IMMUN-PHD - Immunology (PhD)
Program Overview
Doctor of Philosophy in Immunology
See Graduate Degrees for the university’s basic requirements for the PhD degree.
Admissions
Students seeking admission to the Immunology PhD program typically have an undergraduate major in biological sciences. Majors from other areas are acceptable if the applicant has sufficient coursework in biology, chemistry, general physics, and mathematics (through calculus). The Immunology Graduate Program committee evaluates applications based on: grades; evidence of research experience; letters of recommendation, including letters from research sponsor(s); and commitment to a career in biomedical research.
The GRE Subject test is optional. Applicants who choose to submit a GRE score should plan on taking the GRE at least one month before the application deadline to ensure that official scores are available when applications are evaluated.
Candidates who are selected to visit Stanford and interview are notified in January. The selected applicants are invited to a Biosciences interview session.
Interested Stanford medical students are welcome to apply to the program and should also submit a formal application by the December deadline.
Prospective graduate students must apply via Stanford’s online graduate application.
Financial Aid
Students admitted to the program are offered financial support for tuition, a living stipend, and health insurance coverage, and for first-year graduate students, a small allowance (tech funds). Applicants are urged to apply for independent fellowships from such entities as the National Science Foundation or the National Defense Science and Engineering Graduate Fellowships. NSF Fellowship applications are due in October of the year before enrollment in the graduate program, and only one more NSF application is permitted in the first or second year. Immunology graduate students may continue to apply for outside fellowships after matriculation. Admitted students are typically offered financial support through Stanford Graduate Fellowships, NIH traineeships, or research assistantships.
General Requirements
Immunology Startup and the First-Year Advising Process
Since students enter with differing backgrounds, each student is assisted by the first-year advisor in selecting courses and lab rotations in the first year and in choosing a lab for the dissertation research. In addition, the Immunology Startup, a five-day introduction to immunology in early September, exposes incoming Immunology PhD students to various techniques and concepts. Students learn basic laboratory techniques in immunology and participate in in-depth discussions with faculty.
All students must be enrolled in exactly ten units during autumn, winter, spring, and summer quarters until reaching Terminal Graduate Residence (TGR) status in the spring or summer quarter of their fourth year. Students must pass all courses they are enrolled in; required and elective courses must be taken for a letter grade. Students must earn a grade of B- or better in all courses applicable to the degree that are taken for a letter grade. Satisfactory completion of each year’s general and track-specific requirements listed below is required. During the first year, degree progress is monitored closely by the first-year advisor in quarterly meetings and by the Stanford Graduate Program Committee in a final advising session in June.
First-year students must complete three rotations in at least two immunology labs. Two mini-rotations of six weeks each may be arranged in the spring quarter. After joining a lab, students must meet with their thesis advisor within 30 days to complete the Individual Development Plan (IDP). Students continue to complete the IDP annually.
Students apply for any fellowships for which they are eligible (NSF, NDSEG, AHA, NIH NRSA are just a few).
A specific program of study for each student is developed individually with the first-year advisor.
Free Form Requisites
Immunology Ph.D. Curriculum:
All students in the two tracks, Molecular, Cellular, and Translational Immunology (MCTI) and Computational and Systems Immunology (CSI) are required to enroll in the following core courses:
Course List | ||
Units | ||
|---|---|---|
Foundations in Experimental Biology | 5 | |
Biostatistics | 5 | |
Advanced Immunology I | 3 | |
Advanced Immunology II | 3 | |
Ethics, Science, and Society | 1 | |
Teaching in Immunology | 1-15 | |
Immunology Journal Club | 1 | |
Seminar in Immunology | 1 | |
Graduate Research | 1-15 | |
The Responsible Conduct of Research | 1 | |
Candidates for Ph.D. degrees at Stanford must satisfactorily complete a program of study that includes 135 units of graduate course work and research. At least 3 units must be taken with each of four different Stanford faculty members. Students in the MCTI track are expected to complete all their core course requirements by the end of their second year; students in the CSI track should complete their core course work by the end of the third year.
In the third through fifth year, students are required to take course Ethics, Science, and Society, a refresher ethics course that is required by NIH and is offered every other year.
Immediately after the final examination period in Spring Quarter of the first year, first-year immunology graduate students are required to give a presentation on one of their three rotations to the Immunology graduate program committee (Qualifying Examination Process, Part I). After the rotation presentation, the first-year student will meet with the Stanford Graduate Program Committee in a one-on-one advising session to review degree progress and choice of a Ph.D. thesis lab.
In Autumn Quarter of the second year, students focus on preparing for Part II of the Qualifying Examination Process, the general oral examination and the Ph.D. thesis dissertation proposal. The student is required to pass the oral examination and write a thesis dissertation proposal which is presented to and evaluated by a qualifying examination committee composed of three faculty members, two of whom must be from the Immunology program faculty and the third faculty member may be from a department outside the program. The Ph.D. adviser is not present for Part II, but is required to submit an evaluation and grade for the Ph.D. thesis dissertation proposal. Upon successful completion of Part II, the student files a petition for Ph.D. candidacy and form their reading dissertation committee.
The dissertation reading committee (generally known as the Ph.D. thesis committee) must be comprised of at least four faculty members who guide the student in the Ph.D. research, and read and approve the final dissertation. Typically three of the four dissertation reading committee members are from the Immunology program faculty.
In the first through third years, the student must meet with the Ph.D. thesis committee at least once a year. In the fourth and fifth years, the student is expected to meet twice a year with the Ph.D. thesis committee. In addition, if requested by the student, a secondary adviser is assigned who can provide additional advice on issues such as career path choices and other non-academic issues.
