General Information

1. Introduction

This handbook serves as a reference manual for the masters and doctoral programs in biostatistics and the doctoral program in epidemiology at the University of Pennsylvania. It covers the graduate experience, from admission through required course work, examinations, and the MS thesis (biostatistics), and PhD dissertation in both programs. This is a living document; please bring errors and omissions to the attention of the Chair of the Graduate Group in Epidemiology and Biostatistics, or to the Chairs of the respective programs.

Many have contributed in ways large and small to this handbook, not least the students in the doctoral program, whose many relevant questions and experiences have led us to review our policies, consider their implications, and write them down clearly. We thank them especially and wish them the best in all their endeavors, at Penn and beyond.

Russell Shinohara, PhD
Professor of Biostatistics 
Chair, Graduate Group in Epidemiology and Biostatistics

Adam Naj, PhD
Assistant Professor of Informatics 
Chair, Doctoral Program in Epidemiology

Michael Harhay, PhD, MPH
Assistant Professor of Epidemiology and Medicine
Associate Chair, Doctoral Program in Epidemiology

Mingyao Li PhD
Professor of Biostatistics
Chair, Graduate Program in Biostatistics

2. Graduate Group in Epidemiology and Biostatistics

2.1 Overview

The Graduate Group in Epidemiology and Biostatistics (GGEB) is responsible for developing and administering the PhD degree programs in epidemiology and biostatistics as well as the MS program in biostatistics. The PhD programs train individuals to be rigorous and independent academic investigators, who are able to apply and extend the range of approaches available in epidemiology and biostatistics to address questions in biomedical research. The objective of the MS program in biostatistics is to train individuals in the basic theory and applications of statistical methods, especially as applied to problems in the health sciences.

The GGEB is a member of the Biomedical Graduate Studies Program (BGS) in the Perelman School of Medicine of the University of Pennsylvania. It is comprised of faculty from across the university with interests in biostatistics and epidemiology. Notably, many of the members of the Graduate Group have academic appointments within the Department of Biostatistics, Epidemiology and Informatics (DBEI). The Office of Biomedical Graduate Studies provides oversight and coordination for the GGEB and six other graduate groups offering PhD degrees in the biomedical sciences.

Biomedical Graduate Studies (BGS) was established in 1985 and serves as the academic home within the University of Pennsylvania for roughly 700 students pursuing a PhD in the basic biomedical sciences. Although BGS is housed within the School of Medicine, it is composed of more than 600 faculty members across seven Penn schools and several associated institutes. BGS provides training and administration through seven graduate groups, some of which have distinct sub-specialty areas. Each graduate group has its own training mission, leadership, and staff, but there is often significant overlap among the groups in respect to faculty membership, courses offered, policies, and procedures. BGS provides centralized support to the graduate groups for admissions, student fellowships, curricular oversight, record-keeping, and other operations.

Additional, up-to-date information about BGS is available at

3. Application and Admission

3.1 Affirmative Action

The GGEB values diversity and seeks talented students from all backgrounds. The GGEB does not discriminate on the basis of color, sex, sexual orientation, religion, national or ethnic origin, age, disability, or status as a disabled or Vietnam Era veteran in the administration of its educational policies, programs or activities, admissions policies and procedures, and scholarship programs.  Women and minorities are especially encouraged to apply to the GGEB's educational programs.

3.2 The Application Process: All GGEB Programs

Applicants must complete the standard online BGS application form and upload the following documents:

