Overview
The Designated Emphasis in Computational and Genomic Biology (DECGB) was developed to orient students, systematize graduate training, catalyze research collaboration, and enhance an intellectual community which transcends traditional departmental boundaries. Admitted students receive a solid foundation in the different facets of genomic research and the ensuing competitive edge for the most desirable jobs in academia and industry, which increasingly require interdisciplinary training.
The DECGB is available for Ph.D. students in one of our Associated Programs listed below. The requirements for completing the DECGB include course work, particiation in the DECGB seminar series, and attendance at the annual retreat. Students should apply to the DE at least one month prior to taking their Qualifying Examination. The QE committee must include at least member of the CGB Graduate Group faculty.
Upon successful completion of the dissertation, the student's final transcript will include the designation, "Ph.D. in XX with a Designated Emphasis in Computational and Genomic Biology."
Due to the interdisciplinary nature of training and research in the Designated Emphasis, and depending on the background of the student, completion of the DE could add one, possibly two, additional semesters to the student's total program. Please note that no additional time can be added to the normative time of the home department.
*All phone numbers are area code 510.
Admissions
Applications for admissions are reviewed on a rolling basis throughout the year; however, students must apply prior to taking the Qualifying Examination. To be admitted to the Designated Emphasis in Computational and Genomic Biology, students must be a doctoral candidate in one of our Associated Programs. Students are advised to notify both the graduate affairs officer of the home department and the DECGB program administrator of their intent to apply as soon as possible to ensure all paperwork is completed properly and in a timely manner. To this end, students are strongly encouraged to apply a minimum of one month prior to the Qualifying Examination.
Examination and Dissertation Requirements
Both the student's Qualifying Examination committee and Dissertation committee must include at least one, but preferrably two, faculty members participating in the DECGB. The DE member(s) may represent either the student's home department or serve as an outside member. Satisfactory performance on the Qualifying Examination for the doctorate will be judged independently from the Designated Emphasis.
To Apply
The following materials are required to apply to the DECGB:
- DE CGB Petition (.pdf)
- Graduate Petition for Change of Major or Degree Goal (.pdf)
- Letter of Recommendation from the student's Faculty Advisor
- One page Statement of Purpose, describing background in Computational and Genomic Biology and outlining short- and long-term training and research goals in computational biology
- Most recent copies of all undergraduate and graduate transcripts
- Curriculum Vitae
Submit materials to:
DECGB Administrator
c/o California Institute for Quantitative Biosciences (QB3)
304 Stanley Hall MC 3220
University of California
Berkeley, CA 94720.
Course Requirements
The curriculum of the Designated Emphasis consists of coursework which may be either independent from, or an integral part of, a student's Associated Program. Our goal is to provide students with a broad education in Computational and Genomic Biology. Students are thus required to take one class from three of the following five categories (A-E). At least two of the courses must be outside of the sudent's Associated Program.
NOTE: Click on the category name to expand/contract course list.
A. Computer Science and Engineering
- Computer Science (COMPSCI) 170: Efficient Algorithms and Intractable Problems
- Computer Science (COMPSCI) 186: Introduction to Database Systems
- Electrical Engineering (EL ENG) 120: Signals and Systems
- Electrical Engineering (EL ENG) 170A, 180A: Introduction to Modeling and Simulation
- Electrical Engineering (EL ENG) 170B, 180B: Introduction to Modeling and Simulation
- Electrical Engineering (EL ENG) 221A: Linear System Theory