Individual Development Plan: Graduate students are required to meet with their faculty mentors once a year to discuss an individual development plan (IDP). The IDP is intended to help the students take ownership of their training and professional development. The goals of the IDP are to: 1) pause, reflect and intentionally think on short-, mid- and long-term goals; 2) identify resources that help to achieve these goals; and 3) have open and direct dialogue with the Ph.D. thesis adviser and establish clear expectations and steps.
Track Specific Requirements
In addition to the general requirements listed above, students must also complete requirements within their track. Written petitions for exemptions to core curriculum and lab rotation requirements are considered only in the first year by the advising committee and the chair of the Graduate Program committee. Approval is contingent upon special circumstances and is not routinely granted.
Molecular, Cellular, and Translational Immunology
In addition to the core courses listed above, MCTI first-year students are required to take the following courses in their first year for a letter grade:
Course List | ||
Units | ||
|---|---|---|
Advanced Immunology III | 3 | |
Take one of the following courses: | ||
Advanced Cell Biology | 4 | |
Introduction to Applied Computational Tools in Immunology | 2 | |
Advanced Pathogenesis of Bacteria, Viruses, and Eukaryotic Parasites | 4 | |
Electives:
One elective (see suggested elective list below)
Course List | ||
Units | ||
|---|---|---|
Molecular and Genetic Basis of Cancer | 4 | |
Cell Signaling | 4 | |
Developmental Biology | 4 | |
Biology and Disease of Hematopoiesis | 3 | |
Tumor Immunology | 3 | |
Biological Macromolecules | 5 | |
Computational and Systems Immunology
In addition to the core courses listed above, the CSI curriculum trains students to be computational and experimental scientists, who are expected to identify important problems in immunology and to devise integrated computational/ experimental plans for addressing them.
CSI Core (Required):
Students in the CSI track are required to take the following core courses in their first and second years, unless demonstrated by proficiency or coursework. For example, a student, with proficiency in concepts taught in CS 106A, may petition to be exempt from this course and go on to take CS 106B. Petitions to exempt from the courses CS 106A, CS 109, and CS 161 must be approved by the Chair of the CSI track.
Course List | ||
Units | ||
|---|---|---|
Representations and Algorithms for Computational Molecular Biology | 3-4 | |
Programming Methodology | 3-5 | |
Programming Abstractions | 3-5 | |
Introduction to Probability for Computer Scientists | 3-5 | |
Design and Analysis of Algorithms | 3-5 | |
Introduction to Applied Computational Tools in Immunology | 2 | |
Essential Methods in Computational and Systems Immunology | 3 | |
CSI Electives:
Two electives (see suggested elective list below):
Course List | ||
Units | ||
|---|---|---|
Introduction to Biomedical Informatics Research Methodology | 3-5 | |
Translational Bioinformatics | 4 | |
Computational Methods for Biomedical Image Analysis and Interpretation | 3-4 | |
Introduction to Numerical Methods for Engineering | 3 | |
Introduction to Linear Dynamical Systems | 3 | |
Randomized Algorithms and Probabilistic Analysis | 3 | |
Convex Optimization I | 3 | |
Applied Fourier Analysis and Elements of Modern Signal Processing | 3 | |
Information Theory | 3 | |
Introduction to Statistical Signal Processing | 3 | |
Theory of Probability | 4 | |
Data Mining and Analysis | 3 | |
Introduction to Statistical Learning | 3 | |
Introduction to Stochastic Processes I | 3 | |
Other | ||
Journal Clubs
Both MCTI and CSI students are required to attend the IMMUNOL 305 Immunology Journal Club for their first through third years. Attendance is optional for fourth year and above graduate students.
Immunology Seminar Series
Graduate seminars are an important means of attaining a broad and comprehensive exposure to all areas in immunology as well as gaining a professional perspective and competence in the field. First-year students are required to attend all immunology seminars (IMMUNOL 311 Seminar in Immunology). Students in their second year and above are required to attend 50% of the seminar series each academic year until the last quarter in which their Ph.D. oral defense takes place.
Immunology Scientific Retreat
The annual Scientific Retreat is usually held in Autumn Quarter, and is attended by students, staff, postdocs and faculty of the Stanford immunology community. All immunology graduate students are required to attend. In the third through fifth years, students will present a poster and give a talk on their graduate research.
Teaching Assistantships
Teaching experience and training are part of the graduate curriculum. Each student assists in teaching two courses in the immunology core or electives. MSTP students are only required to do one TAship. A TA match process is held in summer quarter in order to match the graduate student's research and teaching preferences to the appropriate courses. Before beginning their assigned teaching assistantships, students are required to attend a TA orientation workshop held by VPTL before the teaching quarter begins. Teaching Assistants are also required to register for course Teaching in Immunology under the instructor they are TAing for and in the quarter they are TAing.
First Author Paper Submission
By the fourth or fifth year, graduate students are expected to submit a first author paper for publication. This milestone should be completed before defending a Ph.D. thesis.
Doctoral Dissertation
Before embarking on the dissertation defense process, the graduate student must submit a Petition to Defend to the Director of the Immunology Graduate Program. Important milestones and degree requirements must be met before proceeding to the oral examination. A substantial draft of the dissertation must be turned in to the student's oral examination committee at least one month before the oral exam is scheduled to take place. At the time of the Ph.D. orals defense, an orals chair is chosen to lead the orals committee, which is a distinct committee, but the basic membership is identical to that of the dissertation reading committee. The correct number of faculty committee members for the orals committee is five. For students with two Ph.D. thesis co-advisors, the exact number of faculty committee members is still five. The final written dissertation must be approved by the student's reading committee and submitted to the Registrar's Office. Upon completion of this final requirement, a student is eligible for conferral of the Ph.D. degree.