2021-22 Epidemiology PhD Handbook

One of the degree programs offered by Public Health Sciences at Penn State College of Medicine is the Epidemiology PhD degree. The objectives of the Epidemiology PhD program are to train students to:

• master current quantitative methods, including study designs and appropriate analytic methods in epidemiological research;
• have broad knowledge of the epidemiology of various major human diseases; and
• to become expert epidemiologists in a specific disease/health status topic.

Career opportunities are available in universities, academic medical centers, research organizations, government and private industry.

The mission of the Department of Public Health Sciences at Penn State College of Medicine is to advance health science through:

• the design, conduct and analysis of population-based biomedical research;
• the support of basic science and clinical research; and
• the education of future generations of health professionals.

The mission of the Epidemiology PhD Program in Public Health Sciences is to fulfill the third arm of the departmental mission.

Completion of the degree indicates that the student will have:

• mastered current quantitative methods in epidemiological research to perform in a professional, academic or corporate setting;
• demonstrated the ability to master current knowledge of major public health concerns and demonstrated ability to develop and conduct epidemiological research in a specific topic of major public health relevance; and
• demonstrated a work ethic that supports scholarship and promotes the highest standards of academic integrity.

Each student in the Epidemiology PhD program is assigned an academic adviser upon admission to the program. The assignment is based on matching the student’s research interest and faculty’s expertise in a specific area of research. The role of the academic adviser is as a point of contact for the student as regards to course selection and to help the student with any academic questions or concerns that might arise. Both the student and the adviser are invited to consult with the Graduate Program Director about any issues related to the student’s graduate education experience.

The Epidemiology PhD program encourages students to discuss their research interest with their academic advisors, with the goal of developing the academic adviser and advisee relationship into a PhD dissertation adviser and advisee relationship.

Students also are encouraged to discuss their research interest with other faculty to develop a PhD dissertation adviser and advisee relationship.

After the student has identified a PhD dissertation topic and established a dissertation adviser and advisee relationship, the dissertation adviser replaces the academic adviser as the primary point of contact and to provide academic guidance for the student in regards to completion of the dissertation. The Epidemiology PhD program highly encourages the student to work with their assigned academic adviser to become a dissertation adviser. The dissertation adviser should be identified soon after the student successfully completes the required courses and before the qualifying examination. The qualifying examination is administered after completion of the first three semesters of course work, often in the end of the second fall semester.

The program is designed to be completed in four years, beginning in the fall semester and concluding at the end of the spring semester of the fourth year. It is possible that a student who transfers credits from another institution may finish in less than four years. The typical course sequence is outlined elsewhere in this handbook.

Students planning to graduate in the spring must electronically file their intent to graduate with the Graduate School during January. The PhD dissertation must be written and submitted according to the deadlines outlined by the graduate school. The Graduate School, University Libraries and the graduate faculty of Penn State have established format standards that a dissertation must meet prior to receiving final approval as fulfillment of a graduate requirement. The Office of Theses and Dissertations is the unit of the Graduate School responsible for certifying that the thesis has been prepared in accordance with these established regulations.

The PhD doctoral committee consists of four or more active members of the Graduate Faculty, which includes at least two faculty members in the Division of Epidemiology and one faculty from the Division of Biostatistics and Bioinformatics in the Department of Public Health Sciences. The doctoral committee is chaired by the dissertation adviser. Faculty members with a primary appointment in the Division of Epidemiology are eligible to serve as the doctoral committee chair. Other faculty members who direct and teach a required course for the PhD in Epidemiology program are also eligible to serve as the chair. At least one regular member of the doctoral committee must represent a field outside the candidate’s major field of study in order to provide a broader range of disciplinary perspectives and expertise. This committee member is referred to as the “Outside Field Member.” Additionally, in order to avoid potential conflicts of interest, the primary appointment of at least one regular member of the doctoral committee must be in an administrative unit that is outside the unit in which the dissertation adviser’s primary appointment is held. This committee member is referred to as the “Outside Unit Member.”

