Bioinformatics and Systems Biology Graduate Program

[ undergraduate program | courses | faculty ]

PROGRAM DIRECTOR:
Vineet Bafna, Professor in Computer Science and Engineering

ASSOCIATE DIRECTOR:
Bing Ren, Professor in Cellular and Molecular Medicine

STUDENT AFFAIRS: (858) 822-4948
bioinfo@ucsd.edu
http://www.bioinformatics.ucsd.edu

All courses, faculty listings, and curricular and degree requirements described herein are subject to change or deletion without notice.

Program Focus

We are witnessing the birth of a new era in biology and medicine. The confluence of unprecedented measuring capabilities and computational power has dramatically changed the questions that may be addressed in the biological and biomedical sciences and promises to empower clinical practice in fundamental ways.

On the one hand, recent and novel technologies produce biological data sets of ever-increasing resolution that reveal not only genomic sequences but also RNA and protein abundances, their interactions with one another, their subcellular localization, and the identity and abundance of other biological molecules. This requires the development and application of sophisticated computational methods, encompassed by the field of bioinformatics.

On the other hand, biomedical research has risen to the challenge of understanding the integrated functions of thousands of genes. Physical and functional interaction networks chart connectivities, reveal functional modules, and provide clues on the functioning of specific genes. Using mathematical models of the stochastic and dynamical events of biology reveals fundamental design principles and allows for virtual experimentation. This is a focus of the field of systems biology.

In addition, rapidly increasing capabilities of rapid molecular and genomic analyses in the clinic promise to transform medical practice in unprecedented ways. The ability to cross-query data and knowledge bases provides opportunities and challenges to computational sciences interfacing with medicine to produce support systems for data management, text and language processing, privacy, clinical decision support, and data mining for knowledge discovery. These define the goals of biomedical informatics.

An increasing number of young scientists have integrated the methods and approaches of the physical and life sciences in order to address biological questions in their laboratories. Their science is distinct from other genomic sciences, which typically involve applying quantitative techniques in one lab to the biological data generated in another. The power of math-based reasoning and theoretical physics is harnessed to discover fundamental aspects of biological systems. Iterations between theory and experiment, between mechanistic models and biological validation, are the key feature of Quantitative Biology.

Addressing these challenges requires an interdisciplinary research structure dedicated to developing intellectual and human capacity in Bioinformatics and Systems Biology (BISB), Biomedical Informatics (BMI), and Quantitative Biology (QBIO). As such, there is an enormous need for trained professionals who are experts in biology, biomedicine, and computing. To address this need, the Bioinformatics Graduate Program at UC San Diego was founded in 2001 by Professor Shankar Subramaniam. It now includes five schools and divisions on the UC San Diego campus: the Jacobs School of Engineering (bioengineering, computer science and engineering, and nanoengineering), the Division of Biological Sciences (molecular biology, cell and developmental biology, neurobiology, ecology/behavior/evolution), the Division of Physical Sciences (chemistry and biochemistry, physics, and mathematics), the School of Medicine, and the Skaggs School of Pharmacy and Pharmaceutical Sciences. The graduate program is supported by the respective schools, divisions, and departments as well as by a substantial NIH Training Grant and more than fifty associated faculty.

Participating Departments

Bioinformatics and systems biology (including the graduate biomedical informatics and quantitative biology tracks) is an interdepartmental academic program for undergraduate and graduate students. It is supported broadly at UC San Diego by five schools/divisions and by the faculty from participating departments.

 Jacobs School of Engineering

Division of Biological Sciences

Division of Physical Sciences

School of Medicine

Skaggs School of Pharmacy and Pharmaceutical Sciences

Admissions Requirements

Admission is in accordance with the general requirements of the graduate division. Candidates ought to have a quantitative or computational track record and an inclination to work in interdisciplinary areas across biology, medicine, computational sciences, and engineering. The most competitive applicants have an undergraduate degree majoring in any of the disciplines in the biological sciences, the physical sciences, computer science, or mathematics, and a strong background in the complementary disciplines.

Admission review will be on a competitive basis based on the applicant’s undergraduate track record, Graduate Record Examination General Test (GRE) scores, and other scholastic achievements. Special attention will be given to the quantitative and analytical section scores of the GRE and the formal education in quantitative methods. Attention will also be given to the motivation and career plans of the applicant candidates. Applicants indicate their priority interest in either the bioinformatics and systems biology track, the biomedical informatics track, or the quantitative biology track. The applications will be screened and evaluated by the Admissions Committee with input from program faculty. Applicants must apply online at https://apply.grad.ucsd.edu/home and must submit a completed UC San Diego Application for Graduate Admission (use major code BF76) to include official transcripts (English translation must accompany official transcript written in other languages), TOEFL scores (required only for 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 candidate’s interest in pursuing graduate study. Typically applicants are only considered for admission after interviews at UC San Diego.