  • Personal Statement - Please discuss your academic and career objectives. It should be around 500 words in length. Be as specific as you can about the area in which you plan to study and your reasons for wishing to study at the University of Pennsylvania.
    In addition, if you are applying to a certificate program, your personal statement should include a paragraph (~200 words) reflecting your interest in those programs in addition to the doctoral discipline.
  • Research Statement - Please provide a description of your research experience(s), including the goals of each project, approaches used, results obtained, and implications of the findings for the project and the field at large. You may choose to describe a single research experience or several experiences, but please limit your statement to around 1000 words in length.
  • Resume/CV (Please DO NOT include GPA and/or GRE information)
  • Transcripts - All BGS applicants are required to upload up-to-date unofficial transcripts from all institutions attended. These transcripts must include your Spring 2016 semester grades and indicate the courses you are enrolled in for the Fall 2017 semester. Transcripts from completed programs should show proof of degree conferral. A final, official transcript showing conferral of degree will be required of all accepted students prior to matriculation.
  • Letters of Recommendation - You will also be prompted to send requests to three (3) people who are able to provide letters of recommendation. They will be sent an email notification with a link to the online recommendation form, which will allow them to upload a PDF of the letter. The letters should identify personal attributes, experiences, accomplishments, and goals relevant to success in graduate study in biostatistics or epidemiology, depending on the program.  Applicants who are currently enrolled in a degree program must arrange for at least one letter of recommendation to be sent from a faculty member in that program.
  • Standardized Test Scores – these should be sent directly from the testing service. BGS requires the general GRE for all applicants and an English proficiency exam (either the TOEFL or the IELTS) for applicants for whom English is not their native language. As part of the review process, we will waive the English Proficiency requirement for applicants who have or will have obtained a degree from a US or other approved English-instructed institution. There are no minimum score requirements. BGS does not require any GRE subject tests. In order for your application to be considered complete, official score reports must be received by the application deadline. In order to ensure that your official scores are received in time, we suggest that you take the exam no later than mid-November.
3.2.1 Waiver of Fees for the Application

U.S. citizens and permanent residents may request a waiver in cases of documented financial hardship. To request a waiver, email the admissions coordinator for BGS prior to submitting your application ( Explain your situation and reasons for requesting a waiver of fees. The coordinator may ask for additional documentation e.g. documentation by the Financial Aid Officer from a relevant undergraduate institution, or, if not applicable, documentation of information about income, assets, family situation, etc. University rules prevent the waiver of application fee for international applicants.

3.2.3 Test of English as a Foreign Language (TOEFL)

All applicants whose native language is not English must arrange for ETS to submit an official TOEFL score as part of the application by the application deadline. The TOEFL requirement is waived for a student who has been enrolled in an English-speaking university for at least two years upon application. TOEFL scores are valid for two years.

3.2.4 Application Deadline and Notification

Students are admitted once per year, for the fall term.  Information and application materials are available by October of the preceding year with an application deadline of around December 1. After reviewing the files, the Admissions Committees for the individual programs recommend candidates for the GGEB to bring to the BGS Admissions Committee and the Chair of BGS. Students are usually notified of the decision of the Admissions Committees by the end of March.

3.2.5 Initiating an Application

Those interested in applying for admission to graduate study should contact the Coordinator:

Eli Elliott
Coordinator, Graduate Group in Epidemiology and Biostatistics
Perelman School of Medicine at the University of Pennsylvania
Tel: (215) 573-3881

3.3 Admission Requirements Specific to the Biostatistics Programs

Entering students must have completed at least one year of calculus (including multivariable methods), one semester of linear algebra, and have a working knowledge of a programming language. Previous experience with data analysis and statistical packages is desirable but not required. Advanced courses in mathematics are particularly important for students who intend to pursue the PhD degree.

3.3.1 Applicants from the MS Program

Students in our Biostatistics MS program who seek admission to our PhD program must submit a formal application.  Typically, such students apply in the fall preceding their projected graduation with the MS.  Results on the written qualifications examination are considered in the admission decision (see the section on “Evaluations and Examinations”).

3.4 Admission Requirements Specific to the PhD Program in Epidemiology

Applicants must demonstrate prior training and experience in epidemiology, clinical sciences, or a public health-related field. This requirement can be satisfied by having a Master’s degree in public health, epidemiology, biostatistics, or related field, OR at least two years of relevant work experience. Individuals admitted without clinical or other biomedical training may be required to take biomedical science courses in addition to the courses required for the PhD in Epidemiology. These courses will not count as electives and must be taken in addition to the required courses and credits. The Admission Committee will determine the need for additional courses at the time of acceptance.