When a PhD candidate has substantially completed all coursework and the qualifying examination, a comprehensive examination, in the form of defending the PhD dissertation proposal, is given. The student must be in good academic standing and must be registered as a full-time or part-time student for the semester in which the comprehensive examination is taken.

The Epidemiology PhD Program encourage the student to taken the comprehensive examination in the end of the second spring semester or the beginning of the third fall semester. The doctoral candidate who has satisfied all other requirements for the PhD degree will be scheduled by the Office of Graduate Enrollment Services to take a final examination. Normally the final oral examination may not be scheduled until at least six months have elapsed after the comprehensive examination was passed.

Following admittance to a degree program, the student should confer with the head of that major department or program concerning procedures and the appointment of an academic adviser. Consultation or arrangement of the details of the student’s semester-by-semester schedule is the function of the academic adviser. This person may be a member of the doctoral committee or someone else designated by the head of the major program for this specific duty. The academic adviser may be different from the dissertation adviser.

Doctoral Committee

General guidance of a doctoral candidate is the responsibility of a doctoral committee consisting of four or more active members of the Graduate Faculty, which includes at least two faculty members in the major field. The dissertation adviser must be a member of the doctoral committee. The dissertation adviser usually serves as chair, but this is not required. If the candidate is also pursuing a dual-title field of study, a co-chair representing the dual-title field must be appointed. In most cases, the same individual (e.g., dissertation adviser) is a member of the Graduate Faculty in both the major and dual-title fields, and in such cases may serve as sole chair.

At least one regular member of the doctoral committee must represent a field outside the candidate’s major field of study in order to provide a broader range of disciplinary perspectives and expertise. This committee member is referred to as the “Outside Field Member.” In cases where the candidate is also pursuing a dual-title field of study, the dual-title representative to the committee may serve as the Outside Field Member.

Additionally, at least one regular member of the doctoral committee must have a primary appointment in an administrative unit outside the primary appointment administrative home of the student’s dissertation adviser (e.g., for tenure-line faculty, the tenure home) in order to avoid the potential for conflicts of interest. This committee member is referred to as the “Outside Unit Member.” In some cases, an individual may have a primary appointment outside the administrative home of the student’s dissertation adviser and also represent a field outside the student’s major field of study; in such cases, the individual may serve as both the Outside Field Member and the Outside Unit Member.

If the candidate has a minor, that field must be represented on the committee by a “Minor Field Member.” (See also Major Program and Minor Field under DEd — Additional Specific Requirements.)

This committee is appointed by the graduate dean through the Office of Graduate Enrollment Services, upon recommendation of the head of the major program, soon after the student has passed the qualifying exam. The dean may on occasion appoint one or more members of the committee in addition to those recommended by the program chair.

A person not affiliated with Penn State who has particular expertise in the candidate’s research area may be added as a “Special Member,” upon recommendation by the head of the program and approval of the graduate dean (via the Office of Graduate Enrollment Services). A Special Member is expected to participate fully in the functions of the doctoral committee. If the Special Member is asked only to read and approve the doctoral dissertation, that person is designated a special signatory. Occasionally, special signatories may be drawn from within the Penn State faculty in particular situations.

The membership of doctoral committees should be periodically reviewed by the program chair to ensure that its members continue to qualify for service on the committee in their designated roles. For example, if appointments, employment at the University, etc., have changed since initial appointment to the committee, changes to the committee membership may be necessary. If changes are warranted, they should be made as soon as possible to prevent future problems that may delay academic progress for the student (e.g., ability to conduct the comprehensive or final examinations).

