Doctor of Philosophy in Systems Biology and Disease |
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Director: Alicia A. McDonough, PhD
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Participating Faculty: Biochemistry, Cell and Neurobiology, Microbiology, Pathology, Physiology and Biophysics, Preventive Medicine. |
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During the past few decades, biomedical research has made great strides in genetic, cellular and molecular biology. With this expanded body of information and tools in hand, it is now feasible to tackle unanswered questions concerning how molecules and cells are organized to function as organs and interacting systems capable of maintaining homeostasis and responding to disturbances. The goal of the Ph.D. program in Systems Biology and Disease is to train investigators to develop strategies to implement and integrate the detailed information gained from cellular, molecular and genetic advances into studies of normal system function as well as studies of how and why systems are disrupted in disease.
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The goal of this program is to apply a multidisciplinary approach to understand the human organism as a whole. Breadth of interests and training are major features of this track and wide and varied skills in many research areas characterize the faculty of the program. To facilitate application of multidisciplinary approaches, close and regular contact between participating faculty and students is a major theme of this Ph.D. track. Students are usually admitted to this program through the PIBBS admission mechanism (www.usc.edu/pibbs) and spend their first year rotating through three labs before choosing a lab in which to pursue the degree. Students may also transfer into the program from other biomedical science programs to labs of participating faculty.
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Admission Requirements:
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As noted above, students are usually admitted via the PIBBS admission mechanism (http://www.usc.edu/pibbs). A baccalaureate degree in life sciences or, if not, sufficient courses in mathematics and the life sciences to provide a strong background for studies in biomedical research. Appropriate undergraduate degrees would be biology, physiology, engineering, chemistry, computer science. Successful applicants must have satisfactory performance on the general and advance portions of the GREs and three letters of recommendation. Previous research experience in a related field is expected but not required. Applicants who are accepted with minor deficiencies are expected to correct these during the first year.
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Pre-applications forms can be obtained from the PIBBS program. These may be obtained from: Director of PIBBS, Office of the Associate Dean for Research, University of Southern California Keck School of Medicine, KAM 110, 1975 Zonal Avenue, Los Angeles, CA 90089-9023. email: pibbs@usc.edu.
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USC Degree Requirements:
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These degrees are awarded under the jurisdiction of the Graduate School. Refer to the Requirements for Graduation section and the Graduate School section of the catalogue for general regulations. All courses applied toward the degrees must be courses accepted by the Graduate School.
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SBD Course Requirements:
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A minimum of 60 units is required, consisting of formal courses, seminars and research credits. At least 24 of the 60 units are to be formal graduate course work (lecture or seminar courses). Students must complete 16 units of coursework before they can satisfy the screening requirement. Additional coursework relevant to the research interests of the student may be required by the student’s guidance committee or by the student’s academic advisor in addition to the 24 units.
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Lab rotations: During the first year in PIBBS students sign up for Research Units BIOC 790 (4 units each semester) and rotate through the labs of three Mentor Members of the Program (potential research advisors). By the first summer of graduate study but no later than 18 months in the program, each student is expected to have selected a research advisor. At this point they will notify the SBD Executive committee of their intention to join the SBD training program.
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In the first year students are also required to take two four-unit courses in each semester which usually include one in each of the following areas: Biochemistry, Cell Biology, and Molecular Genetics, and Physiology/Pathology. An Ethics Class is taken in the Summer term. For these required courses, opting out, delaying or substituting a class will require the approval of the Executive Committee of the Program.
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New SBD core courses: The SBD executive committee designed and implemented a required two term core course entitled Systems Physiology and Disease (INTD 562a, 562b) which provides a graduate level analysis of how organ systems operate during health, and complements this with pathophysiologic studies of organ system disease. Taught by faculty from both basic and clinical science departments at HSC and CHLA, the fall term course covers muscle, respiratory, cardiovascular and renal systems and the spring term course covers Immunology/Defense, Nervous system, Endocrine/Reproduction and GI/liver. The two courses are designed to be independent of one another and can be taken in either order. Usually students will take at least one of these courses during their first year.
(INTD 562 Course Syllabus for Fall 2005)
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In the second year, courses are selected with the approval of the student’s Guidance Committee with reference to the research area in which the student is working. To accomplish the goal of having highly interactive faculty and students in the SBD program, in the second and all subsequent years, students are required to take the course entitled PHBI 550 Seminars in Systems Biology and Disease (1 unit). Presentations within this course will be part of the student’s annual research appraisal (ARA), described more fully below. A satisfactory ARA is required of every student for every year in residence. Participation in an organized journal club or working group recognized by the Executive Committee is required each year. Within the first two years, each student is additionally required to take a statistics course.
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Screening Procedure:
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At the end of the first year of graduate study each student is required to pass a screening process. In short, the student’s progress is judged satisfactory if they have maintained a minimum 3.0 GPA in 16 units of classroom work, and satisfactory completion of research rotations. After screening is complete, the student is expected to select an area of research and obtain the consent of a member of the SBD faculty to serve as Mentor. The Executive Committee in consultation with the student’s mentor will select a Guidance Committee appropriate for the student’s selected research area. The Guidance Committee will aid in selecting appropriate coursework and in ensuring suitable progress in the program.
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Qualifying Examination:
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The qualifying examination concentrates on the student’s ability to demonstrate a conceptual grasp of the major area of interest chosen, and an understanding of the general framework and approaches of hypothesis-driven research. The qualifying exam will be administered by the Guidance Committee. The examination is partly written and partly oral and is designed to test the student’s ability to meet the demands of the profession. Directly at the end of the second year (e.g. May/June) the student and mentor form a 4 member committee that designs a comprehensive exam based on student’s coursework and research area that will test for mastery and overall knowledge of the major area, ability to unravel complex problems, ability to think creatively and critically. These 4 questions will be answered in a 1½ day formal exam. Upon passing the comprehensive exam, the student writes a proposal in the format of an NIH Ruth L. Kirschstein National Research Service Award. The student first develops and presents 3 testable hypotheses to the committee, distinct from the PI mentor’s grants or applications, and the committee chooses one for the student to address. The student has 5 weeks to complete the proposal. After the written portion is judged satisfactory, the student has an oral exam with the committee on the proposal.
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Annual Research Appraisal (ARA):
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After advancing to candidacy, progress on dissertation research by each student is evaluated annually with an Annual Research Appraisal (ARA). Prior to the meeting, students submit a short written document describing their research (significant experiments, problems, projected studies) to the Dissertation Committee, give an open seminar (as part of PHBI 550 course), then have a closed meeting with the Dissertation Committee. The ARA meeting is intended to be a working session between the student and his or her committee in which results and problems are discussed and the student presents a plan for the next year of work. A satisfactory ARA is required of every student for every year in residence.
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Dissertation:
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At the last ARA before the defense of the thesis, the student submits an outline draft of the thesis document to the Dissertation Committee prior to the ARA seminar. After the ARA, the Dissertation Committee will meet in closed session to determine if additional experiments or revisions to the thesis document are needed or approve the document and give permission for writing the dissertation.
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Thesis defense:
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An acceptable dissertation based upon completion of an original investigation is required. The candidate must defend an approved draft of the dissertation in a public oral defense. The Dissertation Committee will then meet with the student in a closed session to complete the oral examination.
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