Immunology

Courses offered by the Immunology Program are listed under the subject code IMMUNOL on the Stanford Bulletin's ExploreCourses web site.

Stanford Immunology is home to faculty, students, postdocs, and staff who work together to produce internationally recognized research in many areas of immunology. The long tradition of collaboration among the immunology laboratories at Stanford fosters productive interdisciplinary research, with an emphasis on the application of current approaches to problems in cellular, molecular and clinical immunology. Faculty research interests include both bench-to-bedside and basic science research. Graduate students and postdoctoral scholars receive outstanding training through their participation in research, teaching, seminars, journal clubs, and the annual Stanford Immunology Scientific Conference.

Mission of the Ph.D. Program in Immunology

The Immunology doctoral program offers instruction and research opportunities leading to a Ph.D. in Immunology. Two tracks are offered:

1. Track 1: Molecular, Cellular, and Translational Immunology
2. Track 2: Computational and Systems Immunology

The goal of the Ph.D. Program in Immunology  is to develop investigators who have a strong foundation in Immunology and related sciences in order to carry out innovative research. The program features a flexible choice of courses and seminars combined with extensive research training in the laboratories of participating Immunology faculty. Specifically, immunology graduate students:

1. acquire a fundamental, broad, and comprehensive body of knowledge and skills through an extensive curriculum.
2. identify important scientific questions, design, and conduct experiments using the most appropriate methods.
3. read and critically analyze current literature in immunology and other relevant fields.
4. present research findings and communicate ideas effectively to a variety of audiences.
5. prepare manuscripts that will be published in leading journals.
6. learn to teach effectively.  

Master of Science in Immunology

Students in the Ph.D. program in Immunology may apply for an M.S. degree in Immunology only under special circumstances, assuming completion of appropriate requirements. Students must complete:

1. At least 45 units of academic work, all of which must be in courses at or above the 100 level, 36 units of which must be at or above the 200 level.
2. 3 quarters of graduate research (IMMUNOL 399 Graduate Research), consisting of rotations in the labs of three faculty members.
3. Participation in the Immunology journal club (IMMUNOL 305 Immunology Journal Club), and attendance at the Immunology seminar series and at the annual Stanford Immunology Scientific Conference.
4. First Year Rotations Presentations and General Advising Sessions, June. Students present on one of three lab rotations.
5.  Students must submit a master's thesis paper on one of their rotations. This requirement may be waived under special circumstances.

Course work in Immunology as follows:

Track: Molecular, Cellular and Translational Immunology

Track: Computational and Systems Immunology

Doctor of Philosophy in Immunology

Courses offered by the Stanford Graduate Program in Immunology are listed under the subject code IMMUNOL on the Stanford Bulletin’s ExploreCourses web site.

Admissions

Students seeking admissions to the Immunology Ph.D. Program typically have an undergraduate major in biological sciences, but majors from other areas are acceptable if the applicants have sufficient coursework in biology, chemistry, general physics, and mathematics (through calculus). Applications are evaluated by the Immunology Graduate Program committee based upon: GRE scores; 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 not required. Applicants should plan on taking the GRE at least one month prior to the application deadline of December 2nd to ensure that official scores are available when applications are evaluated. Interested Stanford medical students are welcome to apply to the program and should also submit a formal application by December 2.

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, insurance coverage, and a small allowance for books/travel. Applicants are urged to apply for independent fellowships such as from the National Science Foundation or National Defense Science and Engineering Graduate Fellowships. NSF Fellowship applications are due in November of the year prior to matriculation in the graduate program, but Immunology graduate students may continue to apply for outside fellowships after matriculation. Admitted students are typically offered financial support in the form of 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 adviser 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 six-day long introduction to immunology in the second week of September, exposes incoming Immunology Ph.D. students to a variety of 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 10 units during Autumn, Winter, Spring, and Summer quarters until reaching TGR status in the spring quarter of their fourth year. Students are required to pass all courses in which they are enrolled; 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 adviser in quarterly meetings and by the Stanford Graduate Program Committee in a final advising session in June.

First-year students are required to complete three rotations in at least two immunology labs. In the spring quarter, two mini-rotations of six weeks each may be arranged.

A specific program of study for each student is developed individually with the first-year adviser.

