Designated Emphasis in Computational and Genomic Biology

Overview

The Designated Emphasis, referred to as the “DE”, is a specialization offered adjunct to affiliated doctoral degrees for students with research interests in computational biology and genomics. DE students receive a solid foundation in the different facets of computational/genomic research and the ensuing competitive edge for the most desirable jobs in academia and industry, which increasingly require interdisciplinary training. Upon successful completion of the dissertation, the student’s final transcript will include the designation, “Ph.D. in [Home Program] with a Designated Emphasis in Computational and Genomic Biology.”

Associated Programs

This list is representative, not comprehensive, and we consider students from most relevant programs on campus:

• Bioengineering Graduate Group (Berkeley campus based students only)
• Biophysics Graduate Group
• Biostatistics Graduate Group
• Chemistry Department
• Computer Science Division, Department of Electrical Engineering and Computer Science
• Integrative Biology Department
• Mathematics Department
• Microbiology Graduate Group
• Molecular and Cell Biology Department
• Physics Department
• Plant Biology Graduate Group
• Public Health – Graduate Group in Epidemiology
• Public Health – Graduate Group in Environmental Health Sciences
• Statistics Department

Normative Time

No additional time can be added to the normative time of your home department; however, due to the interdisciplinary nature of training and research in the Designated Emphasis, and depending on the student’s background, completion of the DE could add one, possibly two, additional semesters to the student’s total program.

Coursework

The DE curriculum consists of a Doctoral Seminar in computational biology composed of separate Fall and Spring components, plus three courses, one each from the three broad areas listed below, which may be independent from or an integral part of a student’s Associated Program. The three courses should be taken in different departments, only one of which may be the student’s home program. These requirements must be fulfilled with coursework taken with a grade of B or better while the student is enrolled as a graduate student at UC Berkeley. S/U graded courses do not count. See below for recommended coursework.

Students do not need to complete all of the course requirements prior to the application or the qualifying exam. The Doctoral Seminar may be taken in different academic years (and does not need to be taken in order, ie either Spring/Fall or Fall/Spring are ok), with at least one of the two semesters being prior to the Qualifying Exam. The DE will be rescinded if coursework has not been completed upon graduation (students should report their progress each year to the DE advisor, especially if they wish to change one of the courses they listed for the requirement).

1. Computer Science and Engineering: A single course at the level of CS61A or higher will fulfill this requirement. Students can also take CS 88 (as an alternative to CS61A), though depending on their background, Data 8 may be necessary to complete this course. Students with a more advanced background are recommended to take a higher level CS course to fulfill the requirement.
2. Biostatistics, Mathematics and Statistics: A single course at the level of Stat 131A, 133, 134, or 135 or higher will fulfill this requirement. Students with a more advanced background are recommended to take one of either Stat 201A & 201B or a higher level course to fulfill the requirement. Statistics or probability courses from other departments may be able to fulfill this requirement with prior approval of the program.
3. Biology: please select an appropriate biology course from the list linked below (not up-to-date), or choose a course from current course listings.
4. Computational Biology: CMPBIO C293, Doctoral Seminar, Fall & Spring.

Recommended Coursework

Seminars & Retreat

Students must attend the annual Computational Biology Retreat (generally held in November) as well as regular CCB Seminar Series, or equivalent, as designated by the Curriculum Committee. Students are also strongly encouraged to attend or volunteer with program events during Orientation, Recruitment, Symposia, etc. Available travel funds will be dependent upon participation.

Qualifying Examination and Dissertation

The qualifying examination and dissertation committees must include at least one, but preferably two, Core faculty members from the Computational Biology Graduate Group. The faculty member(s) may either represent the home department or serve as an outside member (Academic Senate Representative). The Qualifying Examination must include examination of knowledge within the area of Computational and Genomic Biology. The Comp Bio Doctoral Seminar must be completed before the QE, as it will be important preparation for the exam.

How to Apply

Applications are due July 15th, the academic year (approx 2 semesters) before the qualifying exam takes place. Students are advised to notify both the graduate affairs officer (GSAO) of the home department and the DE program coordinator of their intent to apply as early as possible.

Electronic copies of the following materials must be submitted to Kate Chase, Graduate Program Coordinator, to apply to the DE in Computational and Genomic Biology:

1. DE CGB Petition (.pdf)(fillable form! Updated 3/15/19)
2. Letter of recommendation from the student’s faculty advisor (which includes approval to participate in the DE)
3. One page letter of intent summarizing the student’s background in computational and genomic biology, and outlining short- and long-term training and research goals in the field
4. Most recent copies of all undergraduate and graduate transcripts
5. The student’s curriculum vitae

Please note that review may take up to one month.