Bioinformatics and Systems Biology Graduate Program
Alexander Hoffmann, Professor in Chemistry and Biochemistry
Pavel Pevzner, Professor in Computer Science and Engineering
All courses, faculty listings, and curricular and degree requirements described herein are subject to change or deletion without notice. Updates to curricular sections may be found on the Academic Senate website: http://senate.ucsd.edu/Curriculum/Updates.htm.
The Bioinformatics and Systems Biology Graduate Program draws upon the expertise of affiliated faculty from the Division of Biological Sciences; Departments of Bioengineering, Chemistry and Biochemistry, Computer Science and Engineering, Mathematics, Physics, and the Biomedical Sciences Graduate Program.
The University of California, San Diego is a premier research institution that has fostered interdisciplinary research since its inception. Specifically, bioengineering (at the interface of biology, medicine, and engineering), neuroscience (at the interface of biology and medicine), biophysics (at the interface of chemistry, biology, and physics), and cognitive science (at the interface of medicine and computer science) are all nationally ranked interdisciplinary graduate research programs. This has led to growth and innovation in many new areas of science and engineering research and the training of an exceptionally high caliber of graduate and postdoctoral students.
In recent years, bioinformatics and systems biology have been identified by the UC San Diego administration as two of the most important growth areas for the campus. With several recent new faculty hires, UC San Diego has seen a significant increase in the research activity associated with bioinformatics and systems biology—these transcend traditional disciplines.
Development of a Field
We are witnessing the birth of a new era in biology. The ability to decipher the genetic code of living organisms is dramatically changing our understanding of the natural world and promises to improve substantially the quality of human life. Understanding how genomes work requires sophisticated computer-based information handling tools (bioinformatics), and new high throughput technologies for understanding the function of genes on a genome-wide scale (functional genomics). The combination of experimental and modeling approaches to understand the functioning of genomes and cellular systems is often call systems biology.
The most pressing problem in the systems biology era will be to understand the integrated functions of thousands of genes. Dealing with this problem will require an interdisciplinary research structure dedicated to developing intellectual and human capital in bioinformatics and genome science. Due to the complexity of this new paradigm in biology, entirely new sets of tools and human resources will be necessary. Thus, future developments will be dependent upon the scientific progress at the interface of three major disciplines—biology, engineering, and computer science. The accelerated growth of modern biology warrants revolutionary changes in academic curricula.
Each department represented in this program participates in various interdisciplinary graduate programs in addition to providing very strong interdisciplinary graduate training. One example is the La Jolla Interfaces in Science program (LJIS), a campus- and mesa-wide fellowship opportunity sponsored by the Burroughs Wellcome Fund. LJIS supports exploration of interfaces between the biological and biomedical sciences and the physical, computer, and mathematical sciences at UC San Diego, The Scripps Research Institute (TSRI), the Salk Institute, and the San Diego Supercomputer Center.
Bioengineering, consistently ranked among the top three programs nationally by U.S. News & World Report, has several new faculty hires in the area of bioinformatics and computational biology and has identified bioinformatics as a major area of focus.
Biological Sciences, a premier division at UC San Diego, will spearhead the interdisciplinary, undergraduate specialization in bioinformatics and is planning to hire new faculty in bioinformatics fields.
Biomedical Sciences is an interdisciplinary PhD program, based in the School of Medicine, with tracks in pharmacology, physiology, and cellular and molecular medicine. It will be closely linked to the planned new School of Pharmacy and Pharmaceutical Sciences. In addition to a strong computational biology presence amongst its faculty, there are plans to hire more faculty whose main interests are in computational pharmacogenomics and bioinformatics.
Chemistry and Biochemistry, the home of the Molecular Biophysics Training Grant, is highly recognized for its strong computational biology program with plans to further expand in chemo and bioinformatics areas.
Computer Science and Engineering (CSE) is unique in having a critical mass of faculty whose research interests focus on biology. These faculty have very strong collaborative research interactions with biology, chemistry, and engineering researchers. CSE is currently recruiting for a senior faculty member with computational biology expertise.
Mathematics has expressed strong interest in building in the area of bioinformatics with emphasis on statistics and probability. This focus is one of fundamental importance for the future of bioinformatics, and the department is committed to both hiring new faculty and launching new courses in statistics pertinent to bioinformatics.
Physics is the home of leaders in the field of computational statistical mechanics applied to biology and provides the foundation for sophisticated modeling of complex biological systems. Physics also plans to recruit new faculty members whose research focus will be on development of information/theory-based models of biological systems.