Core Courses:

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:  

In the third week of June, 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 PhD thesis lab. The first-year graduate student is asked to complete a “Big Picture” advising document, which takes stock of the first year student’s accomplishments in the past year, discusses near- and long-term plans, and serves as a transitional document for the PhD thesis adviser.

Once a dissertation adviser has been selected, a dissertation committee, including the dissertation adviser and two additional Immunology faculty, is constituted to guide the student during the dissertation research. The student must meet with the dissertation committee at least once a year. In the first through third years, the student must meet with the dissertation committee at least once a year. In the 4th and 5th years, students are expected to meet twice a year with their thesis committees. For students in their 5th years and above, a member of the Immunology Graduate Program Committee will also attend these bi-annual thesis committee meetings. In addition, 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 will help achieve these goals; 3) have open and direct dialogue with the PhD 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

MCTI first-year students are required to take the following courses in their first year for a letter grade:

Electives:

One elective (see elective list below)

Computational and Systems Immunology

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 students are required to take the following courses in their first and second years.

First Year:

Second Year: 

Electives:

Two electives (see elective list below)

Qualifying Exam and Admission to Candidacy

Second-year students are required to pass a general orals examination and write a thesis dissertation proposal, which will be presented to and evaluated by a committee of three faculty members (the dissertation advising committee). All students must be admitted to candidacy by the end of their second year. This is contingent upon satisfactory completion of course work, all first and second year requirements, the dissertation proposal, and the University's requirements for candidacy outlined in the Candidacy section of this bulletin. If a student does not meet the requirements for admission to candidacy by the end of the second year, the student is subject to dismissal from the PhD program.

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. All core course requirements must be completed by the end of the second year.

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 and CSI 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, Tuesdays, 4:15 pm) and the companion immunology seminar discussions course (IMMUNOL 311A Discussions in Immunology, Mondays, 10:00 am); in the latter, the seminar speakers’ papers are discussed. Students in their second year and above are required to attend 50% of the seminar series each academic year.  Students in the CSI track are required to attend the IMMUNOL 311 Seminar in Immunology for the Autumn and Winter quarters of their first year.  In the Spring quarter, attendance in IMMUNOL 311 Seminar in Immunology is optional so that graduate students in the CSI track may attend IMMUNOL 310 Seminars in Computational and Systems Immunology for the Spring and Summer quarters. 

Immunology Scientific Retreat

The annual Retreat is held at the Asilomar Conference Grounds, Pacific Grove, CA, 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. 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.

First Author Paper Submission

By the 4th or 5th year, graduate students are expected to submit a first author paper for publication. This milestone, the submission of a first author paper, should be completed before defending a PhD thesis.

Doctoral Dissertation

Before embarking on the dissertation defense process, the graduate student must submit a Petition to Defend to the Chair 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. In addition, 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 degree.

The Reading Dissertation Committee must be comprised of at least four faculty members. The minimum number of faculty members in the immunology program may be 2, but typically, 3 of the 4 Reading Dissertation Committee members are from the Graduate Program in Immunology. At the time of the PhD orals defense, an Orals Chair is chosen to lead the Orals Committee (distinct from the Reading Dissertation Committee), and the minimum number for this committee is 5. 

Faculty

Director, Executive Committee for the Immunology Program: Patricia Jones (Professor, Biology)

Chair for Immunology Graduate Program: Olivia Martinez (Professor, Research, Surgery, Transplantation)

Participating Departments and Faculty (Molecular, Cellular, Translational Immunology)

Biochemistry: Peter Kim (Professor)

Bioengineering: Stephen Quake (Professor, and Applied Physics and Physics)

Biology: Patricia P. Jones (Professor)

Genetics: Leonore A. Herzenberg (Professor, Research), Karla Kirkegaard (Professor), Michael Snyder (Professor)

Med/Biomedical Informatics:  Purvesh Khatri (Assistant Professor)

Medicine/Blood and Bone Marrow Transplantation Program: Everett Meyer (Assistant Professor), David Miklos (Assistant Professor), Robert Negrin (Professor), Judith Shizuru (Associate Professor)

Medicine/Cardiovascular Medicine: Joseph Wu (Professor, and Radiology)

Medicine/Endocrinology: Joy Wu (Assistant Professor)

Medicine/Gastroenterology and Hepatology: Aida Habtezion (Assistant Professor)

