The main objective of the Computational Biology PhD is to train the next generation of scientists who are both passionate about exploring the interface of computation and biology, and committed to functioning at a high level in both computational and biological fields.
The program emphasizes multidisciplinary competency, interdisciplinary collaboration, and transdisciplinary research, and offers an integrated and customizable curriculum that consists of two semesters of didactic course work tailored to each student’s background and interests, research rotations with faculty mentors spanning computational biology’s core disciplines, and dissertation research jointly supervised by computational and biological faculty mentors.
The Computational Biology Graduate Group facilitates student immersion into UC Berkeley's vibrant computational biology research community. Currently, the Group includes over 44 faculty from across 14 departments of the College of Letters and Science, the College of Engineering, the College of Natural Resources, and the School of Public Health. Of these, 26 faculty (Core Members) are available as potential dissertation research advisors for Computational Biology PhD students, with more available for participation on doctoral committees.
The First YearThe time to degree (normative time) of the Computational Biology PhD is five years. The first year of the program emphasizes gaining competency in computational biology, the biological sciences, and the computational sciences (broadly construed). Since student backgrounds will vary widely, each student will work with faculty and student advisory committees to develop a program of study tailored to their background and interests. Specifically, all first-year students must:
- Perform three rotations with Core faculty (one rotation with a non-Core faculty is acceptable with advance approval)
- Complete course work requirements (see below)
- Complete a course in the Responsible Conduct of Research
- Attend the computational biology seminar series
- Complete experimental training (see below)
Laboratory RotationsEntering students are required to complete three laboratory rotations during their first year in the program to seek out a Dissertation Advisor under whose supervision dissertation research will be conducted. Students should rotate with at least one computational Core faculty member and one experimental Core faculty member.
Course Work & Additional RequirementsStudents must complete six courses in the first three (up to four) semesters:
- CMPBIO 293, Doctoral Student Seminar (required Fall/Spring Semester). This one-year interactive seminar builds skills, knowledge and community in computational biology for first year PhD and second year DE students. Topics covered include concepts in human genetics/genomics, laboratory methodologies and data sources for computational biology, workshops on use of various bioinformatics tools, critical review of current research studies and computational methods, preparation for success in the PhD program and career development. Faculty members of the graduate program in computational biology and scientists from other institutions will participate.
- STAT 201A/B Intro to Probability at an Advanced Level/Intro to Statistics at an Advanced Level. It is recommended to take A & B in the same semester; however, it is possible to take them in separate Fall semesters. Alternatively, students can demonstrate they have completed the equivalent by passing a proctored assessment exam on Campus the week before instruction begins. Information about the time/location/content of exam will be provided to each student before the semester begins. NOTE: Students who are offered admission and are not prepared to complete STAT 201A/B will be required to complete STAT 134 or PH 142 first.
- CS61A, The Structure and Interpretation of Computer Programs (Fall Semester) or demonstrate they have completed the equivalent in another course; a syllabus is required for approval. Note: Students will need to complete CS61B and CS70 or the equivalent in order to enroll in upper division CS courses (see proposed CS coursework).
- At least three additional courses, drawn from existing campus offerings. These courses are intended to resolve deficiencies in training and ensure competency in the fundamental knowledge of each discipline. Students are expected to develop a course plan for remaining program requirements (such as biology coursework) and any additional electives, and to consult with the Head Graduate Advisor before the Spring semester of their first year for formal approval (signature required). The course plan will take into account the student's undergraduate training areas and goals for PhD research areas.
- Attend the computational biology seminar series. A schedule is circulated to all students by email and is available on the Center website.
- Complete a Responsible Conduct of Research course, most likely through the Department of Molecular and Cell Biology.
- Complete an experimental training component in one of three ways: 1) complete a laboratory course at Berkeley (or equivalent) with a minimum grade of B, 2) complete a rotation in an experimental lab (w/ an experimental project), with a positive evaluation from the PI, 3) demonstrate proof of previous experience, such as: a biological sciences undergraduate major with at least two upper division laboratory-based courses, a semester or equivalent of supervised undergraduate experimental laboratory-based research at a university, or previous paid or volunteer/internship work in an industry-based experimental laboratory. Students will provide a brief summary of this experience to the Head Graduate Advisor for approval before taking the QE.
Second Year & BeyondAt the beginning of the fall of the second year, students begin full-time dissertation research in earnest under the supervision of their Dissertation advisor. It is anticipated that it will take students three (up to four) semesters to complete the 6 course requirement. Students are required to continue to participate annually in the computational biology seminar series.
Qualifying ExaminationStudents are expected to take and pass an oral Qualifying Examination (QE) by the end of the spring semester (June 15th) of their second year of graduate study. Students must present a written dissertation proposal to the QE committee no fewer than four weeks prior to the oral QE. The write-up should follow the format of an NIH-style grant proposal (i.e., it should include an abstract, background and significance, specific aims to be addressed (~3), and a research plan for addressing the aims) and must thoroughly discuss plans for research to be conducted in the dissertation lab.