- Electrical Engineering (EL ENG) 222: Nonlinear Systems - Analysis, Stability and Control
- Electrical Engineering (EL ENG) 223: Stochastic Systems: Estimation and Control
- Electrical Engineering (EL ENG) 227A, B: Introduction to Convex Optimization
- School of Information Management Science (SIMS) 255: Foundations of Software Design
B. Biostatistics, Mathematics, and Statistics
- Mathematics (MATH) 110: Linear Algebra
- Mathematics (MATH) 127: Mathematical and Computational Methods in Molecular Biology
- Mathematics (MATH) 128A, B: Numerical Analysis
- Mathematics (MATH) 228A, B: Numerical Solution of Differential Equations
- Mathematics (MATH) 290: Hidden Markov Models in Comparative Genomics
- Public Health (PB HLTH) 142A, B: Introduction to Probability and Statistics in Biology and Public Health
- Public Health (PB HLTH) 143: Introduction to Statistical Methods in Computational and Genomic Biology
- Public Health (PB HLTH) 240C: Biostatistical Methods: Computational Techniques
- Public Health (PB HLTH) 240D: Biostatistical Methods: Applications of Statistics to Genetics and Molecular Biology
- Public Health (PB HLTH) 243A: Multivariate Statistical Methods in Genomics
- Public Health (PB HLTH) 244A, B: Stochastic Processes in Biology and Health
- Public Health (PB HLTH) 248: Statistical/Computer Analysis Using SPLUS
- Public Health (PB HLTH) 252B: Modeling the Dynamics of Infectious Disease Processes
- Statistics (STAT) 101: Introduction to the Theory of Probability
- Statistics (STAT) 102: Introduction to the Theory of Statistics
- Statistics (STAT) 134: Concepts of Probability
- Statistics (STAT) 135: Concepts of Statistics
- Statistics (STAT) C141 / Bioengineering (BIO ENG) C141: Statistics for Bioinformatics
- Statistics (STAT) 200A, B: Introduction to Probability and Statistics at an Advanced Level
- Statistics (STAT) 210A, B: Theoretical Statistics
- Statistics (STAT) 215A, B: Statistical Models: Theory and Application
- Statistics (STAT) 232: Experimental Design
- Statistics (STAT) 241A, B, C: Statistical Learning Theory
- Statistics (STAT) 242A, B: Analysis of Multidimensional Data
- Statistics (STAT) 243: Introduction to Statistical Computing
- Statistics (STAT) 244: Statistical Computing
- Statistics (STAT) 246: Statistical Genetics
D. Chemistry, Chemical Engineering, and Physics
- Chemistry (CHEM) 120B: Physical Chemistry
- Chemistry (CHEM) 130A: Biophysical Chemistry
- Chemistry (CHEM) 212: Bioorganic Chemistry
- Chemistry (CHEM) 220B: Statistical Mechanics
- Chemistry (CHEM) 223A: Chemical Kinetics
- Chemistry (CHEM) C230: Protein Chemistry, Enzymology, and Bio-organic Chemistry
- Chemistry (CHEM) 231A: Advanced Biophysical Chemistry
- Chemical Engineering (CHM ENG) 142: Chemical Kinetics and Reaction Engineering
- Chemical Engineering (CHM ENG) 150A, B: Transport Processes
- Chemical Engineering (CHM ENG) 162: Dynamics and Control of Chemical Processes
- Chemical Engineering (CHM ENG) 244: Kinetics and Reaction Engineering
- Physics (PHYSICS) 205A, B: Advanced Dynamics
E. Computational Biology
- Bioengineering (BIO ENG) 131: Introduction to Computational Biology
- Bioengineering (BIO ENG) 142: Programming and Algorithm Design for Computational Biology & Genomics Applications
- Bioengineering (BIO ENG) 143: Computational Methods in Biology
- Bioengineering (BIO ENG) 144: Introduction to Protein Bioinformatics
- Molecular and Cell Biology (MCELLBI) 137: Computer Simulation in Biology
- PLANTBI C246 (also MCELLBI C246, BIOENG C246): Topics in Computational Biology & Genomics
Prior coursework may be used to fulfill the requirements if the coursework is found to be equivalent to those classes listed below. The selection of courses will be maintained and regularly updated to follow the rapid pace of research in genomics and the offering of new courses on campus. Students are required to earn letter grades (A-F) for coursework.
Seminars
In addition to the coursework requirement, students must attend regular seminar series, or equilvalent, as designated by the Curriculum Committee.
Annual Retreat
Each year, the DE faculty and students convene for a two-day retreat. The retreat program includes student presentations, poster session, student meeting and faculty meeting. For information on the next retreat, please click here.
