PhD in Bioinformatics

The PhD in Bioinformatics program offers unique interdisciplinary training for graduate students in the science, engineering, medicine, and ethics of twenty-first-century cell biology jointly through the College of Engineering and the Graduate School of Arts & Sciences. The program aims to prepare top researchers for careers in both academia and industry in the areas of molecular life sciences. In order to be admitted, students need at least a bachelor’s degree in a field related to bioinformatics, preferably one with a strong component in mathematics and computer science.

Learning Outcomes

Students graduating with a PhD in Bioinformatics are expected to:

• Demonstrate mastery of the core concepts of Bioinformatics: These include (a) advanced methods in computational biology, (b) the chemical principles that underlie biochemistry, molecular biology, and genomics, (c) the design and implementation of relational databases, (d) fundamental methods in probability and statistics, and (e) the construction of predictive mathematical models of biological systems.
• Be capable of using critical thinking and research methods in Bioinformatics to understand computational and experimental data. In addition to formal coursework, this ability will be learned and demonstrated in (a) dissertation research and (b) presentations at scientific meetings, graduate seminars, student seminars, and qualifying examinations.
• Demonstrate the ability to produce and present original research in Bioinformatics. The most important manifestation of this outcome is publication of peer-reviewed research papers on dissertation research, and, in particular, papers with the trainee as first author. The Challenge Project, seminar presentations, and presentations at meetings also demonstrate this outcome.
• Conduct scholarly activities in a professional and ethical manner.
• Develop the ability to communicate clearly the meaning, potential impacts, and risks associated with one’s research activities to a nontechnical audience in ways that confer a sense for its value to society.

Course Requirements

The PhD requires a total of 64 course credits, consisting of the 36 required credits listed below, or their equivalents, and additional elective lecture, laboratory, and research credits. The precise course of study will be determined in consultation with faculty advisors and will reflect the student’s background and interests. In order to be admitted to PhD candidacy, students must demonstrate mastery of the required subject matter (no lower than a B in each of the required courses). Course requirements are as follows:

• ENG BE 562 Computational Biology: Genomes, Networks, Evolution (4 cr)
• Choose one Comp/Math core course:
  • CAS CS 542 Machine Learning (4 cr)
  • ENG BF 571 Dynamics and Evolution of Biological Networks (4 cr)
  • ENG BF 768 Biological Database Systems (4 cr)
  • GRS MA 770 Mathematical and Statistical Methods of Bioinformatics (4 cr)
• Choose one Biology core course:
  • CAS BI 565 Functional Genomics (4 cr)
  • ENG BF 751 Molecular Biology and Biochemistry: Molecules and Processes (4 cr)
• ENG BF 690 Bioinformatics Challenge Project (2 cr each; 4 total)
• ENG BF 752 Legal and Ethical Issues of Science and Technology (4 cr)
• ENG BF 810 Laboratory Rotation System (1 cr each, 3 total)
• ENG BF 820 Research Opportunities in Bioinformatics (1 cr)
• ENG BF 821 Bioinformatics Graduate Seminar (2 cr each)
• GRS MA 681 Accelerated Introduction to Statistical Methods for Quantitative Research (4 cr)
• One nonresearch elective course (4 cr)
• A minimum of 2 research credits

Fulfillment of required course equivalents will be determined based on documented previous academic and/or work experience. The student and their advisors will petition the curriculum committee for such equivalencies. When either past work or an alternate course has been accepted as a required course equivalent, the student’s advisors will recommend another course to fulfill the 36 core credit hours. Advanced elective courses should be taken in place of any waived course requirements.

Qualifying Examination

Students must pass an oral qualifying exam in order to advance to the level of PhD candidacy. The goal of the exam is for the student to demonstrate their general proficiency in bioinformatics, as well as command of the area(s) in which they intend to conduct research. All parts of the qualifying examination must be passed before the dissertation or thesis prospectus will be accepted by the Graduate School of Arts & Sciences.

Students must schedule their qualifying exam by March 31 of their second year, and must take the exam by June 30. Students who fail to pass the exam on their first try are allowed a second attempt, to be scheduled and completed by the end of the first semester of their third year.

Language Requirement

There is no foreign language requirement for the bioinformatics degree. However, basic mastery of spoken and written English, as determined by oral presentations, written reports, and publishable manuscripts, is a requirement for the PhD.

Dissertation and Final Oral Examination

Candidates shall demonstrate their abilities for independent study in a dissertation representing original research or creative scholarship. A prospectus for the dissertation must be completed and approved by the readers, the Director of Graduate Studies, and the Department Chair/Program Director. Candidates must undergo a final oral examination in which they defend their dissertations as a valuable contribution to knowledge in their field and demonstrate a mastery of their field of specialization in relation to their dissertation. All portions of the dissertation and final oral examination must be completed as outlined in the GRS General Requirements for the Doctor of Philosophy Degree.

Students who complete the required core courses but are unable to successfully complete all of the requirements for the PhD will be eligible to be awarded a master’s degree.