PhD in Infectious Diseases and Immunity

The IDI Program intends to create opportunities for students to gain new and advanced knowledge about infectious disease agents and how they interact with host cells, human populations, and the environment. Our goal is to improve public health by increasing our understanding of infectious diseases and human immunology through basic and translational research that contributes to developing new diagnostics, treatments, and methods to prevent or control diseases. Because the IDI Graduate Group is administratively managed by the School of Public Health, we follow the School of Public Health application process and deadlines.

Program Objectives

The objective of this program is to provide students with research-oriented training that will enable them to design and implement independent investigations and advance the fundamental knowledge of infectious disease agents and their interactions with the human host and the environment. The IDI PhD program is five to six-year program. Students in the program are fully funded throughout their time in the program, and are provided with a competitive monthly stipend.

We strive to promote health by integrating basic research and applied technologies to develop new approaches for the diagnosis, treatment, prevention, and control of infectious disease in humans. This program combines clinical, epidemiological, and basic laboratory research strategies in order to apply these methods to specific infectious disease problems affecting human populations. In addition, students have opportunities to interact with faculty members from multidisciplinary centers involved in global infectious disease research. These include the Center for Global Public Health and Center for Emerging and Neglected Diseases. Students matriculating through this program will acquire expertise in not only fundamental infectious disease research, but also learn how their research relates to other disciplines. Students matriculating through this degree program will acquire expertise in fundamental infectious diseases research for which there is demand from academic institutions, local and national government agencies, and biotechnology companies.

Curriculum

The PhD program in Infectious Diseases and Immunity (IDI) is a laboratory based infectious disease research program that spans immunology and microbiology with a public and global health focus. It usually takes about 5.5 years to complete the IDI PhD degree. The Graduate Group in Infectious Diseases and Immunity, administered by the School of Public Health, is an interdepartmental graduate program that is unique in its emphasis on integrated multidisciplinary training. Important areas of inquiry include the biology of host-pathogen interactions, molecular and cellular aspects of pathogenesis, the ecology and evolution of disease agents, environmental factors in transmission, intermediate hosts and vectors, the biology of surveillance and epidemiological analysis, and vaccine and disease prevention and control. The program follows the Admission application process and requirement of the School of Public Health which requires the applicant to complete both the SOPHAS and UC Berkeley Graduate Admission applications.

In addition to the minimal core course requirements (listed below) each student shall take additional courses selected in consultation with the major professor and/or Graduate Advisor and approved by the Group Executive Faculty Committee. The specific courses will not be listed here since this part of the student’s curriculum will be tailored to meet identified professional career goals. In addition, laboratory rotations, two GSI teaching, qualifying examination, research resulting in a dissertation, and enrollment and participation in the IDI Doctoral Seminars are required for completion of the Ph.D. degree.

The minimum requirements include core training in molecular biology, epidemiology, statistics, and research ethics. Specific training in infectious disease is also available related to a student’s major interest for more specialized preparation.

It is expected that students will complete a minimum of 30 units of predominantly graduate-level courses, in addition to 4 units of graduate seminar. During the first three to four semesters of the program, doctoral students complete all or most of the course work required for the degree and rotate through the research laboratories of one to three faculty members, who evaluate the student’s ability to conduct laboratory research. This allows the student to determine what research opportunities are available to them, to learn new research methods that will be of value in their subsequent dissertation research, and to decide on a suitable research project for their dissertation.

Required and recommended courses, including teaching requirement:

The following minimum core graduate courses, or their equivalent, are required of all students in the Graduate Group. These courses should be taken before the Qualifying Examination Committee is appointed, and the student must receive a “B” or higher grade average in these courses, except seminars that can be taken on a Satisfactory or Unsatisfactory basis (S/U).

  • PH 260A Principles of Infectious Disease (4 units)

And one of the following:

  • PH 260B Principles of Infectious Disease (4 units)
  • PH 266B Zoonotic Diseases (2 units)
  • PH 262 Molecular Basis of Bacterial Pathogenesis (3 units)
  • PH 265 Molecular Parasitology (3 units)

One of the Following:

  • PH 263 Public Health Immunology (3 units)
  • MCB 250 (4 units)

One of the following:

  • PH 145 Statistical Analysis of Continuous-Outcome Data
  • PH 245 Introduction to Multivariate Statistics

And one of the following:

  • PH 253B Epidemiology and Control of Infectious Diseases (3 units)
  • PH 260E Molecular Epidemiology
  • PH 293 Monday IDI Doctoral Seminar, for all IDI students
  • PH 293 Wednesday IDI Doctoral Seminar for pre-QE students

It is suggested that, students will elect to take at least a few additional advanced courses appropriate to the student’s area of research interest and fill in the gap of knowledge in areas such as cell biology, genetics or biochemistry with the guidance of the Graduate Advisor and other faculty. All IDI PhD students must register and attend Monday IDI Doctoral Seminar PH 293. In addition, all IDI pre-QE students must register and attend the Wednesday IDI Doctoral Seminar PH 293 as well.

Lab Rotations

Rotations in lab provide an opportunity for students to experience different research areas and environments. Lab rotation should be arranged by mutual agreement with the faculty and the student in consultation with the IDI Head Graduate Advisor. Each lab rotation may last 10 weeks and should begin as early as the mid part of the first semester. Students are suggested to do three rotations before deciding on the lab for their dissertation research.