Admission is in accordance with the general requirements of the graduate division. Candidates will have an interdisciplinary persuasion to work across computers, biology, medicine, and engineering; with an undergraduate degree majoring in any of the disciplines in biological science, physical science, computer science, mathematics, or engineering with a strong background in quantitative sciences and biology.
Admission review will be on a competitive basis based on the applicants’ undergraduate track record, Graduate Record Examination General Test (GRE) scores, and other scholastic achievements. Attention will also be given to the motivation and career plans of the applicant candidates. Special attention will be given to the quantitative and analytical section scores of the GRE. The applications will be screened and evaluated by the Admissions Committee with input from all program faculty. In addition, applicants must submit a completed UC San Diego Application for Graduate Admission (use major code BF75), official transcripts (English translation must accompany official transcript written in other languages), TOEFL scores (required ONLY for all international applicants whose native language is not English and whose undergraduate education was conducted in a language other than English), and three letters of recommendation from individuals who can attest to the academic competence and to the depth of the candidates’ interest in pursuing graduate study.
For further admission information, students should contact the bioinformatics graduate coordinator via e-mail at firstname.lastname@example.org or at (858) 822-4948. You may also visit our website at http://www.bioinformatics.ucsd.edu.
The Bioinformatics and Systems Biology Graduate Program is organized around a formal course requirement consisting of three quarters of course work, with enrollment in four four-unit courses each quarter. One four-unit course in each quarter will be a research rotation in the laboratory of a program faculty mentor. The remaining nine courses will include four compulsory core courses and five courses to be chosen from a list of electives approved by the Course Committee.
The electives are intended to maximize the flexibility of the program, but at least one course must be chosen from the biology field and one from the computer science and engineering field. The faculty adviser(s) will pay particular attention to deficits in the background of each student and will assist in making appropriate course choices from the elective fields. Students electing to take any of the undergraduate courses listed in these fields will receive an additional course component in order to make it equivalent to a graduate level course. Students have the option to test out of a field by passing an exam designed by the faculty committee. This exam will fulfill one of the breadth requirements of the program.
It is the general policy of the program to be as adaptable as possible to the needs of the individual student. The faculty advisory committee will work closely with students to identify what might be lacking in a particular curriculum program.
Core Training Courses
- Bioinformatics I. Biological Data and Analysis Tools (Pharm 201)
- Bioinformatics II. Introduction to Bioinformatics Algorithms (BENG 202/CSE 282)
- Bioinformatics III. Genomics, Proteomics, and Network Biology (BENG 203/CSE 283)
- Bioinformatics IV. Statistical Methods in Bioinformatics (Math 283)
(Each student will select from five of the eight elective fields below. One must be from the biology field and one from the computer science field. For each elective, multiple course options currently available are listed).
Elective 1: Biochemistry
- BENG 230. Biochemistry
- BIBC 100. Structural Biochemistry
- Chem 114A. Biochemical Structure and Function
- Chem 213. Chemistry of Macromolecules
- Chem 218. Macromolecular Biochemistry
Elective 2: Data Structures
- CSE 100. Data Structures
- CSE 200. Computability and Complexity
- Math 176A. Computer Implementation of Data Structures
Elective 3: Algorithms
- CSE 101. (also Math 188) Design and Analysis of Algorithms
- Math 173. Mathematical Software Scientific Programming
Elective 4: Information Retrieval, Databases, and Data Mining
- CSE 132A. Database System Principles
- CSE 133. Information Retrieval
- CSE 254. Machine Learning
Elective 5: Molecular Genetics
- BICD 100. Genetics
- BIMM 100. Molecular Biology
- BIBC 116. Evolution of Genes and Proteins
- BGGN 220. Advanced Molecular Biology
- BGGN 223. Advanced Genetics
Elective 6: Cell Biology
- BICD 110. Cell Biology
- BICD 130. Embryos, Genes, and Development
- BIOMED 210. Cellular Biology
- BIOMED 212. Cellular and Molecular Pharmacology
- BGGN 222. Advanced Cell Biology
Elective 7: Physics and Engineering
- BENG 253. Biomedical Transport Phenomena
- BENG 275. Computational Biomechanics
- Phys 210A. Equilibrium Statistical Mechanics, or higher
Elective 8: Mathematics and Statistics
- Math 174. Numerical Methods in Science and Engineering
- Math 181E. Mathematical Statistics
- Math 280A. Probability Theory
Example 1–Sample Program (Year 1)
A student with an undergraduate background in biology might make the following course selections:
|Bioinformatics I||Bioinformatics II||Bioinformatics III|
|CSE 100||CSE 101|
|Test out—Chem 114A||Test out—BENG 275||Test out—BICD 110|
|Research Rotation||Research Rotation|
Example 2–Sample Program (Year 1)
A sample program for a student with an undergraduate degree in computer science and engineering might be structured as follows:
|Bioinformatics I||Bioinformatics II||Bioinformatics III||Bioinformatics IV|
|BIOMED 210||Chem 213|
|Test out-CSE 101||Math 280A||Elective|
|Elective||Elective||Test out—CSE 132A|
|Research Rotation||Research Rotation|
All students, regardless of their background and elective track, will be expected to begin working in the laboratory of their choice by the second year. Additionally in Year 2, students will begin preparing for their qualifying examination and will participate in advanced seminar courses and journal clubs identified by program faculty.