For further admission information, students should see the Admissions FAQ on our website http://www.bioinformatics.ucsd.edu or contact the bioinformatics and systems biology graduate coordinator via e-mail at bioinfo@ucsd.edu or at (858) 822-4948.

Curriculum

The bioinformatics and systems biology graduate program is organized around three disciplinary tracks that have distinct yet overlapping faculty and curricular requirements:

Students indicate their interest in one track but are able to request a switch at any time during their study. For each track there are four required core courses and sixteen units to be chosen from a list of elective fields to be completed within the first two years. All required core and elective courses for the degree must be taken for a letter grade. Students must obtain a B or better in courses taken for the degree.

The core curriculum and elective requirements are specified for each track below.

Bioinformatics and Systems Biology Track

Core Courses
Other Required Courses
Elective Courses

Sixteen units of elective courses are to be selected from the elective fields (BIO, CS, SB, BMI, QBIO) delineated below, with at least four units from the CS series and four units from the BIO series. For example, a student interested in systems biology could take one, four-unit class from the CS series, one from the BIO series, one from SB-1, and one from SB-2.

Biomedical Informatics Track

Core Courses
Other Required Courses
Elective Courses

Sixteen units of elective courses are to be selected from the elective fields (BIO, CS, SB, BMI, QBIO) delineated below, with at least four units from the CS series and eight units from the BMI series.

Quantitative Biology Track

Core Courses
Colloquia
Student Seminars
Lab Training
Other Required Courses
Elective Courses

Sixteen units of Elective Courses selected from Elective Field QBIO-1 (listed below) are required. QBIO students may choose from one of the following elective tracks:

Elective Fields

It is the general policy of the program to be as adaptable as possible to the needs of the individual student. The curriculum committee is receptive to students petitioning to satisfy an elective requirement by taking a course not listed among the electives. If a class is available both as an elective and as a core class, it may only be used to satisfy one of those requirements, not both.

Elective BIO-1: Biochemistry
Elective BIO-2: Molecular Genetics
Elective BIO-3: Cell Biology
Elective CS-1: Algorithms
Elective CS-2: Machine Learning and Data Mining
Elective CS-3: Mathematics and Statistics
Elective SB-1: Biological Systems
Elective SB-2: Kinetic Modeling
Elective BMI-1: Biomedical Informatics
Elective QBIO-1: Quantitative Biology

Sample Schedules

Please note that the quarters in which classes are offered may vary each year, some classes may not be offered every year, and course offerings may change. Electives and opportunities for teaching assistantships are likely to be scheduled differently than in the sample schedule.

Example: Bioinformatics and Systems Biology Track
Year 1
FALLWINTERSPRING
Core: Math 283 Core: CSE 280ACore: BENG 203/CSE 283
 Core: BENG 202/CSE 282SOMI 226 or BIOM 219: Ethics
Elective  Elective
BNFO 281: Colloquium BNFO 281: Colloquium BNFO 281: Colloquium
BNFO 283: Student Research Talks BNFO 283: Student Research Talks BNFO 283: Student Research Talks
BNFO 298: Research Rotation BNFO 298: Research Rotation BNFO 298: Research Rotation
Year 2
FALL WINTER SPRING
Elective Elective  
BNFO 281: Colloquium BNFO 281: Colloquium BNFO 281: Colloquium
BNFO 283: Student Research Talks BNFO 283: Student Research Talks BNFO 283: Student Research Talks
BNFO 299: Research BNFO 299: Research BNFO 299: Research
BNFO 500: Teaching Experience BNFO 500: Teaching Experience Qualifying Exam
Example: Biomedical Informatics Track
Year 1
FALL WINTER SPRING
Core: Math 283 Core: CSE 280A  
Core: MED 264 Core: BENG 202/CSE 282 SOMI 226 or BIOM 219: Ethics
Elective Elective Elective
MED 262: Colloquium MED 262: Colloquium MED 262: Colloquium
BNFO 283: Student Research Talks BNFO 283: Student Research Talks BNFO 283: Student Research Talks
BNFO 298: Research Rotation BNFO 298: Research Rotation BNFO 298: Research Rotation
Year 2
FALL WINTER SPRING
Elective Elective Elective
MED 262: Colloquium MED 262: Colloquium MED 262: Colloquium
BNFO 283: Student Research Talks BNFO 283: Student Research Talks BNFO 283: Student Research Talks
BNFO 299: Research BNFO 299: Research BNFO 299: Research
BNFO 500: Teaching Experience BNFO 500: Teaching Experience Qualifying Exam
Example: Quantitative Biology Track

Note that the three quarters of Phys 255 may be started in the first year, concurrent with Phys 270B.

