NYU Structural Biology Program Requirements
Required Courses
- Foundations Course I and II (1st and 2nd semester)
- Principles in Structural Biology (1st semester)
- Seminar in Structural Biology (1st year)
- Advanced Techniques in Structural Biology (2nd semester)
- Tutorial in Structural Biology (3rd or 4th year)
- Sackler Inst requirement is 32 credits of course work out of 72 total credits
Seminar in Structural Biology
The primary goal of this course is to develop your skills in attending
and presenting research seminars. These skills are critical to
developing your career as a research scientist. There are two parts to
the course, which are described below.
In terms of course credits, you are required to enroll in the Sackler
course "Seminar in Structural Biology" (G16.3715) for the fall
semester of your 1st year. After that, you may enroll in this course
at your discretion (i.e., if you need course credits). Regardless of
your course enrollment, you are expected to participate in our seminar
program throughout your tenure at NYU.
First part of the Seminar course:
You are required to attend and report on 10 seminars of your choice
during the fall semester. The seminars must be presented by a faculty
level researcher, preferably someone visiting from another institution
as part of NYUSOM's many seminar series. Student and postdoc
presentations are not acceptable. Outside of this criterion, the
choice of seminars is yours, but I would offer the following
suggestions for seminars that you are likely to find the most
rewarding. Both the Skirball Seminar Series (Friday 12-1) and the
Honors Series Lectures (Monday 4-5) involve eminent researchers who
are encouraged to give somewhat general lectures that are accessible
to a broad audience. Any of these lectures would be an excellent
choice. In addition, the Structural Biology Program will invite a
limited number of speakers who are likely to give more focused
presentations and you are strongly encouraged to attend these lectures
whether or not you choose to use them for one of your 10 reports.
The reports consist of a brief abstract of
the presentation (1 paragraph). These should mention the system
being investigated, its biological and/or medical relevance, one or
two main results, and a take-home message. Much of this
information is likely to be presented in the introduction to the talk . These
don't have to be polished abstracts, but simply prove that you
attended the lecture and were able to understand the important points. Also,
they will instill the good habit of taking notes during seminars,
which you will find greatly increases your retention of the
material.
These abstracts are to be sent to
stokes@nyu.edu within 2 days
of the seminar (otherwise you will certainly forget). Please include
the name of the lecture series, the time and date, the title of the
presentation and the name of the speaker.
NYU has a web site that is reasonably good about listing seminars,
though not necessarily comprehensive:
http://www.med.nyu.edu/calendar.html
Please be aware that the Skirball Seminar series generally provides an
opportunity for students to have lunch with the speakers after the
seminar. You are strongly encouraged to attend these lunches.
Second part of the Seminar Course:
Throughout your tenure at NYU, you will be expected to participate in
our "Research in Progress" seminar series. This series involves
presentations by students and postdocs within the program and takes
place every other Tuesday at 11:00 to describe their ongoing
research. The aim is to have everyone present once each year.
First year students will not
have to present and second year students will be scheduled for the end
of their second year. If you don't have a conflict with another class,
you should start attending these right away. The schedule is posted at
http://saturn.med.nyu.edu/it/schedules
Rotations
Students must complete three 12-week rotations: one in the autumn semester,
one in the spring semester and one in the summer. Students in the NIH GPP program
complete an additional (fourth) rotation in the summer prior to starting at NYU.
At the end of each rotation, students are required to prepare a brief
report (2-4 pages), which is presented to their rotation advisor, the
Graduate Advisor and the Sackler Institute. This report should cover
the background for the rotation project, a description of the
experiments performed and any results obtained, and a discussion of
how this works fits into the broader goals of the laboratory. After
receiving the report, the rotation advisor completes an evaluation of
the students performance during the rotation, which becomes part of
the student's record.
Tutorial in Structural Biology
All students are required to complete a semester long Tutorial in Structural Biology. This course is meant for students in their 3rd or 4th year and is a one-on-one tutorial with a faculty member of their choosing. This faculty member must not be their thesis advisor and the topic should not be closely related to their thesis project. Rather, this course is meant to expand the students knowledge in a useful, but somewhat orthogonal direction. The student should approach a faculty member (any faculty member, not necessarily in the Structural Biology program) and propose to have a semester-long set of discussions. Normally, these discussions will be based on a series of papers proposed by either the faculty member or the student. In some cases, there could be some practical exercises, if for example the student chose to learn a computer programming language or data processing method. However, this course should not become another rotation and the student's main energies should remain focused on their thesis research project. Once completed, an evaluation form should be filled out by the faculty member and submitted to the Course Director (David Stokes).
Qualifying Exam
All students are required to pass the qualifying examination at the end of their second year in order to proceed with their doctoral thesis research. This qualifying examination consists of the preparation of a written research proposal followed by an oral defense before a committee of faculty members. Membership of this Examination Committee is determined by the student in consultation with their mentor. After completing the qualifying exam, this committee generally continues as the Thesis Committee (see below).
