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Course of Study

Overview

With over 100 faculty in the Program, entering students may choose among diverse specializations in the field of genetics.  The courses taken may vary depending on the area of specialization, and every effort is made to tailor the curriculum to students' individual needs.  Regardless of the field of specialization, the Program ensures that its students graduate with an excellent working knowledge of modern genetics and molecular biology.  The primary advisor during the first year is the Program Director, who helps each student to select laboratory rotations and develop an individualized plan of study.  In addition, the heads of the laboratories in which students rotate serve an important advisory role.  Typically, students have chosen a laboratory in which to pursue their dissertation research by May of the first year.  At this time, the dissertation advisor joins the Program Director in mentoring students throughout the remainder of their graduate careers.  Once students have defended their research proposal in their fifth semester, their dissertation research committees also become important supportive resources.

Choosing a Laboratory

We do not expect students to know which laboratory they want to work in at the time that they enter the program. Therefore, we use the Laboratory Rotation course as a vehicle to introduce first-year trainees to the kinds of research conducted in several laboratories within the program. Through the laboratory rotations, students gain a hands-on introduction to the particular experimental systems and methodologies available in each laboratory, along with a general feeling for the ambience of each lab. Typically, a student will rotate in three different laboratories during the first year (Fall, Winter, Spring).

All of the required courses in the first two semesters meet on the Stony Brook campus, although additional electives and journal clubs are also offered at Cold Spring Harbor Laboratory. Because both Cold Spring Harbor Laboratory and Brookhaven National Laboratory are roughly a half hour's drive from Stony Brook, we recommend that students choosing rotations at either facility consider their course loads and time the rotations accordingly. The decision as to where to carry out the first rotation is made by the student in conjunction with the Program Director. By the time second rotation needs to be chosen, students will have had many opportunities to become familiar with the faculty. Through Program retreats, courses, and in-house symposia at Cold Spring Harbor Laboratory, Brookhaven National Laboratory, and Stony Brook, the Program facilitates frequent interactions among faculty and students. Every effort is made to promote student awareness of the research possibilities at all three institutions.

Teaching Assistantships and Student Seminars

Effective teaching and communication skills are assets for career advancement in the sciences. Genetics students typically function for two semesters as Teaching Assistants in the undergraduate Genetics course, where they may conduct discussion sections or study groups, and in introductory biology courses, leading student laboratories or study sessions. In addition, all students participate in the Graduate Student Seminar (BGE 531) throughout their academic careers. This seminar series gives every student the opportunity to present his or her own research to students and faculty, thereby gaining valuable presentation experience and feedback.  Students may also to elect to take courses in the University's Alan Alda Center for Communicating Science to boost confidence in and enhance their presentation skills.

Other Seminars and Symposia

A variety of seminars and symposia featuring speakers from outside the University is available to the students in the Genetics Program. Every department in the Life Sciences Building, School of Medicine, and Centers for Molecular Medicine hosts regular seminars and special symposia conducted by visiting scientists. In addition, Cold Spring Harbor Laboratory and Brookhaven National Laboratory also sponsor numerous seminars by resident and visiting scientists.

Advancement to Candidacy

Most students will complete their formal course requirements by January of the second year. At that time they prepare for a qualifying exam, which takes the form of a National Institutes of Health grant proposal on a topic that is not directly related to the student's dissertation work. A preparatory course (BGE 693) guides students through the process of writing an effective and compelling proposal.  Students then orally defend their proposal to a small group of faculty who assess the student's ability to think critically. 

After passing the qualifying exam and before the end of the fifth semester, each student prepares a dissertation proposal. This proposal also takes the form of an NIH grant application, but this time the topic is what the student intends to pursue for his or her dissertation project.  The written document is prepared in consultation with the research advisor. It is defended orally before a dissertation research committee of four faculty, one of whom must be from outside the Genetics Program.  The research committee is chosen by the student in consultation with his or her advisor.  The dissertation proposal is a valuable means of giving students and their advisors an opportunity to think through the long-term strategy of the dissertation research and receive helpful advice from colleagues. After passing the dissertation proposal, the student advances to candidacy and pursues dissertation research full-time. His/her advisor then becomes a member of the dissertation research committee, which meets at least annually to monitor the student's progress. To be eligible for graduation, each student must also submit as first author at least one manuscript of original research to a suitable peer-reviewed journal, as determined by the Program's Executive Committee.  Moreover, the journal's editors must deem the paper of sufficient quality to merit evaluation by external reviewers.  Students typically complete the entire program and obtain the PhD degree in five to six years.

