Current Students

Curriculum

Lab Research.
Photo courtesy CDC.

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:

 
  1. Core  training in molecular biology, epidemiology, statistics, and research ethics
  2. Specific training in infectious disease related to their major interest to obtain 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).

 
Group I: Infectious Diseases (2 courses)
  PH 260A  Principles of Infectious Disease (4 units)
   
  And one of the following:
  PH 260B Principles of Infectious Disease (4 units)
  PH 261 Advanced Medical Virology (3 units)
  PH 262  Molecular Basis of Bacterial Pathogenesis (3 units)
  PH 265  Molecular Parasitology (3 units)
PH 266  Viruses & Cancer (3 units)
Group II: Immunology (1 course)
 

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

 
   
Group III: Epidemiology and Biostatistics (2 courses)
  PH 145  Statistical Analysis of Continuous-Outcome Data 
or PH 245   Introduction to Multivariate Statistics
  PH 253B  Epidemiology and Control of Infectious Diseases (3 units) or PH 260E Molecular Epidemiology
Group IV: Research (2 courses)
  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 section 4. In addition, all IDI pre-QE students must register and attend the Wednesday IDI Doctoral Seminar PH 293 section 12 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 9 weeks and should begin as early as the later part of the first semester. Students are suggested to do at least one or two lab rotations before deciding on the lab for their research.

Teaching Requirement

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

Qualifying Examination

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 come up with a four-member committee to administer the examination. Students will submit the Qualifying Exam Application, as approved by IDI PhD Program Head, to IDV Office for submission to the Grad Division for approval. The  Qualifying Exam Applications (PDF) must be submitted at least four weeks for approval prior to the proposed exam date. No students can take the QE Exam without the Grad Division approval.

Students wishing to use co-authored or previously published material in their thesis or dissertation must make the request at least three weeks before they file. One member of this committee must be an academic senate member from another department on the Berkeley campus who is not a faculty member in the Graduate Group in Infectious Disease and Immunity. 

The research advisor for the student’s dissertation may not serve on the QE committee.
The Ph.D. qualifying examination consists of an oral defense of two written research proposals (10-15 pages each).  One proposal may be the student’s proposed dissertation research problem, but the other must encompass a research problem in an area unrelated to the dissertation research.  The Chair of the Ph.D. Qualifying Examination Committee must approve the research problems for both propositions.  Final versions of these written proposals must be submitted to the Committee members no later than 2 weeks prior to the date of the qualifying examination. 

During the examination, questions by the Committee dwell on the background and theory of the proposed research, the rationale for the proposed methods of data analysis, etc., and not on actual research results.  The latter is a function of the student’s Dissertation Committee.  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.  With permission of the Dissertation Committee Chair, a student can include in the committee faculty members from outside of the Division of Infectious Disease and Vaccinology as well as those from outside of University of California at Berkeley.  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 by March 31st and send the signed form to the Head Graduae Advisor and IDV Division for record. The student will then initiate and submit the required official Annual Doctoral Progress Report in GLOW by the end of Spring semester every year.

 

Research and Dissertation

The research for the dissertation is conducted under the guidance of a three- (or more) member Dissertation Committee, for which the student’s research mentor is normally the Committee Chair, and that includes an outside member who is a UC Berkeley Academic Senate member and not a member of the Graduate Group in Infectious Diseases and Immunity.  The composition of the committee is subject to the approval of the Dean of the Graduate Division.  One member of the committee may be non-Berkeley Academic Senate with approval of the Dean of the Graduate Division.
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.

The student presents a written research proposal to the committee prior to formally commencing the research.  This proposal results from working closely with the Candidate’s research preceptor and usually involves the acquisition of preliminary data.  The candidate must consult with each member of the committee as soon as possible after advancement to candidacy; and periodically (minimally once per year) thereafter, to evaluate and monitor the student’s progress and provide guidance to the student’s research.  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 three 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 and one of its unique strengths.

Culminating Seminar: 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.

 

Current IDI PhD Students | Fall 2017

 

Year of Admission and lab in parenthesis

Jonathan Portman (2011 Portnoy lab)

Matthew Gardner (2012 Glaunsinger lab)

Nicole Tarlton (2012 Riley lab)

Daniela Andrade (2013 Harris lab)

Dustin Glasner (2013 Harris lab)

Paulina Andrade (2014 Harris lab)

Eric Lee (2014 Portnoy lab)

Alexandra Tsitsiklis (2014 Robey lab)

Derek Bangs (2015 Robey lab)

Gina Borgo (2015 Welch lab)

Milena Dimitrova (2015 Harris lab)

Kristina Geiger (2015 Coscoy lab)

Perri Callaway (2016 Feeney lab, UCSF)

Marissa Foster (2016 Riley lab)

Nicholas Lo Tsu Ning (2017)

 

Seminars/Events

CEND Seminars and Infectious Disease Supergroup
Check http://cend.berkeley.edu for updated schedule.

Resources:

 

Student Groups and Associations
Infectious Disease and Immunity PhD Group

Graduate Division

Guide to Graduate Policy: http://grad.berkeley.edu/policies/guides/category/ggp/
Degrees FAQ: http://www.grad.berkeley.edu/policies/faq.shtml
Fees: http://grad.berkeley.edu/admissions/cost_fees.shtml
Fellowship Office: http://grad.berkeley.edu/financial/fellowships_office.shtml
Information on GSI/GSR/Reader/Tutor appointments: http://grad.berkeley.edu/policies/pdf/apptknow.pdf
Filing Electronic Dissertation: http://grad.berkeley.edu/policies/pdf/disguide.pdf
Filing Dissertation Deadlines: http://www.grad.berkeley.edu/policies/degree_filing_deadlines.shtml
Graduate Diversity Program: How to Establish and Manager the Advisor/Advisee Relationship.pdf
Resources on How to write an Academic Grant Proposal

Resources package-Grant Writing Proposal

 

Registrar
Academic & student calendars, fees, legal residency: http://registrar.berkeley.edu/
Establishing California residency: Guidelines from the Registrar's Office                             

Current Students- Forms and Applications

IDI Guidelines to Qualifying Examination effective 12/16/2015

IDI Guidelines to Qualifying Examination

PhD: Application for Qualifying Examination:  
http://www.grad.berkeley.edu/policies/pdf/qe_application.pdf

Need to know information from the Grad Division for Doctoral Students on Advancing to Candiday

http://grad.berkeley.edu/academic-progress/advanced/

PhD: Advancement for Candidacy form:
Application for Candidacy (Plan B)

Report on Progress in Candidacy in the Doctoral program:
http://grad.berkeley.edu/academic-progress/advanced/academic-progress-report/

IDI Form to prepare for the Dissertation Committee Meeting


Information on writing and submission of dissertation:
http://www.grad.berkeley.edu/policies/pdf/disguide.pdf
Filing Fee Application PDF

Business Forms:
CTS Form: http://controller.berkeley.edu/travel/TravelAgency/CTSForm.pdf
Policies on Travel and Entertainment and the Reimbursement Form:  http://controller.berkeley.edu/travel/

Extramural Resources:
American Society for Microbiology: www.asm.org
Northern California Branch of ASM: www.asm.org/branch/branco/index.html
American Public Health Association: www.apha.org