Bioinformatics Graduate Program
PROGRAM DIRECTOR: Shankar Subramaniam
Professor of Bioengineering and Chemistry and Biochemistry Senior Fellow,
San Diego Supercomputer Center
Student Affairs: (858) 822-4948
bioinfo@ucsd.edu
http://www.bioinformatics.ucsd.edu
Participating Faculty
Program Focus
The Interdisciplinary Bioinformatics 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 Psychiatry; 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 has been identified by the UCSD administration
as one of the most important growth areas for the campus. Several recent
new faculty hires have been targeted in bioinformatics-related fields.
UCSD has also seen a significant increase in the research activity associated
with bioinformatics across the traditional disciplines.
Development of the Field and Departmental Strength in the 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. Recent advances in technology have led to the
creation of a new interdisciplinary sciencegenomics. In simple terms,
genomics is the reading and understanding of the blueprints for 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).
Bioinformatics
characterizes the flow of information in living systems and can
be schematically represented by the following:
The most pressing problem in the post-genome sequencing 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,
i.e., understanding the organization, evolution, and function of whole
genomes rather than single genes, entirely new sets of tools and human
resources will be necessary. Thus, future developments in genomics, and
the applications that derive from genomics, will be dependent upon the
scientific progress at the interface of three major disciplinesbiology,
engineering, and computer science. In addition to the scientific advances
required to understand the functions of genomes, 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
intradisciplinary 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 UCSD, 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 and 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 UCSD, will spearhead
the interdisciplinary, undergraduate specialization in bioinformatics
and is planning to hire new faculty in bioinformatics fields.
Biomedical Sciences, is an interdisciplinary Ph.D. 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 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.
Admissions Requirements
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 UCSD 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.
Acceptance letters to incoming students will indicate academic areas
in which the Admissions Committee believe the individual is deficient
and suggestions for remedial materials to be examined prior to the fall
quarter may be provided.
For further admission information and/or to request an application packet,
students should contact the bioinformatics graduate coordinator via email
at bioinfo@ucsd.edu or
at (858) 822-4948. You may also visit our Web site at http://www.bioinformatics.ucsd.edu.
Foreign Language Requirement
Competence in one or more foreign languages is encouraged but not required.
Curriculum
Specific fields of emphasis:
- biological data and analysis tools
- sequence analysis
- genomic analysis
- statistical methods for bioinformatics
The Interdisciplinary Bioinformatics 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: Sequence and Structure AnalysisMethods and
Applications (BENG 202/CSE 257A)
- Bioinformatics III: Genomic Analysis (BENG 203)
- Bioinformatics IV: Statistical Methods in Bioinformatics (Math 283)
Program Electives
(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 1sample program (Year 1)
A student with an undergraduate background in biology might make the
following course selections:
Year 1
FALL
|
WINTER
|
SPRING
|
|
Bioinformatics I
|
Bioinformatics II
|
Bioinformatics III Bioinformatics IV
|
|
CSE 100
|
CSE 101
|
Test out-Chem. 114A
|
BENG 275
|
Test out-BICD 110
|
Elective
|
Elective
|
Elective
|
|
Research Rotation
|
Research Rotation
|
|
example 2sample program (Year 1)
A sample program for a student with an undergraduate degree in computer
science and engineering might be structured as follows:
Year 1
FALL
|
WINTER
|
SPRING
|
|
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
|
|
Year 2
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: Ph.D.
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.
Research Rotations
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
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 UCSD for one-day talks and discussions.
Besides the activities noted above, UCSD 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.
Research Training
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.
Advancement to Ph.D. 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 Ph.D. 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 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 students research
and dissertation.
It is anticipated that each student will complete the qualifying examination
before the end of the second year of his or her tenure, but no later than
the end of the third year. The student is expected to join a research
laboratory for completing a thesis dissertation no later than the beginning
of the second year of tenure.
Thesis and/or Dissertation
Each graduate student in the program will work on a bioinformatics thesis
project under dual mentorship of the program faculty. As a partial fulfillment
for the Ph.D. degree, the student will submit a complete dissertation
to be evaluated by a doctoral committee chosen by his or her mentors in
consultation with the bioinformatics steering committee. The doctoral
dissertation will be submitted to each member of the doctoral committee
at least four weeks before the final examination. The student will defend
his or her final thesis after the committees evaluation and will
pass or fail depending on the committees decision. The entire graduate
program is expected to be completed within the proposed timeline of the
program.
Final Examination
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 Masters
Theses.
Teaching Requirement
Each graduate student admitted to the Ph.D. 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).
Financial Support
It is expected that all students admitted into the Ph.D. 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.
Employment Prospects
There is enormous demand from industry for trained professionals in
bioinformatics. The pharmaceutical industry, agrobusiness, and biotechnology
companies often look to academia for people with the appropriate interdisciplinary
skills. There is also a great need for academic faculty who have broad,
interdisciplinary training, because much of the success of the next generation
of undergraduate and graduate students will depend on their ability to
master materials in several disciplines. Competition for people skilled
in bioinformatics is so intense that salary offers are being driven sky-high
and there is concern that the universitiesfew of which are training
students in the fieldare rapidly being depleted of the best researchers.
A report from the Working Group of Biomedical Computing of the NIH recognized
the shortage of biologists with appropriate computing expertise and called
for strong NIH support of cross-disciplinary education and training.
Ph.D. Degrees with a Specialization in Bioinformatics
Currently, UCSD offers Ph.D. 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 departmental and the interdisciplinary bioinformatics
graduate program. If you are interested in the Ph.D. 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.
Further Information
For further information please visit our Web site at http:///www.bioinformatics.ucsd.edu,
or contact the bioinformatics student affairs office at (858) 822-4948,
bioinfo@ucsd.edu.
Bioinformatics Graduate Program
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