CHAIR

The chair or at least one co-chair must be a member of the graduate faculty of the specific doctoral program in which the candidate is enrolled. A retired or emeritus faculty member may chair a doctoral committee if they began chairing the committee prior to retirement and has the continuing approval of the department head or program chair. The primary duties of the chair are: (1) to maintain the academic standards of the doctoral program and the Graduate School and assure that all procedures are carried out fairly, (2) to ensure that the comprehensive and final examinations are conducted in a timely fashion, (3) to arrange and conduct all meetings, and (4) to ensure that requirements set forth by the committee are implemented in the final version of the thesis.

RESPONSIBILITIES OF DOCTORAL COMMITTEES

The doctoral committee is responsible for approving the broad outline of the student’s program and should review the program as soon as possible after the student passes the qualifying exam. Moreover, continuing communication among the student, the committee chair, the research supervisor, and the members of the committee is strongly recommended, to preclude misunderstandings and to develop a collegial relation between the candidate and the committee.

DOCTORAL EXAMINATION

The (entire) committee will prepare and administer the examination, and evaluate the candidate’s performance on the examination. If a committee member is unable to attend the final oral defense, the member may sign as a special signatory. A revised committee appointment form will need to be sent to the Office of Graduate Enrollment Services, 114 Kern Graduate Building, removing the faculty member as a regular committee member and if it is desired to designate that individual as a special signatory, a memo must accompany the revised committee form, requesting that the faculty member be moved to a special signatory. If there are then not enough members serving on the committee (i.e., four or more active members of the Graduate Faculty), another Penn State faculty member will need to replace that member to constitute a legitimate doctoral committee. (Substitutes are not permitted.) These changes and approvals shall occur before the actual examination takes place. The program administrator will notify the Office of Graduate Enrollment Services, providing two weeks’ notice, when the candidate is ready to schedule the comprehensive and the final oral examinations and will report the results of these examinations to that office.

The dissertation adviser, as well as the chair of the doctoral committee (if not the same individual as the dissertation adviser), along with additional members of the committee to total a minimum of three (3), must be physically present at the final oral examination. The graduate student must also be physically present at the exam. (Thus for a five-person committee, two could participate via distance.) No more than one member may participate via telephone; a second member could participate via interactive videoconferencing. The examination request and a request for exceptions must be submitted to the director of Graduate Enrollment Services for approval at least two weeks prior to the date of the exam. Special arrangements, i.e., requirements for meeting participation via distance, must be communicated to the student and the doctoral committee members well in advance of the examination.
A favorable vote of at least two-thirds of the members of the committee is required for passing a comprehensive or a final oral examination. If a candidate fails an examination, it is the responsibility of the doctoral committee to determine whether another examination may be taken.

The committee examines the dissertation, administers the final oral examination, and signs the approval page of the dissertation. At least two-thirds of the committee must approve the dissertation.

Each student in the Epidemiology PhD program is expected to acquire breadth of knowledge in the discipline of Epidemiology. Each student must complete:

• at least 28 didactic credits as described elsewhere in this handbook; and
• an original dissertation that involves a specific research topic in an epidemiological area that is worthy of publications of at least two original research manuscripts in peer-reviewed scientific journals.

Students enrolled in the Epidemiology PhD program will be required to successfully complete a minimum of 28 accumulated course credit hours. Specifically, students are required to take the “Required Core Methodology” courses (16 credits), and the one-credit Research Ethics course (PHS 500), which is a required course to meet the SARI requirements.

Students are also required to take three 3-credit “Required Core Substantive Epidemiology” courses (9 credits). Students can also take one Elective Substantive Epidemiology courses, including individual studies (EPID596) with their research mentor.