The content of the additional courses required for those admitted without prior clinical or other biomedical training will be determined by a committee consisting of the student’s advisor and two additional epidemiologists who are members of the Graduate Group. The advisor will be responsible for identifying those two faculty members. At least one of the three members of this committee must hold a clinical doctorate and at least one member of the committee must hold a doctorate in epidemiology or a related field, without a clinical doctorate. This committee will identify specific courses to be taken on the basis of a review of the candidate’s academic record/transcripts and research interests, as well as interactions with the candidate. The candidate will be informed of the additional required courses prior to enrollment. It is likely that this additional coursework will increase the amount of time it takes for the candidate to successfully complete the PhD degree requirements.

Combined degree (MD-PhD, VMD-PhD, and DMD-PhD) applicants are exempt from this requirement since they will have had at least two years of relevant coursework in their professional degree program prior to starting coursework for the PhD.

4. Financial Obligations and Support

Tuition costs are determined each year. The Trustees of the University of Pennsylvania reserve the right to increase tuition and fees and to otherwise amend the regulations concerning tuition and fees at any time and to make such changes applicable to students in the University at that time. PhD students receive up to 21 months of funding from BGS. During the initial 21 months, students identify a PhD advisor and work with the advisor and the program to develop a funding plan for the remainder of their graduate program. Most PhD students receive financial support through one or more of the following sources:  assistantships supported by research grants, training grant fellowships, and fellowships from research institutions or private industry. A limited number of teaching assistantships are available.  These sources are described in more detail below. Students who receive full-time support may accept no additional employment during the period of the support. Support for Biostatistics MS students depends on the availability of funds, with priority given to PhD students.

4.1 Financial Aid

The University’s Office of Student Financial Services provides information on student expenses and billing; processes financial aid applications, awards financial assistance; and administers the Penn Plan payment programs.  Students may contact the Office directly at:

Office of Student Financial Services 
University of Pennsylvania 
Room 100 Franklin Building 
3451 Walnut Street 
Philadelphia, PA 19104-6270 
Tel: 215-898-1988 

5. Resources for Students

5.1 Penn Card

The PennCard is the official identification card of the University of Pennsylvania. The PennCard Center is located on the second floor of the Penn Bookstore, 3601 Walnut Street. A valid, government-issued photo I.D. is required in order to pick up a PennCard. The first PennCard is free. Information about the PennCard and its use is provided at

5.2 PennKey

The PennKey name and password provides access to PennNet, a Penn e-mail account, and many other essential services managed through the PhD Program. All students are required to have a current, active PennKey and password. Students are issued a PennKey Setup Code when they pick up their PennCard.

5.3 The PennPortal

The PennPortal webpage bundles together links to important information for students. To access the PennPortal (, students should log in with their PennKey name and password. If the “Graduate Students” tab does not automatically appear, students should click on the “My Tabs” button to add the “Graduate Students” tab from the available tabs.

5.5 Health Care Coverage

Penn students are automatically eligible for Penn Student Health Services and Chickering Health Insurance. Once a student is matriculated, the University will assume that this health coverage is needed and they will bill for the service. Students who wish to waive the Penn sponsored insurance should log onto PennPortal at to do so. It is necessary that students watch their bill to ensure that no health insurance fee is incurred. If one is charged to the student account, the GGEB Coordinator should be notified.

5.6 Student Travel Funds

BGS allows doctoral students to apply for partial reimbursement (currently, up to $500/year) for travel to professional meetings if they are making a presentation.  Applicants must justify the expenses prior to attending the meetings.  Dissertation advisors sometimes are able to augment these travel funds. In addition some training grants provide funds for student travel. Information and application provided at:

6. Academic Policies

Students in the PhD program are subject to academic policies of BGS ( as well as the specific policies of the GGEB and PhD program as defined below.

