PhD in Computational Biology

About the Program

About the Program

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 30 faculty from across 10 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.

Curriculum

Curriculum

The First Year

The 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 ten-week rotations with core faculty,
  • take six courses,
  • take a course in the Responsible Conduct of Research, and
  • attend a Computational Biology-related seminar series.

Laboratory Rotations

Entering students are required to complete three ten-week laboratory rotations during their first year in the program to seek out a Major 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

Students must complete six courses in the first two semesters.

  • A Core Course, Classics in Computational Biology, in which students examine the history and state of the art of computational biology through presentation and discussion of the primary literature.
  • Three Foundation courses drawn from existing departmental offerings and selected in consultation with a faculty advisory committee. These courses are intended to resolve deficiencies in training and ensure competency in the fundamental knowledge of each discipline. These courses are categorized broadly as either computational or biological and students must take one course from each category.
  • Two advanced Elective Courses likewise drawn from existing departmental offerings and selected in consultation with a faculty advisory committee.
  • Attend a computational biology seminar series.
  • Attend at least eight sessions of the Responsible Conduct of Research seminar series.

Satisfactory completion of all first year requirements will be evaluated at the end of the spring semester of the first year. If all requirements are satisfied, students will formally choose a Major dissertation advisor from among the core faculty and begin dissertation research. Prior to the beginning of the third semester, each student and their Major advisor will identify a Minor advisor whose research represents a complementary yet distinct area (from that of the Major advisor) that will be integrated in the student’s dissertation research.

Second Year & Beyond

At the beginning of the fall of the second year, students begin full-time dissertation research in earnest under the joint supervision of their Major and Minor advisors. Although no didactic courses are required beyond the first year if the 6 course requirement has been met, students are required to continue to participate annually in computational biology seminar series.

Qualifying Examination

Students are expected to take and pass the the Oral Qualifying Examination by the end of the spring semester of their second year of graduate study (June 15th). Prior to the oral examination, students must successfully present a written dissertation proposal to the Qualifying Examination committee no fewer than four weeks prior to the Oral Qualifying Examination. The proposal 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, and a research plan for addressing the aims) and must thoroughly discuss plans for research to be conducted in both the Major and Minor advisors’ laboratories and their integration.

Advancement to Candidacy

After successfully completing the written and Oral components of the Qualifying Examination, 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.

Meetings with the Dissertation Committee

After Advancing to Candidacy, students are expected to meet with their Dissertation Committee at least once each year.

The Dissertation

Dissertation 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 Requirements

Students will be required to present their research either orally or via a poster at the annual retreat beginning in their second year. Also, students for whom the advisory committee deem it necessary will be required to take the Biocomputing Bootcamp, an intensive two-week summer workshop aimed at students with minimal computing experience that teaches the rudiments of data structures, python scripting, and genome analysis tools.

Admissions

Admissions

We 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.

Application Requirements

Undergraduate Preparation

Minimum 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. 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).

Application requirements:

  • 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 $90; students may request a fee waiver as part of the online application. For all other students the fee is $110 (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.
  • Transcripts: Unofficial copies of all relevant transcripts, uploaded as part of the online application (see application for details). Do not send official transcripts to Grad Division or Computational Biology. 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.
  • (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.

GRE: 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/IELTS: Adequate 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 Deadlines

The 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.

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.

Interviews

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.

