Introduction

This handbook describes general information, requirements, regulations, and procedures for the Ph.D. program in Biostatistics, a program jointly offered by the Department of Mathematical Sciences in the Purdue School of Science at Indianapolis and the Division of Biostatistics in the Indiana University School of Medicine. This unique program combines the strength in statistical theory of the Department of Mathematical Sciences with the biostatistical methods research and life sciences experience of the Division of Biostatistics.

The program is designed for individuals with strong quantitative and analytical skills and a strong interest in biological, medical and/or health related sciences. It provides rigorous training in statistical theory and methodologies that are suitable for applications in research, collaboration and consulting on a broad spectrum of health and life science problems. The program stresses the theory and concepts underlying statistical methods, the interpretation of results from experimental as well as observational studies, and the practical realities of health-related studies and their analysis. The primary goal is to prepare the students for independent careers as biostatisticians in any professional health-related or biomedical environment, such as in medical research institutes, universities, government agencies and private health-industries or organizations.

Additional information regarding specific policies of the Indiana University University Graduate School can be found in the University Graduate School Bulletin.

Program Requirements

Required Coursework

Every student in the program is required to complete the following 11 courses for a total of 33 credits:

• STAT 51200 Applied Regression Analysis
• BIOS-S 515 Biostatistics Practicum
• STAT 51900 Introduction to Probability *
• STAT 52500 Intermediate Statistical Methods *
• BIOS-S 527 Introduction to Clinical Trials
• STAT 52800 Mathematical Statistics I *
• STAT 53600 Introduction to Survival Analysis *
• BIOS-S 546 Applied Longitudinal Data Analysis *

Any three of the following:

• STAT 61900 Probability Theory
• BIOS-S 621 Advanced Statistical Computing
• STAT 62800 Advanced Statistical Inference
• BIOS-S 636 Advanced Survival Analysis
• BIOS-S 646 Advanced Longitudinal Data Analysis

(* indicates the Program's Core Courses)

In addition, every student must take an additional 12 credit hours of statistics/biostatistics courses. At most six credit hours of these electives may be taken from 500-level courses.

Qualifying Examination

Students must pass an initial qualifying examination on the five core courses: STAT 51900, 52500, 52800, 53600 and BIOS-S 546. The qualifying examination is a written examination offered once a year during a two-day Qualifier Exam Session the week before classes start in August and is administered in two sections – Theoretical Biostatistics and Applied Biostatistics. The preparation and the administration of the qualifying examination is overseen by the Graduate Examination Committee.

Students are expected to have completed and passed both sections of the qualifying examination on or before their qualifier deadline.

Deadline for full-time students:

The deadline for passing the qualifying examination for full-time students who enter the program with a master's degree or equivalent is August at the end of their second year; the deadline for full-time students who enter the program without a master's degree is August at the end of their third year.

Deadline for part-time students:

The deadline for passing the qualifying examination for part-time students who enter the program with a master's degree or equivalent is August at the end of their third year; the deadline for part-time students who enter the program without a master's degree is August at the end of their fourth year.

If students do not pass both sections of the examination by their qualifier deadline, they will have their privilege to continue in the program terminated.

A student will have at most two attempts to pass the examination. The first attempt must include the entire examination, i.e. both the Theoretical and Applied sections. If one or both sections are not passed on the first attempt, then a second attempt on or before the deadline is allowed. During the final attempt, the student may only sit for the section(s) not passed in the first attempt.

A student’s first attempt at the qualifying examination will result in one of the following three outcomes:

1. Pass Both Sections: The student has demonstrated fundamental understanding of the core material and the examination committee believes he/she will be successful in completing the Ph.D. program.
2. Pass One Section: The student has demonstrated fundamental understanding of one section, but lacks adequate understanding of the other section. The student must sit for the section not passed at a future examination session.
3. Fail: The student has failed to demonstrate an adequate understanding of the material from the core courses and thus fails the examination. The student must sit for both sections at a future examination session.

