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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 15 tenured/tenure-track and 2 teaching core faculty, 2 emeritus professors, and 20 joint faculty from the Dornsife College of Letter, Arts and Sciences, the Viterbi School of Engineering, the Keck School of Medicine, and other USC Schools. 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: CSCI 570, MATH 505A, MATH 541A, QBIO 502, QBIO 542, QBIO 547, QBIO 577, QBIO 578A, QBIO 578B, and QBIO 593. An additional 6 units of elective courses will be taken from the following list: BISC 502A, BISC 502B, BME 530, CSCI 521, CSCI 559, CSCI 567, CSCI 596, MATH 502A, MATH 505B, MATH555A, MATH 565a, PHYS 516, PHYS 518, or other BISC, BME, CSCI, MATH, or PHYS courses that are approved by the student’s research advisor and the Director of Graduate Studies (DGS). 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

QBIO 505A

CSCI 570

QBIO 547

QBIO 577

UNITS

3

4

1

2

SPRING SEMESTER

QBIO 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

QBIO 578B

QBIO 542

QBIO 593

1ST ELECTIVE

UNITS

3

1

2

3-4

SPRING SEMESTER

QBIO 542

QBIO 790

2ND ELECTIVE

UNITS

1

3

3-4

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.

  • BISC 502a Molecular Genetics and Biochemistry  Units: 4

  • BISC 502b Molecular Genetics and Biochemistry  Units: 4

  • 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 670x 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 565a Ordinary Differential Equations  Units: 3

  • PHYS 516 Methods of Computational Physics  Units: 3

  • PHYS 518 Thermodynamics and Statistical Mechanics  Units: 3

  • OR other graduate courses in BISC, BME, CSCI, MATH, PHYS selected in consultation with your research adviser and approved by the Director of Graduate Studies (DGS)

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

Lab Rotation

Students in the CBB program rotate with faculty for two primary reasons:

  • Rotations allow the student and prospective advisor to learn if they would be a good mutual fit as advisor/advisee.

  • Rotations ensure that each first-year student is in regular communication with a QCB faculty member, so the student can easily and quickly find guidance when needed. (Note: all CBB students may also consult with the GAA or DGS at any time.)

Although rotations are typically only done by first year students, if a CBB student past their first year is without an advisor (dissertation chair) for any reason, that student must start a rotation. 3 Note that the regulation on joint QCB faculty advising at most two CBB students does not extend to rotations. Students may rotate with a joint QCB member who is already advisor (dissertation chair) to two CBB students. However, this is not recommended unless there is strong evidence that one of those two CBB students is nearing graduation.

All first-year students need to complete at least two faculty rotations during their first two semesters. Students and rotation advisors must both confirm the rotation arrangement to the Department by email to the GAA. Rotation advisors must be eligible as dissertation advisors for CBB students (see Section 1.4). The requirements of a rotation differ depending on the rotation advisor. For example, the student may be expected to participate in research activities, interact with other students or collaborators, or have assigned lab responsibilities during a rotation. In other cases, a rotation advisor may only require the student to attend regular meetings. Rotation advisors will respect the course load of CBB students during their first two semesters. Students are discouraged from changing rotation advisor mid-semester. Even the optimal relationship may take some time to evaluate. Such a change can lead to incomplete assessment, both for the rotation that concludes early, and for the new rotation that begins late. If a student or rotation advisor feels they must conclude a rotation mid-semester, the Department must be informed by communication with the GAA.

 

Rotations need not be with different rotation advisors to fulfill the requirement of two rotations indicated above. Students should not rotate with any faculty member if they are already certain they would not want that faculty member as dissertation advisor (e.g., if they have no interest

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.

This webpage is for short information purposes. The detailed CBB graduate program’s regulations are provided in  our PhD Program Handbook.