Curriculum

The required courses in the Genetics Program are Molecular Genetics, Cell Biology, and Graduate Genetics. The last course covers the major areas of modern genetics in a comprehensive fashion.  These courses include lectures given by different faculty, who address topics within their own field of expertise and interest. Students must achieve a grade of B or better in each of these three courses. In addition to the required courses, students must take at least six credits of specialized electives, which can be chosen from an extensive array of offerings in consultation with the research advisor and Program Director. Students must attain an overall average of B (3.0) or better in these elective courses. 'Readings in Genetics' is a journal club designed to teach students to critically evaluate scientific literature, and it is taken for three semesters (typically the second, third, and fourth semesters). Listed below are the core courses and some of the specialized courses that are available. However, students who enter the program with particular academic strengths may be exempted from one or more courses; therefore, the actual course of study may be adjusted to accommodate a trainee's specific interests and previous training. The times at which electives are taken are also quite flexible, although the electives must be completed before a student can advance to candidacy.

First Year, Fall (12 credits total)

BGE 510 Graduate Genetics (3 credits)
HBM 503 Molecular Genetics (3)
GRD 500 Responsible Conduct of Research and Scholarship (0-1)
BGE 531 Graduate Student Seminar (1)
BGE 530 Laboratory Rotation (1-5)

First Year, Spring (12 credits total)

MCB 656 Cell Biology (4)
BGE 531 Graduate Student Seminar (0-1)
BGE 691 Readings in Genetics (1)
BGE 530 Laboratory Rotation (1-6)
BIO 600 Practicum in Teaching (0)

Second Year, Fall (9 credits total)

BGE 531 Graduate Student Seminar (1)
BGE 691 Readings in Genetics (1)
BGE 599 Graduate Research (1-7)
BIO 600 Practicum in Teaching (0)
Elective(s)

Second Year, Spring (9 credits total)

BGE 693 Research Proposal Preparation (1)
BGE 531 Graduate Student Seminar (1)
BGE 691 Readings in Genetics (1)
BGE 599 Graduate Research (1-6)
Elective(s)

Third Year (9 credits per semester)

Dissertation Research Proposal (due by end of December)
BGE 531 Graduate Student Seminar (1)
BGE 599/699 Graduate Research (1-8)
Elective(s)

Fourth Year (9 credits per semester)

BGE 531 Graduate Student Seminar (1)
BGE 699 Graduate Research (8)

Fifth Year (9 credits per semester)

BGE 531 Graduate Student Seminar (1)
BGE 699 Graduate Research (8)
Submission of a first-authored manuscript
Defense of the dissertation

Summer, all years

BGE 800 Summer Research (0)

Program Courses

Core Courses

Core courses include: Cell Biology, Molecular Genetics, Graduate Genetics, Laboratory Rotation, Graduate Research (once a dissertation lab is chosen), Graduate Student Seminar in Genetics, Readings in Genetics (Journal Club), Integrity in Science, Practicum in Teaching, and Research Proposal Preparation.

Elective Courses

With consent of the dissertation advisor and Program Director, students may choose electives from among graduate-level courses at the University in other programs, including those in Applied Mathematics and Statistics, Molecular and Cellular Biology, Neurobiology and Behavior, Pharmacological Sciences, and Ecology and Evolution.  Cold Spring Harbor Laboratory also offers courses that may be eligible for elective credit.  The Alan Alda Center for Communicating Science is an exceptional resource for students who wish to improve their oral and written communication.  Courses such as 'Distilling Your Message' and 'Improvisation for Scientists' build students' skills in describing their research to peers and the general public.  These courses are popular with students who plan to teach or work in biotechnology careers and can be counted as electives with permission of the research advisor and Program Director.

A partial listing of popular electives includes:

AMS 534  Introduction to Systems Biology (3 cr) [Cross-listed as BGE 534]
AMS 572  Data Analysis 1 (3 cr)
BEE 551   Principles of Evolution (4 cr)
BEE 554   Population Genetics & Evolution (3 cr)
BEE 575   Evolutionary Ecology (3 cr)
BME 503  Cell & Molecular Imaging (3 cr)
BME 534  Functional Genomics (3 cr)
CHE 543  Chemical Approaches to Biology (3 cr)
CSE 549  Computational Biology (3 cr)
HBH 550  Statistics in Life Sciences (1 cr)
HBM 522  Biology of Cancer (2 cr)
HBM 640  Molecular Mechanisms of Microbial Pathogenesis (3 cr)
HBM 692  Experimental Methods in Molecular Microbiology (1 cr)
HBP 533  Immunology (3 cr)
HBY 561  Statistical Analysis of Physiologic Data (1 cr)
MCB 517  Biomembranes (1 cr)
MCB 520  Graduate Biochemistry I (3 cr)
MCB 657  Principles of Development (3 cr) [Cross-listed as BGE 657]
WRT 621  Graduate Level Writing (3 cr)

BGE 510 Graduate Genetics (3 credits)
HBM 503 Molecular Genetics (3)

GRD 500 Responsible Conduct of Research and Scholarship (0-1)
BGE 531 Graduate Student Seminar (1)
BGE 530 Laboratory Rotation (1-5)

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