Medicine/Hematology: Ravi Majeti (Assistant Professor)

Medicine/Immunology and Rheumatology: C. Garrison Fathman (Professor), Jorg Goronzy (Professor), William Robinson (Associate Professor), Samuel Strober (Professor), Paul J. Utz (Professor), Cornelia Weyand (Professor)

Medicine/Infectious Diseases: Catherine Blish (Assistant Professor), Paul Bollyky (Assistant Professor)

Medicine/Oncology: Ash Alizadeh (Assistant Professor), Gilbert Chu (Professor, and Biochemistry), Dean Felsher (Professor, and Pathology), Holbrook Kohrt (Assistant Professor), Ronald Levy (Professor), Shoshana Levy (Professor, Research)

Medicine/Pulmonary and Critical Care Medicine: Mark Nicolls (Associate Professor)

Microbiology and Immunology: John Boothroyd (Professor), Yueh-Hsiu Chien (Professor), Mark M. Davis (Professor, and Director, Institute for Immunity, Transplantation and Infection), Juliana Idoyaga (Assistant Professor), Holden Maecker (Associate Professor, Research), Hugh McDevitt (Professor, Emeritus), Denise Monack (Associate Professor), Garry P. Nolan (Professor), David Schneider (Associate Professor)

Molecular and Cellular Physiology: K. Christopher Garcia (Professor, and Structural Biology), Richard S. Lewis (Professor)

Neurology and Neurological Sciences: May Han (Assistant Professor), Lawrence Steinman (Professor, and Pediatrics), Tony Wyss-Coray (Professor)

Neurosurgery: Theo Palmer (Associate Professor)

Otolaryngology/Head and Neck Surgery (ENT): Jayakar Nayak (Assistant Professor), John B. Sunwoo (Associate Professor)

Pathology: Sean Bendall (Assistant Professor), Scott Boyd (Assistant Professor), Eugene C. Butcher (Professor), Michael Cleary (Professor), Gerald R. Crabtree (Professor, and Developmental Biology), Edgar G. Engleman (Professor, and Medicine/Immunology and Rheumatology),  Andrew Fire (Professor, and Genetics), Stephen Galli (Professor and Chair), Sara Michie (Professor), Raymond A. Sobel (Professor), Irving Weissman (Professor, and Director, Stem Cell Institute)

Pediatrics: Manish Butte (Assistant Professor), Christopher Contag (Professor, Research, and Microbiology and Immunology, and Radiology), David B. Lewis (Professor), Maria Grazia Roncarolo (Professor, and Medicine/Blood and Marrow Transplantation), Elizabeth Mellins (Professor), Kari Nadeau (Associate Professor)

Psychiatry and Behavioral Sciences: Firdaus Dhabhar (Associate Professor), Emmanuel Mignot (Professor)

Radiology: Parag Mallick (Assistant Professor and Diagnostic Radiology)

Structural Biology: Peter Parham (Professor, and Microbiology and Immunology), Theodore Jardetzky (Professor)

Surgery/Multi-Organ Transplantation: Sheri Krams (Associate Professor, Research), Olivia Martinez (Professor, Research)

Participating Departments and Faculty (Computational and Systems Immunology)

Bioengineering: Stephen Quake (Professor, and Applied Physics and Physics)

Genetics: Michael Snyder (Professor), Karla Kirkegaard (Professor)

Med/Biomedical Informatics:  Purvesh Khatri (Assistant Professor)

Med/Immunology and Rheumatology: Paul J. Utz (Professor)

Med/Oncology: Ash Alizadeh (Assistant Professor)

Microbiology and Immunology: John Boothroyd (Professor), Mark M. Davis (Professor, and Director, Institute for Immunity, Transplantation and Infection), Holden Maecker (Associate Professor, Research), Garry Nolan (Professor)

Pathology: Sean Bendall (Assistant Professor), Scott Boyd (Assistant Professor), Andrew Fire (Professor, and Genetics)

Radiology:  Parag Mallick (Assistant Professor, and General Radiology)

Affiliate Members:

Biochemistry: Ron Davis (Professor, and Genetics)

Bioengineering: Russ Altman (Professor, and Genetics and Computer Science)

Health and Research Policy - Biostatistics: Robert Tibshirani (Professor, and Statistics)