Year 1
FALL WINTER SPRING
Core: Math 283 Core: CSE 280A Core: BENG 203/CSE 283
  Core: BENG 202/CSE 282 SOMI 226 or BIOM 219: Ethics
Elective   Elective
BNFO 281: Colloquium BNFO 281: Colloquium BNFO 281: Colloquium
Phys 270A: QBIO Techniques Phys 270B: QBIO Techniques Phys 270B: QBIO Techniques
Year 2
FALL WINTER SPRING
Elective Elective Elective
Phys 254: QBIO Seminar Phys 254: QBIO Seminar Phys 254: QBIO Seminar
Phys 255: QBIO Research Talks Phys 255: QBIO Research Talks Phys 255: QBIO Research Talks
Phys 256: Critical Reading in QBIO Phys 256: Critical Reading in QBIO Phys 256: Critical Reading in QBIO
BNFO 299: Research BNFO 299: Research BNFO 299: Research
BNFO 500: Teaching Experience BNFO 500: Teaching Experience Qualifying Exam
Year 2 through 5

All students, regardless of their background and elective track, are expected to identify a dissertation research adviser and laboratory prior to the start of the second year. This is an academic requirement to be in good academic standing.

In Year 2, students will begin preparing for their qualifying examination, to be completed before the end of the spring quarter of the second year.

In Year 3, students will begin preparing for their advancement to candidacy examination, to be completed before the end of the spring quarter of the third year.

The goal of the PhD program is that all students complete their dissertation and hold the public dissertation defense by the end of fifth year.

Research Requirement

During the academic year, all students must be enrolled in the appropriate research course for their level. Students in the BISB and BMI tracks typically do three rotations in Year 1 (BNFO 298), while students in the QBIO track typically do one quarter of Phys 270A and two quarters of Phys 270B. Students typically join a lab at the end of Year 1 and then enroll in research units (BNFO 299) with their dissertation adviser in Years 2 and later. BNFO 299 units may be varied to meet the full-time enrollment requirement of twelve units per quarter in fall, winter, and spring. During the summer, students are expected to do research as well, but should not enroll in BNFO 298, Phys 270B, or BNFO 299. During all quarters and the summer, students are responsible for satisfying program requirements, including proposals, reports, presentations, committee meetings, notifying the graduate coordinator when joining/changing labs, etc.; the only difference is that students do not enroll in BNFO 298, Phys 270B, or BNFO 299 in the summer.

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.

Year 1 (BISB and BMI tracks):
Year 1 (QBIO track):
Years 2 and later (all tracks)
The Research Rotation Program

The Research Rotation Program is an integral component of the first year in our program. Each first-year student in the BISB and BMI tracks is required to undertake and pass three quarter-long (ten week) Research Rotations, one in each of the fall, winter, and spring quarters. For fall, winter, and spring rotations (but not summer rotations), students should register for BNFO 298.

The aims of the Research Rotation Program are

The QBIO track has a separate lab training program. For more information, students should contact the Student Affairs office.

Research Rotation Program Guidelines (BISB and BMI tracks)

Students are responsible for identifying laboratories/faculty they are interested in joining for a Research Rotation. Students may only rotate with faculty who could also function as their dissertation advisers. All rotations must be with different faculty.

Faculty are encouraged to develop short projects for rotation students so that students can get a sense of the lab and learn research skills. Rotation projects may or may not be related to possible PhD dissertation projects. Students should check the rotation projects descriptions on the program website to identify projects of interest. Please refer to our faculty directory for a full list of program faculty contact information and research interests. If faculty do not have a rotation project listed online, please contact them directly to discuss available projects.

Second-Year Qualifying Examination

The second-year qualifying examination (BQE) is designed to examine the student’s ability to think critically, analytically, and independently, and to apply the skills acquired in classes to a real research project. The subject of the exam is the student’s current research project. But the focus is the student’s critical analytical ability and command of relevant methods and subjects. The exam is normally taken before the completion of spring quarter in the student’s second year; however, requirements for the first two years must be completed before or in the quarter it is taken, including core classes, rotations (BISB and BMI tracks), or Phys 270A-B (QBIO track), colloquia and student seminars, and ethics.

The exam consists of two components: a ten-page project proposal and an oral exam. The proposal must be submitted at least one week prior to the oral exam. The proposal will have the following sections, in line with NIH proposals: Specific Aims, Significance and Preliminary Data, Approach, and References. The references are not included in the ten-page limit. The second component is the oral exam, where the student defends their proposal.