Required Core Methodology courses (16 credits)

• PHS 500: Research Ethics (1 credit)
• PHS 510: Grant Writing Methods (3 credits)
• PHS 518: Scientific Communications (3 credits)
• PHS 554: Statistical Methods in Public Health I (3 credits)
• PHS 555: Statistical Methods in Public Health II (3 credits)
• PHS 560: Epidemiological Research Methods (3 credits)

Required Core Substantive Epidemiology courses (9 credits)

• PHS 503: Nutritional epidemiology (3 credits)
• PHS 556: Cancer epidemiology (3 credits)
• PHS 558: CVD epidemiology (3 credits)

Elective Substantive Epidemiology courses (3 to 9 credits)

• PHS 561: Chronic disease biomarkers epidemiology (3 credits)
• PHS 562: Environmental epidemiology (3 credits)
• PHS 563: Infectious disease epidemiology (3 credits)
• EPID 596: Individual Studies (3 to 9 credits)

Elective Biostatistics courses (12 credits)

• PHS 523: Multivariate Analysis (3 credits)
• PHS 524: Longitudinal Data Analysis (3 credits)
• PHS 526: Categorical Data Analysis (3 credits)
• PHS 527: Survival Analysis (3 credits)

Other Requirements

Students are required to fulfill the following requirements:

• Epidemiology and biostatistics seminar series: Students are required to attend. Each student is required to present at least one seminar each year after their qualifying examination.
• Qualifying examination: This is taken after completion of the first three semesters of course work. The topics for the qualifying examination will be posted in the last week of the third semester (second fall semester). Student will choose a topic area, and write an Investigator-Initiated Research Proposal (R01).
• Comprehensive exam: This will be a defense of the dissertation research proposal, administered by the entire doctoral committee. The comprehensive examination can takes place sometime in between six to 12 months after the qualifying examination.
• PhD dissertation (PHS 601).
• Final oral dissertation defense: This is administered by the entire doctoral committee.

Proposed Schedule of Coursework

Fall semester, Year 1 (9 credits)

• PHS 554 – Statistical Methods for Public Health I (Required course)
• PHS 556 – Cancer Epidemiology (Required course)
• PHS 558 – Cardiovascular Disease Epidemiology (Required course)

Spring semester, Year 1 (10 credits)

• PHS 500 – Research Ethics (Required course)
• PHS 555 – Statistical Methods for Public Health II (Required course)
• PHS 560 – Epidemiological Research Methods (Required course)
• PHS 562 – Environmental Epidemiology (Elective course)

Fall semester, Year 2 (9 or more credits)

• PHS 503 – Nutritional Epidemiology (Required course)
• PHS 510 – Grant Writing (Required course)
• PHS 518 – Scientific Communications (Required course)

Spring semester of Year 2 or early fall semester of Year 3

• Comprehensive exam

Years 3 and 4

• Dissertation research and final defense

Students are also required to fulfill the following requirements:

1. Students are required to attend the epidemiology seminar series. To enable our PhD students to be excellent communicators in professional settings, we require each PhD student to give at least two presentations in the seminar series.
2. A qualifying examination is taken after completion of the first three semesters of coursework. The topics for the qualifying examination will be posted after the third semester (second fall semester), usually in June. Students write a NIH investigator initiated research proposal (R01) based on their intended dissertation research topic. Students are the PI of the proposed study. Specifically, this is a full R01 proposal, just as an individual would submit to one of the NIH study sections. All major components of the study are required and the PI are responsible for including the project summary, abstract (30 lines), a short project narratives (3-4 sentences), biosketch (4 pages), specific aims (1 page), the research plan (12 pages), a projected budget and a budget justification, references, protection of human subjects and enrollment table. Proposals are evaluated according to the NIH’s R01 review criteria. Because this is a qualifying examination, students are not allowed to consult with others on the proposal. Students are not allowed to ask others to review proposals before they are submitted. Violation of these rules can lead to a proposal’s disqualification.
3. A comprehensive exam, which will be a defense of dissertation research proposal, will be administered by the entire doctoral committee. The comprehensive examination can take place six to 12 months after the qualifying examination. In the period between passing the qualifying exam and before taking the comprehensive exam, a student should work closely with their primary mentor(s) in forming a dissertation committee and in preparing the dissertation research proposal. Oftentimes, students are encouraged to focus on their dissertation research proposals, the full literature review to support their dissertation research hypotheses, the details of study populations, methods on study design and data collection, major preliminary data supporting the feasibility of the proposed research, major statistical methods to be used, and finally, the expected results, potential difficulties and alternative approaches. In planning for the comprehensive exam, students must prepare a written document (about 30 pages) and submit it to the members of the dissertation committee two weeks in advance of the comprehensive exam. The comprehensive exam has two parts:
   • Part One: A 45- to 60-minute public presentation of the dissertation research proposal.
   • Part Two: A closed-door meeting with the dissertation committee members.