A student’s second and final attempt at the qualifying examination will result in one of the following two outcomes:

1. Pass: The student has demonstrated fundamental understanding of the core material and the examination committee believes he/she will be successful in completing the Ph.D. program.
2. Fail: The student has failed to demonstrate an adequate understanding of the material from the core courses and thus fails the examination, with privilege to continue in the program terminated.

Minor Area

In addition to the 45 credits of formal statistics/biostatistics coursework, the student must complete a minor (9 – 15 credits) in an area related to any of the health and life sciences disciplines. The minor may be obtained in areas such as pharmacology and toxicology, epidemiology, genetics, biology, physiology, bioinformatics, public health and health economics, among many others, and it must be approved by the student’s advisory committee. The minor must contain a minimum of three graduate level courses (nine credits) in the chosen area and it must comply with the minor requirements of the respective department/unit.

Ph.D. Advisor and Advisory Committee

Within one year of admission, each student must select an advisory committee, consisting of at least two members of the program’s graduate training faculty, and at least one member from outside the program, preferably from the student’s minor area. The student should select at least one member to be the primary advisor.

Preliminary Examination and Research Committee

A student becomes eligible to take the Preliminary Examination after passing the qualifying examination. The student must prepare and pass a preliminary examination, which consists of an oral presentation on an advanced research topic suggested by the student to an appointed committee of at least four faculty members, including the student’s advisor and at least one member from the student’s minor area. The committee may consist of the same members as the student’s original advisory committee, but is not required to. This committee will serve as the research committee for the student, and must be approved by the dean. Prior to the examination, the student must provide the committee with a paper (10 – 15 pages) outlining the topic to be covered, clearly indicating the scope and depth of the planned research along with relevant references. In the examination, the student is expected to display an in-depth understanding of the chosen subject matter. The committee may ask the student questions which normally will be directed to the subject matter of the research but may, by natural extension, also cover any other relevant topic.

Admission to Candidacy

Following the passing of the preliminary examination and the completion of all required coursework, the student's advisory committee will nominate the student to candidacy. Upon approval of the dean of the IU Graduate School, the student will be admitted to candidacy.

Dissertation

A Ph.D. dissertation is a document authored by an individual, describing results of original research undertaken by that individual, and asserting a position which that individual is willing to defend. A dissertation must be submitted in final form presenting new results of sufficient importance to merit publication.

After consultation with and approval by the student’s advisor and research committee, the student will submit to the University Graduate School (at the IUPUI Graduate Office, UN 207) a one- or two-page prospectus of the dissertation research. If the proposed research involves human subjects, animals, biohazards, or radiation, approval from the appropriate university committee must also be obtained. The dissertation prospectus must be approved by the University Graduate School at least six months before the defense of the dissertation.

The dissertation must meet departmental and University format requirements. Consult the Guide to the Preparation of Theses and Dissertations (“The Format Guide”) - for use by students admitted to IU Graduate School Programs located at IUPUI. The Format Guide is available at the IUPUI Graduate Office website.

Final Examination (Defense)

When the dissertation has been completed, the student should submit an unbound copy to each member of the research committee as the initial step in scheduling the defense of the dissertation. All members of the research committee should read the dissertation in its entirety before attending the defense. At this stage both the student and the faculty members must extend certain courtesies to each other. It is the responsibility of the student to give faculty members sufficient time to read the dissertation without making unreasonable requests of them based upon University Graduate School time limitations, immediate job possibilities, contract renewal, or some other reason. Similarly, a faculty member should not keep a student's work for inordinate periods of time because of the press of other duties. Once a faculty member assumes membership on a research committee, it becomes another part of his or her teaching assignment, comparable to conducting regularly scheduled classes.

After the committee members have read the dissertation, there should be direct communication (either in writing or orally) between the research committee chairperson and the other committee members about its readiness for defense. Readiness for defense, however, is not tantamount to acceptance of the dissertation; it means that the committee is ready to make a decision. The decision to hold a doctoral defense, moreover, is not entirely up to the research committee. If a student insists upon the right to a defense before the committee believes the dissertation is ready, that student does have the right to due process (i.e., to an oral defense) but exercises it at some risk.