Faculty

Core Faculty

Name Affiliation Interest
Doris Bachtrog Integrative Biology Evolutionary significance of sex and recombination, the mode and tempo of genome evolution, the genomics of speciation, and the evolution of epigenetic modifications.
Lisa Barcellos Epidemiology Identification of genetic, social and environmental risk factors for particular autoimmune diseases including multiple sclerosis, systemic lupus erythematosus, rheumatoid arthritis and other conditions.
Steven Brenner Plant and Microbial Biology; MCB Genetics, Genomics and Development (Affiliated); and Bioengineering (Affiliated) Gene regulation by alternative splicing and nonsense-mediated mRNA decay; Prediction of protein function using Bayesian phylogenomics; Medical and environmental metagenomics; personal genomics; Structural genomics and proteins complexes.
Sandrine Dudoit Biostatistics and Statistics Statistical methods in genetics & molecular biology
Michael Eisen MCB Genetics, Genomics and Development Regulatory sequence analysis
Steve Evans Statistics and Mathematics Stochastic processes and their applications
Daniel Fletcher Bioengineering tba
Oskar Hallatschek Physics Biophysics Theory and Experiments
Teresa Head-Gordon Bioengineering and Chemistry Protein folding & hydration
Ian Holmes Bioengineering Evolutionary genomics; post-transcriptional regulation; bioinformatics algorithms.
Haiyan Huang Statistics Regulatory sequences/motifs, SAGE data analysis
John Huelsenbeck Integrative Biology Evolutionary biology, phylogenetics theory
Nicholas Ingolia Molecular and Cell Biology Translational control of gene expression
Michael Jordan Electrical Engineering and Computer Science, and Statistics Machine learning and bioinformatics
Richard Karp Electrical Engineering and Computer Science Algorithms for computational biology
Sung-Hou Kim Professor of the Graduate Studies, Dept. of Chemistry I. Structural Genomics: Mapping of protein structures coded by whole genome;
II. Computational Genomics: (a) Whole genome phylogeny by alignment-free method; (b) Phenotype classification by whole genome variations
Lexin Li School of Public Health, Biostatistics Neuroimaging data analysis, networks data analysis, personalized recommendation; Statistical genetics, computational biology; Dimension reduction, variable selection, high dimensional regressions; Statistical machine learning, data mining, computational statistics
Rasmus Nielsen Integrative Biology and Statistics Evolutionary genomics
Lior Pachter Mathematics; MCB Genetics, Genomics and Development; and Computer Science Comparative genome analysis
Elizabeth Purdom Statistics Statistical methods for high-dimensional biological and genetic data
Jasper Rine MCB Genetics, Genomics and Development Yeast genetics & genomics, human genetics
Daniel Rokhsar MCB Genetics, Genomics and Development; Physics Genome assembly & comparative genomics
Kimmen Sjölander Bioengineering, and Plant and Microbial Biology Machine learning methods for (meta)genomics and protein functional and structural evolution
Montgomery Slatkin Integrative Biology Population Genetics and Evolutionary Theory
Yun Song Electrical Engineering and Computer Science, and Statistics Computational biology, population genetics, algorithms, applied probability
Nir Yosef Electrical Engineering and Computer Science Biological networks, algorithms, transcriptional regulation, immune cells

Affiliate Faculty

Name Affiliation Interest
Adam Arkin Bioengineering Systems modeling
Peter Bickel Statistics (Emeritus), and Professor in the Graduate School Statistical methods in genomics
Carl Boettiger Environment Science, Policy and Management Applying data science on ecological forecasting and decision making under uncertainty, with applications for global change, conservation and natural resource management
Perry de Valpine Environment Science, Policy and Management Experimental population dynamics, mathematical modeling and statistics
Phillip Geissler Chemistry Theoretical Chemistry
Wayne Getz Environmental Science, Policy and Management Quantitative Population Biology and Disease Ecology
Alan Hubbard Biostatistics Biostatistics; Environmental Health Sciences; Epi/Biostat
Nicholas Jewell Biostatistics and Statistics Statistical analysis & epidemiology
Susan Marqusee MCB Biochemistry and Molecular Biology Protein folding, stability & function
John Marshall Biostatistics Utilize mathematical models to predict the utility of genetic control strategies for a variety of mosquito-borne diseases
Elchanan Mossel Statistics and Computer Science Combinatorial Statistics, Discrete Fourier Analysis and Influences, Randomized Algorithms, Computational Complexity, MCMC, Markov Random Fields, Social Choice, Game Theory, Evolution
Michael Nachman Integrative Biology Evolutionary Genomics and Genetics
George Oster Environmental Sciences, Policy and Management; and MCB Cell and Developmental Biology (Affiliated) Mathematical models of molecular, cellular and organismal systems
David Patterson Computer Science Cancer Tumor Genomics
John Taylor Plant and Microbial Biology Fungal evolution and genomics
Mark van der Laan Biostatistics and Statistics Statistics in biology & causality

Financial Support

Financial Support

The Computational Biology Graduate Group provides a competitive stipend (the stipend for 2015-16 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 one semester 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 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:

For more information concerning financial support and fellowships, please read the Graduate Division’s Guide to Financial Support.

Tips for the Application Process

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.

Contact

Contact

Graduate Program Coordinator:

Kate Chase
University of California, Berkeley
574 Stanley Hall, MC 3220
Berkeley, CA 94720
(510) 642-0379
katechase@berkeley.edu
Office Hours: M-F, 8-4:30 (12-1 lunch)

Program Chair:

Lisa Barcellos, Ph.D.

Head Graduate Advisor:

Haiyan Huang, Ph.D.