4. A PhD dissertation (PHS 601)
5. A final oral dissertation defense administered by the entire doctoral committee.

Students are allowed to transfer up to 10 credits from an external graduate program to fulfill the 28-credit course requirements for the Epidemiology PhD program. The Admissions Committee will review the syllabus for the equivalent courses to determine their eligibility for transfer.

All PhD candidates are required to demonstrate high-level competence in the use of the English language, including reading, writing, and speaking. All PhD candidates will be evaluated on their English competency (1) by their presentations in epidemiology seminar series before their qualifying exam by the program director; and (2) by the required course instructors at the time of grading their homework, class presentations, and class examinations. The program director and these course instructors will be asked to identify any potential English competency concerns based on both oral and written interactions with students. If any concerns are raised, the program director will determine subsequent steps including possibly additional testing and remediation steps. If no concerns are raised, then the student is found to have sufficient English competency per the graduate school requirement.

An original PhD dissertation is required for completion of the Epidemiology PhD. Details about the dissertation requirements are available on the Graduate School website.

The Graduate School reviews the format of the dissertation and does not provide edits to the dissertation for spelling, grammar or punctuation. A PhD dissertation must be submitted electronically. See details on electronic thesis (eTDs) submissions.

A minimum grade-point average of 3.0 for all coursework is required to fulfill the graduation requirements. One or more failing grades or a cumulative grade-point average below 3.0 may be considered evidence of unsatisfactory scholarship and be grounds for dismissal from the University (see the Graduate Programs Bulletin).

If, for reasons beyond the student’s control, a student is prevented from completing a course within the prescribed time, the grade in that course may be deferred with the concurrence of the instructor.

The period during which a grade may be deferred shall not extend, without further approval of the dean of the college, beyond the end of the sixth week of the next semester in which the University is in session. A deferred grade that is not changed to a passing grade by the instructor before the end of this period automatically becomes an F.

Academic Integrity at Penn State is defined in Faculty Senate Policy 49-20 as “the pursuit of scholarly activity in an open, honest and responsible manner.” The University’s Code of Conduct states that “all students should act with personal integrity, respect other students’ dignity, rights and property, and help create and maintain an environment in which all can succeed through the fruits of their efforts.

Academic integrity includes a commitment not to engage in or tolerate acts of falsification, misrepresentation or deception. Such acts of dishonesty violate the fundamental ethical principles of the University community and compromise the worth of work completed by others”. Academic dishonesty (including, but not limited to cheating, plagiarism, or falsification of information) will not be tolerated and can result in academic or disciplinary sanctions such as a failing (F) grade in the course.

Teaching Assistant (TA)

An excellent PhD-level epidemiologist should be an excellent teacher as well. To gain such experience during the PhD training period is an important step towards such an expectation. Therefore, all students in the PhD Epidemiology program are required to serve as a Teaching Assistant (TA) in an epidemiology course for at least three consecutive years. The TA position is assigned by the PhD program director. The program expects the TA to attend all lectures of the course that they are assigned to be the TA. The first year TA will run the Lab and grade the homework as directed by the course director. The course director will perform assessment of the TA performance and decide to offer the opportunity of allowing the second- and third-year TA to give 1-2 lectures in the last two years.

