether or not the quality of the written document is sufficient to warrant exemption from the required course on Proposal Writing. At the end of this session, the committee chairperson will discuss with the student the strengths and weaknesses found in the examination, and will inform the student of the intended recommendation (pass or fail) to the Steering Committee. The chairperson cannot tell the student at this time whether or not s/he will be able to continue in the program, which is based on additional factors.

Soon after all the first-year oral examinations have been completed, the Biophysics Program Steering Committee will meet to hear the reports from the examining committees and to examine the records (course work, rotation evaluations, etc.) of each student. Based on these discussions, the Steering Committee will determine whether a student should remain in the program, be re-examined on a new paper (by the same preliminary exam committee or by a different one), or in unusual cases, leave the program. The decision of the Steering Committee will be reported to the students as quickly as feasible by the Director of Graduate Studies.

Student teaching is viewed as an integral part of student learning, both as a means of consolidating one’s own knowledge and as a means of learning how to convey effectively that knowledge to others. Each (non-M.D./Ph.D.) biophysics student is required to act as a teaching assistant for at least one semester. Usually, this will be during the second year.

After completing three research rotations (usually at the end of May), passing all courses (as stated above), and successfully passing the first-year examination, students may submit in writing their choice for thesis advisor to the Graduate Studies Coordinator. Every attempt will be made to place students in their first-choice laboratory, but limitations of space and funding may, in some cases, make it necessary to assign a student to a second choice. If a student does not feel prepared to choose a thesis advisor at this time, s/he may elect to do an additional rotation in the summer after the first year. Final choices of thesis advisor are subject to the approval of the Steering Committee of the BSCB Program.

The research advisors currently in the BSCB program are: Andrew Berger, Paul Boutz, Kara Bren, Regine Choe, Mark Dumont, Dmitri Ermolenko, Sina Ghaemmaghami, Alan Grossfield, Jeffrey Hayes, Paul Kammermeier, Clara Kielkopf, Todd Krauss, David MacLean, Lynne Maquat, David Mathews, David McCamant, James McGrath, Anne Meyer, Benjamin Miller, Joshua Munger, Mitchell O’Connell, Eric Phizicky, Lewis Rothberg, Gaurav Sharma, Juilee Thakar, Eric Wagner, Rick Waugh, Joseph Wedekind, Andrew White, Axel Wismüller and David Yule.

The BSCB program provides a broad array of opportunities for graduate education in the areas of biophysics, structural biology, and computational biology. Students in the BSCB program are free to choose any of the faculty advisors within the BSCB program as their Ph.D. advisor. In the unusual situation where a student wishes to select a thesis advisor who is not a member of the BSCB Program, the student  formally has two options. First, the student may request to join the degree program of the intended thesis advisor. That program must approve the request of the student. In this situation, the student would no longer be capable of pursuing a Ph.D. in Biophysics. A second option is to appoint the chosen advisor to the BSCB program as a member. This process requires formal approval by the steering committee and the existing BSCB members. Under these circumstances, the student may remain in the BSCB program under the supervision of the chosen advisor.

Conditions under which a thesis advisor can resign. A faculty advisor may resign as the advisor of a student because they believe that the student’s performance or behavior is unsatisfactory or because of incompatibility between the advisor and the student. Before asking the student to leave his or her laboratory, the advisor should discuss the problem with the student and must discuss the problem with the Director of the BSCB Program and the Dean of Graduate Studies and Postdoctoral affairs to obtain approval. The Director will consult with the members of the Steering Committee to obtain approval. The purpose of this consultation is to seek a resolution to the issue(s) that are leading to the advisor resigning. The student must be given 60 days warning in writing before termination of the student stipend. The student may attempt to find a new research advisor during this period; if a BSCB advisor is found, the student will be allowed to remain in the program.

Following selection of the research advisor, the student's thesis advisory committee is selected. The thesis advisory committee performs several functions. The thesis advisory committee serves the student by providing additional mentoring to that provided by the thesis advisor. It could help the student choose specific elective courses in preparation for the chosen field of research. It provides advisory input during the development of the thesis research project with respect to scientific merit, techniques and methodology, relevant literature, etc. It gives final approval of the specific program presented for the thesis topic to be developed. The members (other than the thesis advisor), along with a faculty member selected by the BSCB Education Chair, serve on the committee for the Qualifying Examination. Finally, the student’s chosen committee members, along with a representative appointed by the Dean's Office, compose the examining committee for the final thesis defense. By September 30th of the second year, the student and the research advisor must submit a list of suggested committee members to the program administrator. The Program Director must approve this thesis advisory committee.

The thesis advisory committee must have a minimum of four members, including the thesis advisor, at least one member who is a faculty member in the Biophysics Program, one faculty member of the “primary” faculty in the Department of Biochemistry and Biophysics who is also a mentor in the BSCB program (see appendix), one faculty member from “outside” the Department and Program (who, by University rules, can also be a faculty member at another university) and a 4th member who can be primary or outside. 

The advisor will be either: 

1. a mentor in the Biophysics Program or 
2. member of the “primary” faculty in the Department of Biochemistry and Biophysics (see appendix, this person must also be a mentor in the BSCB Program). 

At least one member of the advisory committee must have trained a graduate student through completion of the Ph.D. Additional committee members may be included from either within or outside the University if it is considered useful or necessary. The minimum size of the committee will be four members, but five (or more) is possible. Finally, when choosing a committee, each member must be informed that they will need to attend the student’s yearly meetings (as stipulated below), which will last 1 h or more.

A yearly progress report must be submitted to the Associate Dean for Graduate Studies by June 1 of each academic year in order to satisfy the uniform standards required for accreditation of the doctoral program have stipend funding approved for the following year. Students should plan to meet with their thesis advisory committee and file a Graduate Student Research Review form (see appendix) in the Department Office during each academic year. In the first year of studies, the laboratory rotation evaluations will be used to fulfill this requirement (see above).

The annual meeting with the thesis advisory committee should be held immediately following the student's seminar, provided that all committee members are able to attend. Otherwise, the committee meeting must be scheduled to take place within one month of the student’s seminar date or before June 1, whichever comes first. When scheduling a meeting, students should request that members be available for at least 1 h or possibly more.

At the end of the annual thesis committee advisory meeting, the thesis advisor will leave the room to give the student an opportunity to meet privately with the remaining members of the thesis committee. Additionally, thesis committee members who are family members with the advisor will also leave the room. This will give the student the opportunity to obtain mentoring from his or her committee in the absence of the advisor. The thesis committee members will be responsible for following up on any concerns raised by the student during this time. The graduate program director or the Chair of Biochemistry & Biophysics will help to resolve any concerns, as needed.