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 one semester of a Doctoral Seminar in computational biology, 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:

• 1 semester of Doctoral Seminar CMPBIO C293
• 1 course in Computer Science and Engineering
• 1 course in Biostatistics, Mathematics or Statistics
• 1 course in Biology

The three courses should be taken in different departments, only one of which may be the student’s home program.

When do I need to take the courses?

Students do not need to complete all of the course requirements prior to the application or the qualifying exam. The semester of the Doctoral Seminar must be taken before the Qualifying Exam (or in the same semester as the exam). Other coursework can be completed any time before graduation. 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. Graduating students should reach out to the DE advisor (via ccb_de_advising@berkeley.edu) to request updates to their DE APR (Academic Progress Report). The APR is manually updated, so it is important that students request this service.

Coursework Policies

• The coursework must be taken with a grade of B or better. S/U graded courses do not count (an exception was made for courses taken Spring 20, Fall 20 and Spring 21 due to the pandemic).
• Courses must be taken while the student is enrolled as a graduate student at UC Berkeley.
• Appropriate upper-division undergraduate courses can satisfy the requirements; unless noted below, lower-division undergraduate courses will not generally count toward the requirement except with permission of the Head Graduate Advisor. Research units, seminars, reading groups, or other similar courses do NOT satisfy the requirements.
• The three courses should be taken in different departments.
• Only one of the courses may be offered by the student’s home program (unless cross-listed with another department). For students in Public Health, courses offered by their home division within Public Health, not the entirety of Public Health, would count as courses offered by the student’s “home program”.

Your course selection will be subject to review by the head graduate advisor. See the link below of commonly taken courses and the category they satisfy as a useful starting point. Courses not listed here can also count, after approval by the Head Graduate Advisor.

Pre-approved courses

by category (see tabs at bottom of google sheet).
And see below for guidance on course choice by category.

Qualifying Examination and Dissertation

The qualifying examination and dissertation committees must include at least one (but more is fine!) Core faculty members from the Computational Biology Graduate Group (only faculty on the linked page are considered core). The faculty member(s) may either represent the home department or serve as an outside member (Academic Senate Representative) – namely, they can serve any role on the committees and overlap with home program requirements. 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.

Seminars & Retreat

Students should attend the annual Computational Biology Retreat (generally held in November) as well as the 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.

Guidelines on Choosing Courses

Below we give some specific guidelines that can be used to determine which courses can count and toward which categories to aid you in choosing a course for the different categories. This guidance is not intended to be exhaustive, but merely to address common questions (ultimately all course selection is subject to the approval of the Head Graduate Advisor).

Computer Science and Engineering: Any courses offered by EECS, BioEngineering, or other Engineering departments at the level of upper-division undergraduate or higher will count for the CS/Engineering category (excepting research units, seminars, reading groups, or other similar courses). Courses in CS at the level of CS61A or higher will also satisfy this requirement. Students without computing experience may find CS 88 to be a good 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 course to fulfill the requirement.

Biostatistics, Mathematics and Statistics: Any courses offered by the Mathematics or Statistics Departments at the level of upper-division undergraduate or higher will count for this requirement (excepting research units, seminars, reading groups, or other similar courses); graduate courses offered by Public Health through Division of Biostatistics (Public Health courses numbered 240-249) will count for this requirement. Lower-division undergraduate Statistics courses numbered STAT 2-88 do NOT count nor does Public Health 142. Other lower-division undergraduate courses in these departments must be assessed by the head graduate advisor.

For students with limited statistics/math background, we recommend Stat 131A, 133, 134, 135 or STAT 200C; note that the course STAT 100, while an upper-division course, has a graduate version (STAT 200C) for which graduate students should register. Students from a biology background may also want to consider IB C201/CMPBIO C210. 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.

Biology: Most courses at the upper-division undergraduate level offered through the biology departments MCB, PMB, and IB will count towards this requirement (excepting research units, seminars, reading groups, or other similar courses). The main exceptions will be courses that are primarily computational or statistically oriented, an example being IB C201/CMPBIO C210 mentioned above. Courses in other departments can also count toward the biology requirement, for example courses in Public Health, ESPM, or NST are often appropriate; again this is subject to approval by the HGA. The above spreadsheet indicates some commonly approved courses as a starting point.

Distinguishing between Biostatistics/Statistics/Math and CS/Engineering: There are many courses whose topics do not clearly divide between CS/Engineering and BioStatistics/Statistics/Math. The goal in the DE requirements is to have both an appropriate breadth of knowledge, and also a diversity of perspectives on those topics. Therefore courses offered by EECS or other Engineering departments will only count for the CS/Engineering category, and courses offered by the Mathematics or Statistics Department or the Division of Biostatistics will only count for the BioStatistics/Statistics/Math requirement, regardless of the course topics.

Courses that are cross-listed between these departments can count for either category, regardless of which department the student registered with. However, it is the student’s responsibility to make clear on the DE application that the course is cross-listed in the other category and indicate to which category the course should be credited. For example, a student who took STAT C241A, which is cross-listed as CS C281A, must give both numbers on their DE application if they wish for the course to count for the CS/Engineering requirement. Otherwise, the course will not be credited toward the CS/Engineering requirement.

Computationally-oriented courses offered in other departments will be evaluated individually based on both the course topics and the level of the instruction in order to determine to which topic (if any) the course can be credited.

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 (ccb_de_advising@berkeley.edu) of their intent to apply as early as possible. Please use ccb_de_advising@berkeley.edu for all CCB DE related inquiries and updates.

To apply to the DE in Computational and Genomic Biology, the following materials must be submitted to the DE advisors via the application form linked below. Please have your list of proposed courses ready before starting the online application.

CCB DE Application Form

The items listed below should be combined into one pdf and uploaded into the online application linked above:

1. Letter of support from the student’s faculty advisor, which includes PI approval for student to participate in the DE and a concise research summary
2. 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
3. Most recent copy of graduate transcript(s)
4. The student’s curriculum vitae (optional!)

Please note that review may take up to one month.