The exam is intended to evaluate the basic knowledge of the student in his/her research area as well as his/her capacity to cogently formulate specific questions to be approached, and to design and interpret experiments directed towards answering these questions. The thesis proposal must be submitted by August 1 of the second year and the oral exam should be scheduled to take place in the last two weeks of August if the committee members are available.
The proposal should be modeled after an NIH postdoctoral
proposal. Although the NIH have recently reduced the lenght of their
fellowship proposals, the thesis proposal should be about 15 pages in
length (single spaced including any figures). An excerpt from the NIH directions is
included below. The proposal
should have a scope consistent with what an exceptionally competent,
hardworking student can accomplish in a three year period. Detailed
guidelines for preparing the proposal can be to obtained from
the NIH Guidelines for preparing a postdoctoral proposal. Briefly, the
proposal should begin with a one page Specific Aims section that first
outlines succinctly the long range goals of the proposed work and then
the specific short term goals and the specific experimental approaches
that will be carried out. Next is a Background section of
approximately 3-4 pages that cogently discusses the current state of
knowledge in the field and introduces the goals and purposes of the
proposed experiments. This should include ample references to the
literature. The next section will present preliminary results
accomplished by the student himself (prior work by others in the
laboratory should be included in the Background section). Note,
however, that the student need not have any significant results to
submit the thesis proposal for the Qualifying examination. The main
section of the proposal outlines the Research Plan
for the thesis research (7-8 pages). It should consists of a coherent
(i.e. rationally ordered) presentation of the proposed experiments and
a description of the methodology to be used. This section may include
additional background information, not given in the introduction, to
illuminate the rationale for the specific experiments proposed.
Excessive details regarding experimental procedures should be avoided,
instead providing appropriate references to the literature;
nevertheless, appropriate experimental techniques should be specified
and all of the relevant steps in preparing samples and analyzing
results should be enumerated. The student should be prepared to fill
in relevant details during the oral exam. For each experiment
proposed, you should discuss difficulties you expect to encounter, the
possible outcomes and their interpretations. You should show that you
are aware of the limitations of the proposed experimental approaches.
The proposal will be read by the examiners within two to three weeks of receipt and they will then decide if it is satisfactory and warrants proceeding with the defense. If this is the case, a date will be set for the oral defense as soon as possible thereafter. If the committee feels that the proposal needs substantial improvement before it can be considered defensible, the student's advisor, after consulting with the committee members, will provide the student with guidance on how to improve it. The oral defense begins with a 20-30 minute presentation from the student followed by questions from the faculty. The student should be prepared to answer general questions relevant to their field, and to fill in experimental details related to their proposed experiments. The student should demonstrate awareness of the context of their work as well as specific limitations of their proposed experimental approaches. After successful defense of their research proposal, the student becomes an official candidate for the Ph.D. degree. Alternatively, if the committee believes that the student is unsuitable for a Ph.D., they will recommend that the student instead be considered for a Masters degree and dismissed from the program.
After defense of the proposal, the examiners should prepare a written report with copies going to the Graduate Advisor and to the Sackler Institute.
Thesis Committee
The Thesis Committee is responsible for monitoring the progress of the
student during their thesis research and to suggest changes in the
approach should a project become untenable. Ultimately, this
committee will evaluate the Ph.D. thesis and administering the oral
defense. The Thesis Committee will consist of four faculty members,
one of which is the student’s research mentor. One outside
examiner will be added to this committee for the final defense of the
Ph.D. thesis. Members of this committee will be chosen by the student
in consultation with the student’s research mentor. A chairperson
will be chosen by the committee members and should not be the
student’s research mentor. For students in the NIH/NYU GPP
program, there must be at least one member from each campus. For GPP
students who establish collaborative projects between the two
campuses, the co-mentors may both serve on the Thesis Committee. This
committee must meet at least once per year and more often when
research progress becomes problematic. After each meeting, the
committee should complete a written report, giving copies to the
student, to the Graduate Advisor and to the Sackler Institute.
Ph.D. candidates are expected to finish the program in 5-5.5 years,
whereas M.D./Ph.D. candidates are encouraged to finish in 4-5 years,
including writing and defending the thesis. The Structural Biology
Program requires each student to publish two papers, one of which
should be a first author paper, prior to defending their thesis.
Thesis Defense
Permission to write the Ph.D. thesis is granted by the Thesis Committee, which generally goes on to administer the final defense, though membership on this Defense Committee can be reconfigured under certain circumstances. In all cases, an additional member from outside NYU is added to the final Defense Committee in order to provide an additional degree of objectivity to the process. The thesis must represent a significant body of independent research and students are generally expected to graduate with two published papers based on their research. The defense consists of a presentation by the student as a public seminar, followed by a private question and answer session with the committee members.