If the decision to proceed with the defense of the dissertation is made against the judgment of one or more members of the committee, or if one or more members of the committee disapprove of parts or all of the dissertation, the committee member(s) should not resign from the committee in order to avoid frustration or collegial confrontation. The University Graduate School urges that such committee members, after ample communication with both the student and the chairperson, remain on the committee and thus prevent the nomination of a committee that might eventually accept what could be unsatisfactory work. Such a committee member could agree that a dissertation is ready for defense but should not be passed (or should not be passed without substantial modification). There will, of course, be situations in which the membership of research committees should or must be changed (e.g., turnover of faculty), but changes because of modifications in the dissertation topic or some equally plausible reason should be made early in the writing of the dissertation.

Thirty days prior to the scheduled defense of the dissertation, the candidate must submit to the University Graduate School a one-page announcement of the final examination. This announcement must follow a format available in the Guide to the Preparation of Theses and Dissertations (“The Format Guide”) - for use by students admitted to IU Graduate School Programs located at IUPUI. The Format Guide is available at the IUPUI Graduate Office website.

The announcement contains, among other things, a summary of the dissertation (not less than 150 words) which is informative and contains a brief statement of the principal results and conclusions.

Once the final examination has been scheduled, the announced time and place of the defense must not be changed without the approval of the dean. Any member of the graduate faculty who wishes to attend the final examination is encouraged to do so; it is requested, however, that the faculty member notify the chairperson of the research committee in advance so that space can be arranged. With the approval of the research committee and the consent of the candidate, other graduate students may attend the defense of the dissertation; normally such students will act as observers, not as participants.

At the end of the oral examination, the research committee must vote on the outcome of the examination. Four options are available to the committee: (1) pass, (2) conditional pass, (3) deferred decision, and (4) failure. If the decision to pass is unanimous, the dissertation is approved once it is received by the University Graduate School along with an acceptance page signed by the members of the research committee. If the decision is not unanimous, majority and minority reports should be submitted to the dean who, within 10 working days, will investigate and consult with the research committee. Upon completion of the dean's investigation and consultation, another meeting of the research committee will be held, and if a majority votes to pass, the dissertation is approved when it is received by the University Graduate School with an acceptance page signed by a majority of the members of the research committee.

Dissertation Submission

After passing the defense and prior to final submission, all students will meet with the IUPUI Graduate Office for a format review. Following acceptance by the research committee, the dissertation is submitted to the University Graduate School (at the IUPUI Graduate Office, UN 207). Please carefully follow the “Format Guide” - available at the IUPUI Graduate Office website.

General Requirements and Procedures

Transfer Coursework

Candidates for the Ph.D. degree may petition for up to 30 hours of graduate credit from other institutions. Students submit the Petition for Approval of Transfer Course form in order to initiate an appeal process and receive approval to apply a course completed at a different institution towards their degree. Students must provide, at minimum, the syllabus for the course under evaluation. Other documentation may be requested, as needed.

Expired Coursework

Normally, a course may not apply towards degree requirements if was completed more than seven years prior to the passing of the preliminary examination. Students submit the Petition for Course Revalidation form in order to initiate an appeal process and receive approval to apply an expired course towards their degree. Students must provide, at minimum, the syllabus for the course under evaluation. Other documentation may be requested, as needed.

Elective Coursework

Students submit the Petition for Approval of Elective Course form in order to initiate an appeal process and receive approval to apply a course completed in a different department towards their degree. Students must provide, at minimum, the syllabus for the course under evaluation. Other documentation may be requested, as needed.

Time Limits for Completion

The student must receive acceptance of his or her dissertation and must submit a copy to the University Graduate School within seven years after passing the preliminary examination, and complete the degree in entirety within ten years from time of admission into the program. Failure to meet this requirement will result in the termination of candidacy and of the student's enrollment in the degree program. Any student whose candidacy lapses will be required to apply to the University Graduate School for reinstatement before further work toward the degree may be done formally. To be reinstated to candidacy in the University Graduate School, the student must: (1) obtain the permission of the departmental chairperson; (2) fulfill the departmental requirements in effect at the time of the application for reinstatement; (3) pass the current Ph.D. qualifying examination or its equivalent (defined in advance); and (4) request reinstatement to candidacy from the dean. Such reinstatement, if granted, will be valid for a period of three years, during which time the candidate must enroll each semester for a minimum of one credit.