Advancement to CandidacyAfter successfully completing the QE, students will Advance to Candidacy. At this time, students select the members of their dissertation committee and submit this committee for approval to the Graduate Division. Students should endeavor to include a member whose research represents a complementary yet distinct area from that of the dissertation advisor (ie, biological vs computational, experimental vs theoretical) and that will be integrated in the student’s dissertation research.
Meetings with the Dissertation CommitteeAfter Advancing to Candidacy, students are expected to meet with their Dissertation Committee at least once each year.
The DissertationDissertation projects will represent scholarly, independent and novel research that contributes new knowledge to Computational Biology by integrating knowledge and methodologies from both the biological and computational sciences. Students must submit their dissertation by the May Graduate Division filing deadline (see Graduate Division for date) of their fifth–and final–year.
Special RequirementsStudents will be required to present their research either orally or via a poster at the annual retreat beginning in their second year.
Financial SupportThe Computational Biology Graduate Group provides a competitive stipend (the stipend for 2016-17 is $34,000) as well as full payment of fees and non-resident tuition. Students maintaining satisfactory academic progress are provided full funding for five and a half years. The program supports students in the first year, while the PI/mentor provides support from the second year on. A portion of this support is in the form of salary for a minimum of two semesters of teaching assistance as a Graduate Student Instructor (GSI) in allied departments, such as Molecular and Cell Biology, Integrative Biology, Plant and Microbial Biology, Mathematics, Statistics or Computer Science. Teaching is part of the training of the program and most students will not teach more than one semester, unless by choice. Due to cost constraints, the program admits few international students; the average is two per year. Those admitted are also given full financial support: stipend, fees and tuition. Students are also strongly encouraged to apply for extramural fellowships. There are a number of extramural fellowships that Berkeley students apply for that current applicants may find appealing. Please note that the NSF now only allows two submissions – once as an undergrad and once in grad school. All eligible students should take advantage of both opportunities to apply.
- National Science Foundation Graduate Research Fellowship (app deadlines in Oct)
- Hertz Foundation Fellowship (app deadline Oct 30, 2015)
- National Defense Science and Engineering Graduate Fellowship (app deadline in Dec)
- DOE Computational Science Graduate Fellowship (Krell Institute) (app deadline in Jan)
AdmissionsWe invite applications from students with distinguished academic records, strong foundations in the basic biological, physical and computational sciences, as well as significant computer programming and research experience. Admission for the Computational Biology PhD is for the fall semester only, and Computational Biology does not offer a Master’s degree. We are happy to answer any questions you may have, but please be sure to read this entire page first, as many of your questions will be answered below.
IMPORTANT: Please note that it is not possible to select a specific PhD advisor until the second year in the program, so contacting individual faculty about openings in their laboratories will not increase your chances of being accepted into the program. You will have an opportunity to discuss your interests with relevant faculty if you are invited to interview in mid-February.
Undergraduate PreparationMinimum requirements for admission to graduate study:
- A bachelor’s degree or recognized equivalent from an accredited institution.
- Minimum GPA of 3.0.
- Undergraduate preparation reflecting a balance of training in computational biology’s core disciplines (biology, computer science, statistics/mathematics), for example, a single interdisciplinary major, such as computational biology or bioinformatics; a major in a core discipline and a combination of interdisciplinary course work and research experiences; or a double major in core disciplines.
- Basic research experience and aptitude are key considerations for admission, so evidence of research experience and letters of recommendation from faculty mentors attesting to the applicant’s research experience are of particular interest.
- Acceptable GRE scores (general exam). Average GRE scores considered for admissions are in the 80th percentile. We do not have set requirements for GRE scores, but generally admit students in the 80th and 90th percentile.
- TOEFL scores for international students (see below for details).
- A completed graduate application: The online application open the first week of September and is located on the Graduate Division website. Paper applications are no longer accepted.
- A nonrefundable application fee: The fee can be paid by credit card online as part of the application process, or as a check made out to the Regents of the University of California. For US citizens and permanent residents, the fee is $105; students may request a fee waiver as part of the online application. For all other students the fee is $125 (no waivers).
- Three letters of recommendation, minimum (up to five are accepted): Letters of recommendation must be submitted online as part of the Graduate Division’s application process. Letters of recommendation may also be mailed directly to Computational Biology, but require advance permission from Computational Biology. Letters are also due December 1st. It is your responsibility to monitor the status of your letters of recommendation (sending prompts, as necessary) in the online system.
- Transcripts: Unofficial copies of all relevant transcripts, uploaded as part of the online application (see application for details). Unofficial copies of official transcripts are strongly preferred, as transcripts must include applicant and institution name and degree goal and should be easy for the reviewers to read (print-outs from online personal schedules can be hard to read and transcripts without your name and the institution name cannot be used for review). Do not send official transcripts to Grad Division or Computational Biology, they will be discarded.
- (Highly, highly recommended) Applicants should also apply for extramural funding, such as NSF Fellowships. Please see Financial Support, below.