6.1 Code of conduct and academic integrity
6.1.1 Code of General Conduct

All BGS students must conduct themselves at all times in a mature and responsible manner. The rights and property of all persons are to be respected regardless of time or place. For dual degree students (MD-PhD, VMD-PhD), or graduate students who conduct research in a clinical venue, this also includes compliance with rules, procedures and accepted practices in the clinical setting. In addition, BGS students must comply with the University's code of general conduct and other University policies related to student conduct that are described in The Penn Book: Policies and Procedures Handbook of the University of Pennsylvania ( These policies include, but are not limited to, policies on sexual harassment, acquaintance rape and sexual violence, open expression, drug and alcohol usage, and the drug-free workplace. The judicial charter contained within that document is not applicable to BGS students; rather, BGS students are subject to the Charter of Biomedical Graduate Studies Student Judicial System which can be found on the BGS website.

6.1.2 Code of Academic Integrity

The most fundamental value of any academic community is intellectual honesty; accordingly, all academic communities rely upon the integrity of each and every member. Students are responsible not only for adhering to the highest standards of truth and honesty but also for upholding the principles and spirit of the following Code. Violations of this Code include but are not limited to the following acts:

A. Cheating: using or attempting to use unauthorized assistance, material or study aids in examinations or any other academic work, or preventing, or attempting to prevent another from using authorized assistance, material, or study aids.
B. Plagiarism: using the ideas, data or language of another without specific and proper acknowledgment.
C. Fabrication: submitting contrived or altered information in any academic exercise.
D. Multiple Submission: submitting, without prior permission, any work submitted to fulfill another academic requirement.
E. Misrepresentation of Academic Records: misrepresenting or tampering with, or attempting to tamper with, any portion of one's own or any other person's transcripts or academic record, either before or after coming to the University of Pennsylvania.
F. Facilitating Academic Dishonesty: knowingly helping or attempting to help another violate provisions of this Code.
G. Unfair Advantage: attempting to gain unauthorized advantage over fellow students in an academic exercise.

Note that it is the policy of the GGEB that students may collaborate on homework/coursework solutions but must submit their own independent response to any homework assignment. Exceptions to this policy may be made explicitly and in writing by the course instructor.

Given our daily reliance on numerous sources of information, it is essential for faculty and students alike to understand their responsibilities in adhering to the University’s Code of Academic Integrity. To ensure that each student’s work represents the effort envisioned by faculty for a given assignment, these two principles must be observed:
  1. It is essential for faculty to indicate in writing for each assignment the parameters for completing that assignment. This should be a statement of exactly what is allowed and what is not allowed in terms of the use of outside material, consultation with other students or faculty, and the use of material previously created by the student for another course.
  2. Students must be sure they understand the parameters for every assignment. While the instructor is responsible for providing a clear description of these parameters, it is the student’s responsibility to understand them, and to discuss with the instructor any concerns or questions about them

The Penn library website has excellent resources on this topic. The links below provide resources on the specific topic of plagiarism:

6.1.3 Code of Clinical Conduct

The relationship of modern biomedical research to the clinical setting may place BGS students in direct contact with patients, patient medical records, or health care workers. BGS students must behave with paramount concern for patients' welfare and with respect for the rights of patients. The expectations of BGS students' conduct in the clinical setting include the following:

A. adherence to appropriate standards of behavior in the presence of patients;
B. adherence to appropriate standards of confidentiality with respect to information about patients;
C. honesty in interactions with clinical colleagues and in recordkeeping;
D. respect for the limits of responsibility and activity set forth by supervisors;
E. appropriate interactions with colleagues and co-workers.

6.2 Academic standards
6.2.1 Course grades and Academic Probation

Grades for all formal courses are assigned as follows: “A,” distinguished; “B,” good; “C,” unsatisfactory; “D,” poor; “F,” failure. Course directors may award pluses and minuses at their discretion. Grades of B− or above are considered acceptable; grades of C+ or below are unacceptable. A student who receives an unacceptable grade (C+ or lower) in any course is automatically placed on academic probation, an enrollment status that indicates an unsatisfactory level of academic performance. A student who is on probation may take other courses and exams but may not graduate. The probation is automatically lifted when the student has made up the deficient work by receiving an acceptable grade. The student must arrange with the chair of the course in question a program of study that will accomplish this end. One option is to redo the assignments or exams that led to the unsatisfactory grade.