Affiliated Faculty
Thomas C. Alber, Ph.D., Molecular and Cell Biology, Lawrence Berkeley National Laboratory
Adam P. Arkin, Ph.D., Bioengineering, Chemistry, Lawrence Berkeley National Laboratory
James J. Berger, Ph.D., Molecular and Cell Biology, Lawrence Berkeley National Laboratory
Peter J. Bickel, Ph.D., Statstics
Rachel Brem, Ph.D., Molecular and Cell Biology
Steven E. Brenner, Ph.D., Plant and Microbial Biology, Bioengineering, Molecular and Cell Biology, Lawrence Berkeley National Laboratory
Sandrine Dudoit, Ph.D., Biostatistics, Statistics
Michael B. Eisen, Ph.D., Molecular and Cell Biology, Lawrence Berkeley National Laboratory
Steven Evans, Ph.D., Statistics, Mathematics
Teresa Head-Gordon, Ph.D., Bioengineering, Lawrence Berkeley National Laboratory
Ian Holmes, Ph.D., Bioengineering
Haiyan Huang, Ph.D., Statistics
John Huelsenbeck, Ph.D., Integrative Biology
Nicholas P. Jewell, Ph.D., Biostatistics, Statistics
Michael I. Jordan, Ph.D., Electrical Engineering and Computer Science, Statistics
Richard M. Karp, Ph.D., Electrical Engineering and Computer Science, Bioengineering, Mathematics, ICSI
Sung-Hou Kim, Ph.D., Chemistry, Lawrence Berkeley National Laboratory
David Lindberg, Ph.D., Integrative Biology, Lawrence Berkeley National Laboratory
Susan Marqusee, Ph.D., Molecular and Cell Biology, Lawrence Berkeley National Laboratory
Rasmus Nielsen, Ph.D., Integrative Biology, Statistics
George Oster, Ph.D., Environmental Science, Policy & Management, Molecular and Cell Biology
Lior Pachter, Ph.D., Mathematics, Molecular and Cell Biology, Computer Science
Jasper Rine, Ph.D., Molecular and Cell Biology
Daniel S. Rokhsar, Ph.D., Molecular and Cell Biology, Lawrence Berkeley National Laboratory
Kimmen Sjölander, Ph.D., Bioengineering, Lawrence Berkeley National Laboratory
Montgomery Slatkin, Ph.D., Integrative Biology
Yun S. Song, Ph.D., Electrical Engineering and Computer Science, Statistics
Terry Speed, Ph.D., Statistics, Lawrence Berkeley National Laboratory
Bernd Sturmfels, Ph.D., Mathematics, Computer Science
Mark J. van der Laan, Ph.D., Biostatistics, Statistics
By-Laws
NOTE: Click on Article to expand and contract content.
Article I: Purpose
The goal of the DECGB is to coordinate research and instruction in the area of Computational and Genomic Biology. The faculty members of the DE shall establish and administer a program of instruction and research leading to a Designated Emphasis to be awarded in conjunction with a Ph.D. degree in an Associated Program. The interdisciplinary and diverse nature of the research conducted by the participating faculty shall provide the student with a broad scope of educational opportunities. The appointment of an Executive Committee to monitor the Designated Emphasis will assure rigorous training for all graduates.
Article II: Faculty Membership
Faculty members of the DE must be actively engaged in teaching and research related to Computational and Genomic Biology, and must be deemed qualified by the Graduate Group Executive Committee. Individuals desiring to become a member of the Designated Emphasis in Computational and Genomic Biology may submit a curriculum vitae to the Chair of the Executive Committee, listing their qualifications and stating reasons for seeking membership.
Faculty applicants will be evaluated in terms of their research interests, current teaching commitments, and potential for student guidance. Appointment of faculty members shall be approved by a majority of the faculty membership voting and submitted to the Dean of Graduate Division for final approval. Members who do not participate in research, student advising, committees, and/or the regular teaching of courses germane to the DECGB will be subject to cancellation of membership by the Executive Committee. A member may resign by a written request submitted to the Chair of the Executive Committee.
Article III: Associated Program Membership
Associated Programs must demonstrate commitment to training and research in the area of the DE.
- Associated Programs shall give the Designated Emphasis in Computational and Genomics Biology prominence at least comparable to that of a single faculty member in brochures and website advertisements.
- Applications for admission to an Associated Program must include a check-box for students to indicate their interest in the Designated Emphasis in Computational and Genomics Biology. This check-box is non-binding on either the student’s or Associated Program’s part.
- Associated Programs agree to either distribute DECGB materials (e.g., program brochure) with all corresponding Associated Program materials, or provide such materials upon request.