End of Year 2 through 5
Spring of Year 2: Qualifying Examination
Spring of Year 3: Advance to Candidacy
End of Year 5: PhD
In summary, in addition to three quarters of research rotations, students must complete the four compulsory bioinformatics core courses; and, either test out of, or select at least five courses from the eight elective areas.
Each student in the graduate program will participate in three research rotations, at least two of which will be in the laboratory of mentors other than the thesis directors. The purpose of the research rotation will be to train the students in research methodology in specific bioinformatics areas. At the end of the research rotation period, the student will submit a written report that will be evaluated by the faculty mentor in whose laboratory the project was carried out. The report will also be sent to the Qualifying Examination Committee who will take this into consideration in the assessment of the student for admission to candidacy.
Seminars, Informal Courses, Group Meetings, and Symposia
Students are expected to attend the weekly Bioinformatics and Systems Biology seminars hosted by the program. As well as formally structured courses and research rotations, graduate students will have access to seminars, group meetings, and informal sessions during which they will have frequent opportunities to interact closely with faculty mentors and to present their research plans, problems, and findings. In addition to weekly bioinformatics seminars, the graduate program will launch monthly student/faculty meetings at which students can present their research findings and discuss their progress. Graduate students will also be expected to organize an annual symposium where they will invite leading researchers to UC San Diego for one-day talks and discussions.
Besides the activities noted above, UC San Diego as a premier research institution has many excellent seminar programs sponsored by each research department and organized research group. Several interdisciplinary programs facilitate research meetings. Notable ones include the La Jolla Interfaces in Sciences (LJIS) Program, the Neurosciences Program, the Molecular Biophysics Program, the Whitaker Institute for Biomedical Engineering, the San Diego Supercomputer Center, and the Structural Genomics Program. LJIS, for example, is an extremely successful interdisciplinary program sponsoring stimulating and state-of-the-art seminars. LJIS recently sponsored a well-received symposium on post-genomic bioinformatics. Many program faculty are involved in several of the areas mentioned above, and the bioinformatics graduate program benefits from all of these additional programs and symposia.
Students, upon completion of the appropriate course work, will be given research orientation lectures by the bioinformatics program faculty. Each graduate student will participate in a research experience in the laboratory he or she selects to carry out the research rotation. During this period students will become acquainted with scientific methodology for designing experiments, analyzing the results, organizing the data, conducting research in a responsible manner, preparing oral and poster presentations of research results, and writing scientific papers.
Upon successful completion of the qualifying examination (described in the following section), graduate students will choose their research project from the many possibilities offered in the program and begin to work on a research problem with their faculty advisers. In consultation with their mentors, students will formulate the research activity that will lead to their dissertation. Graduate students will have the opportunity to do internships in the local bioinformatics/ biotechnology industry if the thesis project is of mutual interest to a corporate sponsor and the thesis advisers. The research program is designed with two key objectives in mind: (1) to provide a truly interdisciplinary research training at the interface area between biology and computer science and engineering; and (2) to address fundamentally strong research problems that will lead to the advancement of the field of bioinformatics. We anticipate that every graduating student will emerge as a highly trained bioinformatician who can either pursue an academic career by choosing optimal postdoctoral research positions or enter the next generation biotechnology/biopharmaceutical industry.