For each student, the program will appoint three program faculty to form the second-year qualifying exam committee, one of whom will serve as chair. The student is responsible for scheduling the exam in the fall, winter, or spring quarter of the second year. The student’s dissertation adviser is not included in the qualifying exam committee and does not coach the student’s preparation for the exam. Instead, the student will present a practice talk in the Student Research Talks (BNFO 283).

Advancement to PhD Candidacy

After completing formal course requirements, each student will be required to take a written and oral qualifying examination. It is often known as major proposition or Senate qualifying or advancement to candidacy exam. Prior to this examination, each student, in consultation with his or her faculty advisers, will establish a dissertation committee of five faculty members. One adviser should have a primarily computational research focus, the other a primarily experimental research focus. One of the two advisers will function as chair of the committee. The doctoral committee for students in the bioinformatics and systems biology program should comprise a minimum of five members and at least three must be members of the BISB program. If all members are from the program, then two must have a different home department than the committee chair, and one of these two must be tenured. The dissertation advisers will have the major responsibility for the student’s research and dissertation.

At UC San Diego, the university “candidacy/Senate” examination is a requirement for a graduate student to complete satisfactorily once a dissertation project has been decided upon. It is strongly recommended except in special circumstances that the student complete this examination prior to the end of the first three years in the program to comply with the precandidacy time limit (PCTL). Students will not be permitted to continue in doctoral status if they have not advanced to candidacy before the expiration of the precandidacy time limit. Satisfactory completion of the exam will admit the student to the candidacy of the PhD program.

The format for this examination is consistent with the highest standards held by peer universities. The student must write a candidacy report generally following an NIH grant proposal format. Specifically, the report must contain Specific Aims, Research Design and Methods, and Proposed Work and Timeline; these comprise 12–15 pages. In addition (not counted in the 12–15 pages), the report must also contain a bibliography and, as attachments, any publications/supplementary material. The project and the report should be interdisciplinary in terms of computation and biology and should have input from both dissertation advisers. The report must be submitted at least one week prior to the oral exam.

Finally, the student must defend their thesis proposal to their committee in an oral exam (“Advancement to Candidacy Examination”). Students may schedule their advancement to candidacy examination between quarters (including summer) to accommodate their PhD committee members’ schedules but, in order for any academic event to be recorded, a student must be registered. This means that an advancement can only be posted to the academic record during a quarter of registration. It is also expected that the student will meet at least annually with the committee to update the members on his/her progress.

Thesis or Dissertation

Each graduate student in the program will work on a dissertation project under dual mentorship, consisting of a primary adviser who is program training faculty, and a coadviser who may or may not be program training faculty, but must be from a different disciplinary area.

Final Examination

Bioinformatics graduate students will defend their dissertation in a final oral examination. The exam will consist of (1) a presentation of the dissertation by the graduate student, (2) questioning by the general audience, and (3) closed door questioning by the dissertation committee. The student will be informed of the exam result at the completion of all three parts of the oral examination. All members of the committee must sign the final report of the doctoral 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.

Teaching Requirement

Each graduate student admitted to the PhD program in bioinformatics and systems biology is mandated to serve as a teaching assistant (TA) for at least two quarters. Students should enroll in BNFO 500 (Teaching Experience) or an equivalent course code in another department, during each quarter in which they are a teaching assistant. A typical teaching assistantship is 110 hours per quarter (25 percent load, two units of BNFO 500); however, this varies by class.

Bioinformatics graduate students will also participate in additional TA training provided by the Office of Graduate Studies through the Center for Teaching Development (CTD).

Financial Support

It is expected that all US citizens and residents admitted into the PhD program in bioinformatics and systems biology 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) NIH-funded graduate training grant.

PhD Degrees with a Specialization in Bioinformatics

To harness the unique educational and research training opportunities offered by the campuswide bioinformatics effort, several UC San Diego doctoral graduate programs offer students the option to develop—within their own doctoral degree program—a curriculum and research training that has an emphasis in bioinformatics. Such students may then qualify to earn a PhD from their respective doctoral program with a Specialization in Bioinformatics.

A Specialization is a formal University of California mechanism that allows a graduate student pursuing a PhD in the UC system to obtain the doctoral equivalent of a minor in a particular area of specialization. Students interested in pursuing a PhD with a Specialization in Bioinformatics will satisfy the core curriculum requirement of the bioinformatics and systems biology graduate program and pursue research that involves bioinformatics with an adviser and/or coadviser who is a training faculty of the BISB and BMI track.

The following graduate programs offer a Specialization in Bioinformatics: bioengineering, biology, biomedical sciences, chemistry, computer science, mathematics, and physics.

Further Information

For further information please visit our website at http:///www.bioinformatics.ucsd.edu, or contact the Bioinformatics Student Affairs office at (858) 822-4948 or bioinfo@ucsd.edu.