Another is to take the course again during the next semester in which it is offered. In any event, a student who fails to redress the deficiency within one year of being placed on academic probation will be dismissed and considered ineligible for re-admission. If a student receives a second unacceptable grade in another course while already on academic probation, the Graduate Group Chair will convene a committee to review the case. The committee, which will consist of the student’s academic advisor and two other members of the Graduate Group faculty, is authorized to recommend either immediate dismissal or continuation of the probationary status, subject to approval by the Graduate Group Chair and BGS.

6.2.2 Incompletes

In order to graduate, students must satisfactorily complete their course work. There may be times when, for some reason, a student cannot complete the course work within the allotted time. In this case, the student must formally request, in writing, a grade of Incomplete (I) for the course. Requests for Incompletes are not automatically granted, and the course director must agree to enter the grade for that course. Students and faculty should be aware that incompletes become permanent after a period of one year. Thus, course requirements must be completed and a grade reported within one year or the student will not receive credit for the course even though tuition was paid. If the incomplete is not resolved within the one-year period, then the student will be required to take an additional course to complete the requirements of the curriculum. The student must obtain approvals for the replacement course from the advisor and the respective Program Chair prior to registering for it.

6.2.3 Individual Development Plans (IDPs)

BGS requires an annual IDP for all pre-doctoral students (PhD, MD-PhD, and VMD-PhD). The goals of the IDP are to make sure students and mentors are communicating openly and that students are working proactively toward developing the skills they will need to succeed in their program. Separate forms are used by pre-thesis and thesis level students.Please see for specific requirements regarding the IDP and examples of completed IDP forms.

6.3 Additional Academic Requirements and Policies
6.3.1 Collaborative Institutional Training Initiative (CITI) Training Program

This program is mandatory for all School of Medicine faculty, clinical care associate physicians, physicians at affiliated hospitals, and research staff working with physicians who conduct patient-oriented research.  Researchers conducting clinical studies with federal funding are also required to take human subjects research training.  The Office of the Provost of Research has identified online training devices provided by the CITI program as the accepted standard for fulfilling the requirement for training certification in human research protections. Penn’s IRB requires that researchers conducting clinical trials complete patient-oriented research training, and the CITI program can also fulfill this requirement.

6.3.2 Health Insurance Portability and Accountability Act (HIPAA) training

HIPAA is a federal law that provides for the protection of the confidentiality of patient health records.  All students must complete a University-approved course in HIPAA compliance.

6.3.3 Responsible Conduct of Research

Students are required to take training in the responsible conduct of research (RCR) every academic year. First-year students satisfy this requirement by participating in an on-line Bioethics Symposium. Second-, third-, and fourth-year students attend small-group workshops in which relevant case studies are discussed. Students whose studies extend beyond four years must continue to participate in a yearly training session of their choice. Such students can satisfy the responsible conduct of research requirement by participating in various University-sanctioned bioethics courses and symposia or by serving as an assistant facilitator in a workshop for second-, third-, and fourth-year students.

Faculty must dedicate at least two meetings (1-2 hrs each) per year to RCR training.  To this end, Faculty have access to case studies to use as discussion pieces, in addition to their own resources or examples from their own experience.  The expectation is for these events to be interactive discussions that ideally include all project personnel, but minimally explicitly include all graduate students who work on that project.  After each such event, the Faculty member is expected to fill out the online form found here:

6.3.4 Course evaluations

Students are requested to submit their feedback promptly and completely at the end of each course throughout their time in graduate training. We take seriously what students say about a course and try hard to improve every year based on students’ feedback. 

Students should also be aware that faculty promotions can be affected by how they are evaluated.  This is not meant to dissuade students from honestly rating the course faculty, but rather as an invitation to take this seriously and be thoughtful about how they rate the faculty’s effort, skill, and teaching abilities.  Constructive criticism is helpful and truly appreciated by both faculty and the graduate group.  Disparaging comments are less helpful and are discouraged. The Program Chairs are always ready to discuss in person any concerns that students may have.