It is our belief that active research under proper tutelage is the best means of training and that the foundations of a good graduate training program rest on an outstanding faculty group, an excellent student body, and a strong and well-coordinated research program. Each of the faculty members in this program has expertise and interests that will contribute importantly to the Interdisciplinary Bioinformatics Graduate Program. Participating faculty have pooled their resources in terms of laboratories, and the knowledge and experience to ensure the success of the program. Through daily contact with faculty and other research colleagues, students will learn to develop critical and creative thinking skills, scientific methodology, and a sound knowledge of research problems.
Second-Year Qualifying Examination
The Bioinformatics and Systems Biology Second-Year Qualifying Examination (BQE) is designed in an innovative manner to test the ability of students to think analytically and in an interdisciplinary manner. This method was suggested by students of the program during the first two years after inception.
Students are expected to come up with a research problem different from the one he or she may have been working on with a faculty adviser and write a proposal that can be defended at the oral examination to a faculty committee appointed by the chair of BQE. The written document is expected to be in the form of a proposal to NSF or NIH, where the student provides the specific aims of the project, the background for and significance of the problem chosen, some preliminary results and/or observations and specific details on the design of the research. The student is tested on his or her ability to formulate and design the problem as well as on the interdisciplinary nature of the approach. Once the student passes the oral portion of the exam, the student is deemed to be qualified for advancing into PhD thesis research in bioinformatics. The student can schedule this examination at any time of the year, but with two provisions. First, the student should have completed all the required and most of the elective courses assigned, and second, the examination should be taken before the student completes his or her second year in the program. At the time of BQE, the student should have decided on his or her two mentors/research advisers, and should have discussed with them about joining their laboratories and obtaining guaranteed funding for the duration of research as long as he or she is in good academic standing. The BQE Oral Examination Committee will discuss these specifics and other program requirements with the students at the oral examination.
Advancement to PhD Candidacy
Upon completion of formal course requirements, each student will be required to take a written and oral qualifying examination that will admit the student to the candidacy of the PhD program In advance of the qualifying examination, each student, in consultation with his or her faculty adviser(s), will establish a dissertation committee of five faculty members. The committee will consist of three faculty, at least two of whom are affiliated with the bioinformatics and systems biology program, and two other faculty from departments affiliated with the program, or who are themselves members of the program faculty. At least two of the five committee members must be from a department other than the committee chair’s department and at least one of these two must be tenured. The thesis advisers will have the major responsibility for the student’s research and dissertation.
Thesis or Dissertation
Each graduate student in the program will work on a bioinformatics thesis project under dual mentorship of the program faculty.
Bioinformatics graduate students will defend their thesis in a final oral examination. The exam will consist of (1) a presentation of the thesis by the graduate student, (2) questioning by the general audience, and (3) closed door questioning by the thesis committee. The student will be informed of the exam result at the completion of all three parts of the oral examination. The final report of the doctoral committee will be signed by all members of the committee and the final version of the dissertation will conform to the procedures outlined in the publication, Instructions for the Preparation and Submission of Doctoral and Master’s Theses.
Each graduate student admitted to the PhD program in bioinformatics is mandated to serve as a teaching assistant (TA) for at least two quarters. This will aid in preparing the students for a teaching career. In addition, each student will make periodic research presentations to the graduate program students/faculty. Students will also discuss their progress at the annual program meeting to be held each year. It is anticipated these formal presentations will serve as valuable training in preparing the student for a teaching career.
Bioinformatics graduate students will also participate in additional TA training provided by the Office of Graduate Studies and Research through the Center for Teaching Development (CTD).
It is expected that all students admitted into the PhD program in bioinformatics will receive financial assistance subject to their continuance and performance in the program. The assistance will be provided from (1) departmental financial commitments, (2) university financial commitments, (3) teaching assistantships, (4) research assistantships, and (5) NIH-funded graduate training grant.
PhD Degrees with a Specialization in Bioinformatics
Currently, UC San Diego offers PhD degrees with a specialization in bioinformatics from the participating departments listed in this section. Students are admitted into one of the departmental graduate programs and satisfy the requirements of both the department and the interdisciplinary bioinformatics graduate program. If you are interested in the PhD degree with a specialization in bioinformatics, please consult with the Student Affairs Office of the department you are interested in to obtain further information on admission and individual program requirements.
For course descriptions not found in the UC San Diego General Catalog, 2013–14, please contact the department for more information.
BNFO 281. Seminar in Bioinformatics and Systems Biology (1)
Weekly seminars by faculty and visiting bioinformaticists presenting their research.