Core Requirements

The Ph.D. degree in Bioinformatics and Genomics prepares graduates for research careers in academia, government, and industry. Students who do not select one of the two optional specializations (Algorithms and Computation or Statistical Genomics) may choose elective courses (13 credits) in addition to the required courses (22 credits).

To be awarded a Ph.D. degree, a student must successfully complete:

• Required Courses: Courses in bioinformatics, genomics, statistics, and molecular evolution. Additionally students will attend courses in colloquium, critical analysis, and ethics (22 credits).
• Elective Courses: Advanced courses from diverse areas (13 credits).
• Rotations: Students will participate in three lab rotations, eight weeks duration each, before selecting their doctoral adviser(s).
• Qualifying Examination: Administered at the end of the first year, it includes a written report and an oral examination of candidate’s knowledge of bioinformatics and genomics research gained over the first year.
• Teaching Requirement: Students are required to complete one semester of teaching in a selected course.
• Comprehensive Examination: Administered generally before the start of the third year, it consists of student’s dissertation proposal and an oral presentation.
• Dissertation Defense: Submission of a written dissertation, and its defense before the dissertation committee, are the program’s final requirements.

Sample Schedule

Options

Students may pursue a doctoral program with no options or select one of the available options: Algorithms and Computation or Statistical Genomics

Algorithms and Computation

The Algorithms and Computation Option trains students in the applications of advanced computational techniques, from specialized data structure and algorithms to the use of novel software and hardware frameworks.

Students are admitted to the option after successfully completing the following:

• The first-year curriculum of the Bioinformatics and Genomics program

• Three research rotations, of which at least two must be with faculty members affiliated with the option

• The qualifying examination

Required Courses

• BMMB/CSE 566 Algorithms and Data Structures in Bioinformatics (3)

• CMPSC 465 Data Structures and Algorithms OR CSE 565 Algorithm Design and Analysis (4)

Electives (select two)

• CMPSC 431 Database Management Systems (3)

• CMPSC 450 Concurrent Scientific Programming (3)

• CSE 562 Probablistic Algorithms (3)

• CMPSC 464 Introduction to the Theory of Computation (3)

• CSE 583 Pattern Recognition-Principles and Applications (3)

• CMPEN 454 Fundamentals of Computer Vision

• CHE 512 Optimization in Biological Networks (3)

Statistical Genomics

The Statistical Genomics Option trains students on the principles and applications of advanced statistical techniques, including experimental design, data processing, statistical inference, visualization, and the use of statistical programming tools.

Students are admitted to the option after successfully completing the following:

• The first-year curriculum of the Bioinformatics and Genomics program

• Three research rotations, of which at least two must be with faculty members affiliated with the option

• The qualifying examination

Required Courses

• STAT 501 Regression Methods (3) or STAT 511 Regression Analysis and Modeling (3)

• STAT 557 Data Mining (3)

Electives (select two)

• STAT 414 Introduction to Probability Theory (3)

• STAT 415 Introduction to Mathematical Statistics (3)

• STAT 416 Stochastic Modeling (3)

• STAT 502 Analysis of Variance (3)

• STAT 504 Analysis of Discrete Data (3)

• STAT 505 Applied Multivariate Analysis (3)

• STAT 540 Statistical Computing (3)

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