Normal Progress and Termination

Once students begin research, they must maintain normal progress toward their degree objective to ensure continued financial support and/or active status. If, in the opinion of the research committee, satisfactory research progress is not being made or if the GPA continues to be below 3.0, a meeting of the student's research committee may be convened. This meeting will include a brief presentation by the student on the work accomplished up to that point, and/or a discussion concerning the problems which have hampered progress. If the consensus of the committee is that the student needs to show improvement, he/she will have 60 days to demonstrate a change in performance. At the end of this time, financial support may be discontinued, if applicable.

If a student finds it necessary to withdraw from the graduate program, then he/she should provide as much notice as possible. In the case of teaching or research assistants, students are expected to complete the semester once it has begun. Similarly, the program will provide a student with as much advance notice as possible if the student is dropped from the program for reasons of poor performance.

In addition, the student must maintain continual enrollment in the program after passing the preliminary examination, not including summer sessions. The student must also be registered during the semester of graduation.

Resources

List of Required Forms

Throughout the period of enrollment in the Ph.D. program, specific forms must be filled out at certain points in the program. It is the student’s responsibility to complete the forms, as required. Below is a list of all required forms with an explanation. All forms are available at the IUPUI Graduate Office website and must be filed with the Graduate Programs Coordinator in the Math Department.

Appointment of Advisory Committee Form

Within one year of admission, each student must select an advisory committee, consisting of at least two members of the program’s graduate training faculty, and at least one member from outside the program, preferably from the student’s minor area. The student should select at least one member to be the primary advisor.

Nomination of Candidacy Form

Following the passing of the preliminary examination and the completion of all required coursework, the student's advisory committee will nominate the student to candidacy. Upon approval of the dean of the IU Graduate School, the student will be admitted to candidacy.

Nomination of Research Committee Form

The research committee is selected when the student begins to prepare for the preliminary examination and consists of at least four faculty members, including the student’s advisor and at least one member from the student’s minor area. The committee may consist of the same members as the student’s original advisory committee, but is not required to. The nomination form is filed after successful completion of the preliminary exam, and includes a one- to two-page summary of the proposed dissertation. The signatures of the faculty members on this form indicate that they agree to supervise the research.

PhD Minor Form

This form is filed as soon as a minor area has been agreed upon, and must be signed by the student’s major advisor and the faculty member selected to be the student’s minor advisor. Should the coursework selected for the minor change, a new form must be filed.

Change of Research Committee Member Form

The membership of the research committee may be changed. However, the final version of the research committee must be fixed no later than six months prior to the defense.

Announcement of Dissertation Defense

Thirty days prior to the scheduled defense of the dissertation, the candidate must submit to the University Graduate School (at the IUPUI Graduate Office, UN 207) a one-page announcement of the final examination. This announcement must follow Guide to the Preparation of Theses and Dissertations (“The Format Guide”) - for use by students admitted to IU Graduate School Programs located at IUPUI. The Format Guide is available at the IUPUI Graduate Office website. The announcement contains, among other things, a summary of the dissertation (not less than 150 words) which is informative and contains a brief statement of the principal results and conclusions. Once the final examination has been scheduled, the announced time and place of the defense must not be changed without the approval of the dean.