Teaching Requirement

At least two semesters as a Graduate Student Instructor (GSI) are required.

Qualifying Examinations

A qualifying examination (QE) should be taken no later than the second year (4th semester) of graduate study, and only after all course requirements have been completed with a minimum grade-point average of at least 3.0 (4-point scale), excluding lower-division courses, seminars and research.  The graduate advisor and the student will select a four-member committee to administer the examination. The Ph.D. qualifying examination consists of an oral defense of two written research proposals (10-15 pages each).  One proposal describes the student’s proposed dissertation research, and the other must encompass a research problem in an area unrelated to the dissertation research.  The purpose of the examination is to test the student’s mastery of a broad area of knowledge reflecting the interdisciplinary preparation of an approved course of study.

Advancement to Candidacy

Within one semester of passing the qualifying examination, students must apply for advancement to candidacy for the Ph.D. degree. At this point, the student must identify a Dissertation Committee comprised of faculty members who can contribute to the dissertation research work.  The Dissertation Committee Chair is the student’s primary research mentor. PhD candidates are required to meet with their dissertation committee at least once a year to discuss research progress, manuscripts in preparation, a proposed timeline for graduation, and post-graduation plans.

Research and Dissertation

The research preceptor is typically selected by the student after obtaining research experience through laboratory rotations.  The student is thus acquainted with the research opportunities available in several laboratories and can evaluate these opportunities in the context of their personal interests.  Students with interests that are clearly defined and are not identified among the Graduate Group faculty, but can be identified among faculty at Berkeley or UCSF outside of the Graduate Group, may elect through direct mentorship of a Graduate Group member to conduct their research in a laboratory other than one represented in the Graduate Group. It is expected that the student’s research will be of sufficient quality to be accepted for publication in peer-reviewed journals.  A goal of at least one, but preferably two or more first-author publications are typically considered sufficient to write the dissertation.  The emphasis on publication of student research, rather than merely completing a dissertation, is an intrinsic component of the Program’s training experience. Within three months of filing the student’s dissertation, the student will give an oral seminar to the members of the Graduate Group describing the dissertation research conducted.

Admissions Statistics

5% Admissions Ratio: (3/64)
3.77 Average GPA of admitted applicants
75% Average Verbal GRE scores of admitted applicants
70% Average Quantitative GRE scores of admitted applicants

Qualifications

The following subjects are normally required as undergraduate preparation for all candidates. Deficiencies must be made up early during the graduate program.

Mathematics: Calculus; one course in probability or statistics.

Physics: General physics.

Chemistry and biochemistry: Inorganic chemistry; organic chemistry; biochemistry; and associated laboratories.

Biology: General biology lecture and laboratory; genetics; and a basic course(s) in molecular biology.
Common undergraduate majors for admitted applicants: Biology, integrative biology, microbiology, biological sciences, biology and communications

Common work experience for admitted applicants: Work experience is not required for admission, but relevant work experience related to infectious diseases, e.g. wet laboratory and/or surveillance work is important for the IDI PhD program. Most of the admitted applicants have strong lab and research experience.

Faculty

IDI Graduate Group faculty come from multiple departmental units spread throughout the departments of Infectious Diseases and Immunity, Plant and Microbial Biology, and Molecular and Cell Biology. In addition, a unique aspect of the IDI program is our affiliation with UCSF faculty who conduct work in the area of global infectious disease. IDI students may choose to join any IDI affiliated lab for their thesis research.

SPH IDI Graduate Group Faculty

UC Berkeley Faculty from Other Departments

Gregory Barton, Molecular and Cell Biology

Steven Brenner, Plant and Microbial Biology 

Laurent Coscoy, Molecular and Cell Biology 

Jeffery Cox, Molecular and Cell Biology 

Michel DuPage, Molecular and Cell Biology 

Suzanne M.J. Fleiszig, Optometry 

Wayne Getz, Environmental Science, Policy and Management 

Britt A. Glaunsinger, Plant and Microbial Biology 

Karsten Gronert, Optometry 

Amy Herr, Bioengineering 

Luke Lee, Bioengineering  

Terry Machen, Molecular and Cell Biology

Kara Nelson, Civil and Environmental Engineering 

Daniel Portnoy, Molecular and Cell Biology/Plant and Microbial Biology

Arthur Reingold, Public Health Epidemiology

Vincent Resh, Environmental Science, Policy and Management 

Ellen A. Robey, Molecular and Cell Biology 

Kimberly Seed,  Plant and Microbial Biology 

Nilabh Shastri, Molecular and Cell Biology 

Kimmen Sjolander, Plant and Microbial Biology/Bioengineering  

John W. Taylor, Plant and Microbial Biology

Russell E. Vance, Molecular and Cell Biology

Matthew D. Welch, Molecular and Cell Biology 

Qiang Zhou, Molecular and Cell Biology

UCSF Affiliated Faculty

Seemay Chou

Margaret Feeney

Brian Greenhouse

Warner Greene

Oren Rosenberg

Phil Rosenthal

Donors

We would like to thank the following funding donors for their generous fellowship support to support our students and our work:

Hillel and Rose Levine Fellowship

The Albert and Mildred Krueger Memorial Fellowship

Sally Anne Bradley Presser and Steven A. Presser Fellowships

Prospective donors, please visit give.berkeley.edu.