Research Assistant

Research is the focus of our PhD in Epidemiology program. Research results are often communicated with other scientists in professional meetings and publishing in reputable peer-reviewed journals. Therefore, all students with a Penn State graduate assistantship are required to serve as a RA in all years in the PhD program, with the first year working in their academic mentor’s ongoing research projects, and the last 2-3 years on dissertation research with their mentor. Students without a graduate assistantship are not required to work as a Research Assistant. In most cases, these students are also full time employees of various research entities. As such, these students will gain their first two years’ research experience from their research work, and their last 2-3 years’ research experience from dissertation research with their mentor.

The research productivity from our PhD students will be presented in our Epidemiology Seminar series. Please refer to Seminar Series for more details.

We highly encourage our PhD students to submit their research work to national scientific meetings. We have created a travel fund to support student attendance at national scientific meetings to present their work. Please refer to Academic Travel Support for more details.

To enable our PhD students to be excellent communicators in professional settings, we require each PhD student to give at least two presentations in our PHS Epidemiology Seminar Series.

The first presentation would be for the second-year PhD students to present the research from their first year as a PhD student. The first presentation should be 30-60 minutes per student.

If a student is in a Graduate Assistantship position (we have four such positions each year), the student is required to work with their primary mentor as a Research Assistant upon enrollment. If you are in this situation, you should work with your academic mentor to learn about your mentor’s research projects upon arrival. As a result, you should have enough material to fulfill your first presentation (given in the second year of your study) requirement.

If a student is self-pay, they are not required to work as a Research Assistant. In most cases, these students are also full-time employees of Penn State. As such, these students are involved in research projects with their job supervisor. If you are in this situation, you should present work-related research material to fulfill your first presentation (given in the second year of your study).

The second presentation would be for the third-year students after passing the qualifying examination. The second presentation can be used to fulfill a PhD candidate’s oral defense of the dissertation research proposal if the dissertation committee chair desires to do so. As such, the second presentation will be more concentrated on a PhD candidate’s dissertation research. The second presentation will be 60 minutes per student.

The Public Health Sciences (PHS) Epidemiology PhD Program has established an academic travel support fund. The primary purpose of this fund is to provide financial awards for students attending national, highly-reputable scientific meetings that focus on epidemiology.

It is expected that students applying for travel awards will present an oral or poster presentation at such meetings. The level of support is summarized below:

• Abstract submission fee up to $50 plus:
  • Travel expense reimbursement up to $400 for a poster presentation
  • Travel expense reimbursement up to $800 for an oral presentation
  • Travel expense reimbursement up to $1200 if the abstract is accepted for a presentation and the paper is submitted and selected as one of the finalists in a competitive contest.

How to apply for a Travel Award

Advance application to the program director is required. The application shall include:

1. The title of the abstract to be submitted
2. The name and location of the scientific conference
3. The list of all authors in the abstract
4. A copy of the abstract to be submitted
   • A request for financial support for a similar abstract that is currently under consideration by another conference is not allowed.
   • A request for financial support for a similar abstract that was presented at a different conference is not allowed.
   • If an Epidemiology Travel Award is received, the student must also present their research at our Epidemiology Division seminar series, preferably before attending the conference.

As soon as the applicant receives notification of the award, they should schedule a meeting with the Administrative Support Assistant for the PHS Department’s Graduate Program, who will review travel policies with them. This should be done prior to making any travel arrangements.

The student must also submit an online PHS travel request as soon as they receive notification of the award. Travel Awards will be used to reimburse the student for abstract fees and travel expenses after they attend the meeting. If actual costs will exceed the amount of the award, the student should either seek additional funding from their advisor/mentor, or pay for those costs on their own.

The Epidemiology Academic Travel Support Fund was created by the generous contributions of:

• Dr. Vernon Chinchilli, PHS Department Chair
• Dr. Duanping Liao, PhD Program Director and Epidemiology Division Chief