6.3.5 Leaves of absence

During the period prior to dissertation status, the University allows graduate students to take leaves of absence with the permission of the PhD program and BGS. Dissertation level students are allowed leaves of absence only with permission, most notably for medical reasons and for parental leave in association with the birth of a child. Student stipends are suspended during a medical leave period and are re-instated upon return as long as the student is in good academic standing. A student who wishes to take a leave of absence must submit a written request to the Program Chair and the GGEB chair at least one month prior to the beginning of the first semester of the proposed leave. If the leave is for medical reasons, the request must include a note from the student’s doctor. Leaves of absence are granted for no more than one year. The university’s leave of absence policy is provided in the Graduate Catalog Rules and Regulations:

6.3.6 Vacation and Time Away

Graduate fellowships provide tuition, fees, health insurance, and a stipend for eligible full-time doctoral students in residence who remain in good academic standing.   A student who accepts a full-time funded position is expected to devote full time to graduate study.

BGS and GGEB offer a 12-month annual training program for funded students. Students are expected to work full-time toward the degree and are entitled to take University and GGEB staff holidays and two weeks per year for personal vacation time. The timing of the vacation must be approved by the supervisor of the entity that provides financial support for the student.  Students who have not yet passed the candidacy exam (see below) must receive permission from the Chair of the GGEB for any additional time away from the University.  A student who has passed the candidacy exam may schedule time away only with the prior approval of his or her dissertation advisor, the individual who is supporting his or her assistantship or traineeship, the Program Chair and the GGEB Chair.

6.4 Transfer of credit

At least twelve course units must be completed while enrolled in a degree program at Penn; for the PhD degree, a maximum of eight units may be transferred from graduate work done at other institutions. Transfer of credit must be approved by the respective Program Chair, Graduate Group Chair, and the BGS Chair. If the requested transfer of credit is for a required core course, then the current course instructor must approve the transfer as well.

6.4.1 Transfer from other graduate groups

Students who are currently enrolled in another graduate group within BGS may apply for transfer into the GGEB by submitting an application for admission to either the PhD Program in Epidemiology or the MS or PhD programs in Biostatistics. Students wishing to transfer must inform their original program of their intent. The student should have the chair of the original program sign a "Transfer of Graduate Group Form" to release the student from the original graduate group and then have the chair of the new program sign the same form to accept the student into the new graduate group. The GGEB will then request that the student's academic file be transferred from the former graduate group office. A similar procedure will be used for students transferring from other graduate programs within the university.

6.5 Residency, time limits, and fees

Students must complete all course requirements, pass the required examinations, and complete the dissertation within ten years of matriculation. A student who fails to complete the dissertation within the time limit must petition a committee — composed of the student’s academic advisor, the Program Chair (or a designated surrogate if the Chair is also the advisor), and a third member of the faculty designated by the GGEB Chair —to be recertified as a PhD candidate.  The petition must name the student’s dissertation advisor and committee members, describe a plan to finish the research needed to complete the dissertation, and indicate an expected data for the defense and deposit of the dissertation. Should the committee support the petition, it will submit a detailed recertification plan for review and approval by the Director of BGS, as specified in the University-­-Wide Academic Rules for Graduate Degrees.

In addition, PhD candidates must complete the dissertation within five years of passing the Qualifications Examination or being admitted into the PhD program (the latter if admitted to the PhD program after passing the Qualifications Examination at the PhD level as an MS student).  A student who does not complete the degree within five years must petition the GGEB for an extension of the time limit.  The petition must indicate a detailed plan for completing the PhD research, including anticipated dates for defending and depositing the dissertation. The petition will be considered by a committee that includes the student’s academic advisor, the Program Chair (or a surrogate as indicated above) and a third faculty member designated by the GGEB Chair.

A candidate who withdraws from the PhD program after reaching dissertation status and subsequently applies for re-admission must pay the dissertation fees that would otherwise have been due during the withdrawal period