Program Faculty

Statistics Faculty and Biostatistics Faculty

Benzion Boukai,
Program Co-Director, Professor of Statistics; Ph.D., Statistics, 1988, SUNY Binghamton; statistical inference, sequential analysis, Bayesian-frequentist interface

Sujuan Gao,
Professor of Biostatistics; Ph.D., Statistics, 1991, University of Southampton; analysis of complex survey data, statistical methods for longitudinal data and missing data

Samiran Ghosh,
Assistant Professor of Statistics; Ph.D., Statistics, 2006, University of Connecticut; Bayesian decision theory and computation, quality of life assessment, regularization/penalized model selection, statistical learning in bioinformatics, survival and reliability analysis

Jaroslaw Harezlak,
Program Co-Director, Assistant Professor of Biostatistics; PhD, Biostatistics, 2005, Harvard University; nonparametric longitudinal models, high dimensional data, functional and intensively collected data analysis, regularization methods in statistics

Siu L. Hui,
Professor of Biostatistics; Ph.D., Biostatistics, 1979, Yale University; analysis of large clinical databases, health services research

Barry P. Katz,
Director, Division of Biostatistics, IU-SOM, Professor of Biostatistics; Ph.D., Biostatistics, 1984, University of Michigan; modeling of infectious diseases, longitudinal data analysis, health services research

Fang Li,
Assistant Professor of Statistics; Ph.D., Statistics, 2004, Michigan State University; nonparametric models, kernel smoothing techniques, time series, stochastic process

Lang Li,
Associate Professor of Biostatistics; Ph.D., Biostatistics, 2001, University of Michigan; pharmacokinetics, pharmacodynamics, pharmacogenetics, epigenetics

Xiaochun Li,
Associate Professor of Biostatistics; Ph.D., Statistics, 1996, University of British Columbia; design and analysis of clinical trials, bioinformatics, medical informatics, nonparametric regression

Xiaoman Li,
Assistant Professor of Biostatistics; Ph.D., Mathematics, 2002, University of Southern California; comparative genomics, gene regulations, Bayesian statistics

Yunlong Liu,
Assistant Professor of Biostatistics; Ph.D., Biomedical Engineering, 2004, Purdue University; computational biology, bioinformatics, functional genomics, epigenetics

Ryan Martin,
Assistant Professor of Statistics; Ph.D., Statistics, 2009, Purdue University; Bayes/empirical Bayes theory and methodology, bioinformatics, high-dimensional inference, mixture models, Monte Carlo methods

Patrick O. Monahan,
Associate Professor of Biostatistics; Ph.D., Measurement and Statistics, 2002, University of Iowa; psychometric methodologies applied to behavioral research

Hanxiang Peng,
Associate Professor of Statistics; Ph.D., Mathematics, 2001, SUNY Binghamton; asymptotic theory, robust regression and data mining, modeling of correlated binary data, survival analysis

Susan M. Perkins,
Associate Professor of Biostatistics; Ph.D., Biostatistics, 1997, University of Michigan; categorical data analysis, clinical trials design and analysis, behavioral research

Chandan K. Saha,
Associate Professor of Biostatistics; Ph.D., Biostatistics, 2001, University of Iowa; statistical methods for longitudinal studies and clinical trials

Jyotirmoy Sarkar,
Associate Professor of Statistics; Ph.D., Statistics, 1990, University of Michigan; statistics, probability, economics

Changyu Shen,
Assistant Professor of Biostatistics; Ph.D., Biostatistics, 2004, University of Pittsburgh; longitudinal data analysis, analysis of incomplete data, statistical methods in bioinformatics, empirical Bayesian models

Wanzhu Tu,
Associate Professor of Biostatistics; Ph.D., Statistics, 1997, University of South Carolina; longitudinal data analysis, Bayes/empirical Bayes analysis, resampling based inference methods

Constantin Yiannoutsos,
Professor of Biostatistics; Ph.D., Statistics, 1991, University of Connecticut; diagnostic test validation, longitudinal data analysis, clinical trials, HIV epidemiology

Menggang Yu,
Assistant Professor of Biostatistics; Ph.D., Biostatistics, 2003, University of Michigan; clinical trials, survival analysis, semiparametric models, latent variable models

Zhangsheng Yu,
Assistant Professor of Biostatistics; Ph.D., Biostatistics, 2006, University of Michigan; survival analysis, longitudinal analysis, nonparametric repression using local kernel and spline methods, bioinformatics