- Applications indicating interest in the Designated Emphasis shall be made available for review by faculty members of the DECGB. The DECGB may advise the Associated Program regarding those students, though such advice is non-binding.
- Students whose applications indicate interest in the Designated Emphasis and who are invited by the Associated Program to visit the campus (e.g., for interviews) will be encouraged to meet with members of the DECGB, including those outside of the Associated Program.
Article IV: Executive Committee
The administrative leadership of the group offering the Designated Emphasis in Computational and Genomic Biology shall be vested in an Executive Committee consisting of five elected members, one of which is the Chair. Members of the Executive Committee, including the Chair, shall be elected by the full group membership. Elections shall be held in the fall semester in alternate years. The existing Executive Committee shall fill interim vacancies in its membership by appointment from within the appropriate area of specialization, after considering the results of previous elections. Executive Committee members must belong to the Academic Senate.
The principal responsibilities of the Chair of the Executive Committee are to:
- Recommend to the Dean of the Graduate Division the name of the individual who will serve as the Head Graduate Adviser for the DECGB and the names of any additional individuals who will serve as Graduate Advisers;
- Represent the membership in official matters pertaining to the DECGB;
- Conduct administrative and clerical matters related to the activities of the DECGB; and
- Review DECGB membership and maintain an list of active members to be annually reported to the Dean of the Graduate Division for approval.
The principal responsibility of the Head Graduate Adviser is to recommend DECGB faculty members who will serve on the Ph.D. Qualifying Examination and Dissertation Committees. This position may be undertaken by the Chair of the DE Executive Committee, the Chair of the DE Graduate Advising Committee, or any other member of the DECGB.
The principal responsibilities of the DE Executive Committee are to:
- Review the academic program and make appropriate recommendations;
- Establish policies regarding admissions, degrees, and graduate support; and
- Conduct any other business necessary to the administration of the DECGB.
The Chair of the DECGB Executive Committee and the Chairs of the Associated Programs shall meet regularly to discuss administrative, instructional, and research resource needs.
Article V: Other Committees
The following three standing committees shall be appointed by the Executive Committee.
Admissions Committee. The Admissions Committee shall have the following responsibilities:
- Review and approve graduate student applications to the DE;
- Review and approve applications for financial support, when applicable;
- Review student admissions requirements and make appropriate modifications;
- Collaborate with Associated Programs in the recruitment of graduate students.
Curriculum Committee. The Curriculum Committee shall have the following responsibilities:
- Review course requirements for the DE and make appropriate additions/deletions to the list of relevant courses;
- Review Qualifying Examination and Dissertation requirements, make appropriate modifications in consultation with the Head Graduate Adviser in the Associated Program and inform the Graduate Division of any changes for approval by the Dean;
- Develop recommended tracks.
Graduate Advising Committee. The Graduate Advising Committee shall have the following responsibilities:
- Review and approve a student’s course selection and make appropriate recommendations before approval;
- Review and approve a student’s Qualifying Examination and Dissertation Committees and recommend to the Dean of the Graduate Division the members representing the DE Graduate Group on each committee;
- Appoint a secondary Faculty Adviser, as needed;
- Review and approve any variations from the DE standard Curriculum and inform the Graduate Division of any changes for approval by the Dean;
In addition, the Executive Committee may select ad hoc committees as needed including a Funding Committee and Seminar, Publicity & Retreat Committee.
Article VI: Meetings
A regular meeting of the members of the Designated Emphasis shall be held each year. The Chair of the Executive Committee shall call meetings of the membership as are deemed necessary or desirable by the Executive Committee. The Chair shall call a special meeting at any time he or she is so requested by written notice from five or more members. Meetings shall be conducted in accordance with generally-accepted procedures, including a review of the minutes of the previous meeting, report of the Executive Committee, report of the Graduate Advisors, unfinished business, and new business. At meetings, twenty-five percent (25%) of the active members in residence shall constitute a quorum. Minutes of each meeting shall be the responsibility of the Chair.
Article VII: Amendments
Approval of changes in these by-laws shall require a two-thirds majority of the votes cast. Proposed changes shall be submitted to the membership for mail ballot or for vote at a meeting, provided that written notice of the proposed changes are sent to the members at least one week prior to the date of the meeting. Votes cast electronically via e- mail are acceptable.