Doctoral Programs
Physiology, Biophysics & Systems Biology
  • PBSB Gallery 1
    Doctoral Program
    Physiology, Biophysics & Systems Biology
    Top: Somatic duplication found in the PSEN2 gene on chromosome 1 of the HCC1395 cell line. Bottom: This duplication was found using a novel deep learning-based structural variant caller. Courtesy Hajirasouliha Lab.
  • PBSB Gallery 2
    Doctoral Program
    Physiology, Biophysics & Systems Biology
    Top: The breakpoint proximity curve BPpc adjusted by its expected values using multiple tissue-specific breakpoint covariates in a generalized additive model (GAM). Bottom: Partial contribution of the interaction of TAD and gene density as a genomic covariate to predict the expected breakpoint proximity curve. Courtesy Khurana Lab.
  • PBSB Gallery 3
    Doctoral Program
    Physiology, Biophysics & Systems Biology
  • PBSB Gallery 4
    Doctoral Program
    Physiology, Biophysics & Systems Biology

    Program Requirements

    What does PBSB look for in student applicants? 

    We welcome applications from any individual who values the use and development of quantitative experimental, computational, and theoretical approaches for tackling challenging biological problems of medical relevance. Applicants should have demonstrated excellence and intellectual ambition in their previous coursework. We also expect that applicants will have had at least one significant research experience.  

    Our most successful applicants will have had meaningful exposure to and demonstrated aptitude for biochemical principles, molecular biology, chemistry, physics, statistics, calculus, linear algebra, and coding (Python, C, Matlab, R, or similar), either through formal coursework, research, or independent study. We recommend that applicants interested in Bioinformatics have had some exposure to machine learning and that those interested in Biophysics are adept with differential equations.  

    See Doctoral Program Admissions for application deadline, procedures, and requirements.

    The path to the degree

    The program of study consists of didactic courses, seminars and supervised research leading to the preparation of a thesis. Each student works with first-year advisors to design an individualized program of study that reflects his/her specific background and interests. Regularly scheduled meetings with faculty ensure that the student's educational program progresses as planned. 

    Timeline

    Year 1

    Year 2

    Year 3

    Year 4

    Year 5...

    Core Curriculum Courses

    Graduate Research Seminars

    Lab Rotations

    Select Research Focus and Special Committee

    Complete Elective Req. (10 Credits)

    Admission to Doctoral Candidacy Exam, Research
    Proposal, and Oral Examination

    Submit PhD Thesis Description

    Lab Research

    Meetings with Special Committees

    Present at PBSB Program Retreat,
    and du Vigneaud Symposium

    Present at Local and National Meetings

    Develop PhD Thesis

    Continue Research and Defend PhD Thesis

    Classroom education during the first two years consists of core courses, seminar course series, a responsible conduct of research course and electives. In the first year, formal coursework is complemented by participation in journal clubs, as well as laboratory rotations. For information about PBSB program courses, see Curriculum

    During the first year, students rotate in three different labs to explore different possibilities for their research project. By July of the first year, each student selects a thesis lab and major sponsor (thesis advisor). Once they choose their thesis lab, the student selects two additional Graduate School faculty advisors who can contribute their expertise to the student’s project. The thesis advisor and these two additional faculty form the Special Committee, which meets at least once a year to discuss research progress and future directions with the student. The Special Committee also serves as the core group of examiners for the student's Admission to Candidacy Exam (ACE) and thesis defense examination. 

    The ACE consists of two parts: a written exam in the form of an NIH R01 proposal, and an oral exam, which includes discussion of the written research proposal. Students are expected to take this exam by July of their second year. The exam provides an opportunity for students to demonstrate that they have attained the requisite breadth of knowledge to continue in the PhD program and are prepared to undertake full-time thesis research. 

    After completing the ACE, the student's annual (or more frequent) meetings with the Special Committee provide the forum for the student to report on his/her progress and agree upon future research directions. 

    Thesis research is typically completed within four to six years, under the direction of the student's sponsor. The Special Committee advises the student in his/her research and oversees development of the thesis. During this time the student continues to participate as a student within the PBSB Program but works full-time in his/her thesis laboratory. 

    The culmination of the student's successful progression through the program is the final examination (the "defense") and certification by the Special Committee that the thesis represents an official piece of research that satisfies the requirements of the Graduate School for a PhD degree. 

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