- Read and follow all of the “Tips for the Application Process” listed below. This ensures that everything goes smoothly and you make a good impression on the faculty reviewing your file.
Applicants are required to take the Graduate Record Examination and have their exam scores reported to the University. The UC Berkeley school code is 4833; department codes are unnecessary. As long as the scores are sent to UC Berkeley, they will be received by any program you apply to on campus.
The GRE general test is required. GRE subject tests are not required, but can be submitted if taken. It is strongly recommended that applicants take the GRE by November so scores arrive in time to complete application files by early December. Self-reported scores are acceptable until the official scores are available. Current test scores are preferred, but we will accept scores up to five years old.
TOEFL/IELTSAdequate proficiency in English must be demonstrated by those applicants applying from countries where English is not the official language. There are two standardized tests you may take: the Test of English as a Foreign Language (TOEFL), and the International English Language Testing System (IELTS). TOEFL minimum passing scores are 90 for the Internet-based test (IBT), and 570 for the paper-based format (PBT). The TOEFL may be waived if an international student has completed at least one year of full-time academic course work with grades of B or better while in residence at a U.S. university (transcript will be required). Please click here for more information.
Application DeadlinesThe Application Deadline is 11:59 pm Pacific Standard Time, December 1, 2016. Applications must be time stamped online by the deadline or they will be disqualified. All materials must be received by the deadline, including letters. GRE & TOEFL tests must be taken by the deadline, as self-reported scores are acceptable for review. It is your responsibility to ensure and verify that your application materials are submitted in a timely manner. Please be sure to hit the submit button when you have completed the application and to monitor the status of your letters of recommendation (sending prompts, as necessary) and official GRE scores. We do not contact you unless you are missing materials after the deadline. Please include the statement of purpose and personal statement in the online application. Applications that are missing these statements will be considered incomplete and may be disqualified. Please DO NOT send résumés, separate folders of information, or articles. They will be discarded unread.
The Computational Biology recruitment visit will take place February 14-16, 2017. Top applicants who are being considered for admission will be invited to visit campus for interviews with faculty. Invitations will be made by mid-January. Students are expected to stay for the entire event, arriving in Berkeley by 5:30pm on the first day and leaving the evening of the final day. In the application, you must provide the names of between 7-10 faculty from the Computational Biology website with whom you are interested in conducting research or performing rotations. This helps route your application to our reviewers and facilitates the interview scheduling process. An invitation is not a guarantee of admission.
International students may be interviewed by phone, as flights are often prohibitively expensive.
Tips for the Application Process
Uploaded Documents: Be sure to put your name and type of essay on your essays (Statement of Purpose [2-3 pages], Personal Statement [1-2 pages]) as a header or before the text, whether you use the text box or upload a PDF or Word doc. There is no minimum length on either essay, but 3 pages maximum is suggested. The Statement of Purpose should describe your research and educational background and aspirations. The Personal Statement can include personal achievements not necessarily related to research, barriers you’ve had to overcome, mentoring and volunteering activities, things that make you unique!
Letters of Recommendation: should be from persons who have supervised your research or academic work and who can evaluate your intellectual ability, creativity, leadership potential and promise for productive scholarship. If lab supervision was provided by a postdoc or graduate student, the letter should carry the signature or support of the faculty member in charge of the research project. Note: the application can be submitted before all of the recommenders have completed their letters. It is your responsibility to keep track of your recommender’s progress through the online system. Be sure to send reminders if your recommenders do not submit their letters.
Extramural fellowships: it is to your benefit to apply for fellowships as they will facilitate entry into the lab of your choice and often provide higher stipends. Do not allow concerns about coming up with a research proposal before joining a lab prevent you from applying. The fellowships are looking for research potential and proposal writing skills and should be flexible once you have started graduate school.
Calculating GPA: Schools can differ in how they assign grades and calculate grade point averages, so it may be difficult for this office to offer advice. The best resource for calculating the GPA for your school is to check the back of the official transcripts where a guide is often provided or use an online tool.
Faculty Contact/Interests: Please be sure to list faculty that interest you as part of the online application. You are not required to contact any faculty in advance, but are welcome to.
Submitting the application: To avoid the possibility of computer problems on either side, it is inadvisable to wait until the last day to submit your application. It is not unusual for the application system to have difficulties during times of heavy traffic. However, there is no need to submit the application too early. No application will be reviewed before the deadline.
Visits: We only arrange one campus visit for recruitment purposes. If you are interested in visiting the campus and meeting with faculty before the application deadline, you are welcome to do so on your own time.
Name: On the online application, please capitalize the first letter of your first and last name. DO NOT use all caps or no caps. And please double check that you have entered your first and last names in the correct fields. This is our first impression of you as a candidate, so you do want to get your name correct! Be sure to put your name on any documents that you upload (Statement of Purpose, Personal Statement).
California Residency: You must have lived in California previously, and be a US citizen or Permanent Resident, to be a resident. You are not considered a resident if you hope to enter our program in the Fall, but have never lived in California before or are here on a visa. So, please do not mark “resident” on the application in anticipation of admission.