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QCB GRADUATE PROGRAMS

PhD

Since 1982, Computational Biology and Bioinformatics has thrived at USC with a rigorous approach to research and training grounded in problem formulation, an interactive process that involves collaborations between biologists and quantitative scientists.

Ph.D. in Computational Biology and Bioinformatics

Ph.D. QUICK LINKS

Computational Biology and Bioinformatics has been thriving at USC since 1982, when Michael Waterman joined the Department of Mathematics. Since that time the group has grown to include 14 tenured/tenure-track and 2 teaching core faculty, 2 emeritus professors, and 11 joint faculty from the Dornsife College of Letter, Arts and Sciences, the Viterbi School of Engineering, and the Keck School of Medicine. The Department of Quantitative and Computational Biology has on average 60 PhD students and an additional 10 postdoctoral associates.

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Our approach to research and training in the Computational Biology and Bioinformatics program has the work on biological questions as its essential motivation. An important aspect involves problem formulation, an interactive process that can involve collaborations between biologists and quantitative scientists. Once a problem is formulated, the solution involves either the application or development of computational methods often based on a blend of statistics, mathematics and computer science algorithms. Several of the faculty members have joint appointments in mathematics, physics, chemistry, computer science or medicine.

Course Requirements

The students must complete, with a “B” average or better, a minimum of 60 units of courses carrying graduate credit and approved by the guidance committee. The required courses include: BISC 542, CSCI 570, MATH 505A, MATH 541A, MATH 578AB, and QBIO 502. An additional 6 units of elective courses will be taken from the following list: BISC 502AB, BME 530, MATH 502A, MATH 505B, MATH 541B, MATH555A, MATH 650, CSCI 521, CSCI 567, CSCI 670, CSCI 559, CSCI 596, or other BISC, BME, MATH or CSCI that are approved by the student’s advisor. Students must register for a minimum of 4 units of dissertation research (QBIO 790, or following the qualification exam, the QBIO 794 series). Students must be registered in QBIO 542 during 5 semesters in their first 3 years in the program and, in their first semester in the program, in QBIO 547, Ethics and Professional Conduct in Computational Biology. Students are required to enroll in BISC 593 (2 units) during the fall semester of their second year for TA preparation taken before or concurrently with a first TA assignment.

A sample course list for the first four semesters of study:

FALL SEMESTER

MATH 505A

CSCI 570

QBIO 547

BISC 577A

UNITS

3

4

1

2

SPRING SEMESTER

MATH 578A

MATH 541A

QBIO 542

QBIO 502

UNITS

3

3

1

4

SUMMER SEMESTER

QBIO 790

UNITS

2

Registration for second-year students is the following:

FALL SEMESTER

MATH 578B

QBIO 542

BISC 593

ELECTIVE 1*

UNITS

3

1

2

3

SPRING SEMESTER

QBIO 542

QBIO 790

ELECTIVE 2*

UNITS

1

3

3

SUMMER SEMESTER

QBIO 790

UNITS

2

Elective should be determined by consulting with your PI. Choose a minimum of 6 units from the following courses. Please review the most recent catalog HERE.

  • BME 530 Introduction to Systems Biology Units: 4

  • CSCI 521 Optimization: Theory and Algorithms Units: 3

  • CSCI 559 Mathematical Pattern Recognition Units: 3

  • CSCI 567 Machine Learning Units: 4

  • CSCI 596 Scientific Computing and Visualization Units: 4

  • CSCI 670 Advanced Analysis of Algorithms Units: 4

  • MATH 502a Numerical Analysis Units: 3

  • MATH 505b Applied Probability Units: 3

  • MATH 555a Partial Differential Equations Units: 3

  • MATH 650 Seminar in Statistical Consulting Units: 3

  • OR other graduate courses in BISC, BME, CSCI or MATH selected in consultation with an adviser

All of the classes in the sample course list are mandatory. A student may not cancel a course during the semester.

Lab Rotation

All first-year students need to take at least two faculty lab rotations, at least one per semester, in the first year. Rotation advisors must be part of the core or joint QCB faculty (see faculty list here). Students are expected to regularly meet with the advising faculty and participate in the lab meetings during the rotation.

Summer Research

All first-year students need to make arrangements for mandatory summer research at USC before May 1 of the same calendar year. Students should inform the graduate student adviser of the name of the faculty with whom they will work in the summer. Students must have an adviser who is either part of the core QCB faculty or is joint faculty through a courtesy appointment to the QCB section. The student must perform his/her summer research project at USC. Summer internships outside a USC laboratory are not allowed.

Choosing an Adviser

At the end of the summer research period a student has to choose a dissertation adviser. Students must have an adviser who is either part of the core QCB faculty or is joint faculty through a courtesy appointment to the QCB Department.

Timeline to Degree for a Ph.D. in Computational Biology and Bioinformatics

  • 1st Year: Completion of courses with minimum 3.0 grade point average and two rotations.

  • 1st Year: End of the Spring: Complete Screening Examination.

  • 2nd Year: End of the Spring: Complete Qualifying Examination.

  • 3rd Year+: Submission and oral defense of a Dissertation acceptable to Dissertation Committee and the Graduate School.

  • 3rd Year+: Delivery of a dissertation defense seminar to the QCB faculty and students, which will be open to the scientific community.

All additional information can be found in the PhD Program Handbook