Program Overview

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Introduction to the Bioinformatics and Systems Biology Graduate Program

The Bioinformatics and Systems Biology Graduate Program at UC San Diego is an interdisciplinary program that combines the methods and approaches of the physical and life sciences to address biological questions. The program is designed to develop intellectual and human capacity in bioinformatics and systems biology, biomedical informatics, and quantitative biology.

Program Focus

The program focuses on the confluence of unprecedented measuring capabilities and computational power, which has dramatically changed the questions that may be addressed in the biological and biomedical sciences. The program aims to empower clinical practice in fundamental ways by developing sophisticated computational methods, encompassed by the field of bioinformatics, and understanding the integrated functions of thousands of genes, which is a focus of the field of systems biology.

Participating Departments

The program is supported by five schools on the UC San Diego campus:

• Jacobs School of Engineering (bioengineering, computer science and engineering, and nanoengineering)
• School of Biological Sciences (molecular biology, cell and developmental biology, neurobiology, and ecology, behavior, and evolution)
• School of Physical Sciences (chemistry and biochemistry, physics, and mathematics)
• School of Medicine
• Skaggs School of Pharmacy and Pharmaceutical Sciences

Admissions Requirements

Admission to the program is in accordance with the general requirements of the graduate division. Candidates should 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.

Curriculum

The program is organized around three disciplinary tracks:

• Bioinformatics and Systems Biology Track (BISB)
• Biomedical Informatics Track (BMI)
• Quantitative Biology Track (QBIO)

Each track has 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.

Bioinformatics and Systems Biology Track

Core Courses

• MATH 283: Statistical Methods in Bioinformatics
• BENG 202/CSE 282: Introduction to Bioinformatics Algorithms
• BENG 203/CSE 283: Genomics, Proteomics, and Network Biology
• For the fourth core class, choose one of the following:
  • CSE 280A: Algorithms in Computational Biology
  • CSE 284: Personal Genomics for Bioinformaticians
  • ECE 208: Computational Evolutionary Biology
  • ECE 213: Parallel Computing in Bioinformatics
  • BNFO 286/MED 283: Network Biology and Biomedicine

Other Required Courses

• BNFO 281: Seminar in Bioinformatics and Systems Biology in fall, winter, and spring quarters of the first and second year
• BNFO 283: Bioinformatics Student Research Talks in fall, winter, and spring quarters of the first and second year
• BNFO 294: Scientific Ethics (previously SOMI 226 or BIOM 219) must be taken by spring of the second year
• BNFO 298: Research Rotations in the fall, winter, and spring quarters of the first year
• BNFO 299: Graduate Research, for year two and above
• BNFO 500: Teaching Assistantship (or an equivalent course code in another department), for two quarters

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.

Biomedical Informatics Track

Core Courses

• MATH 283: Statistical Methods in Bioinformatics
• BENG 202/CSE 282: Introduction to Bioinformatics Algorithms
• MED 264: Principles of Biomedical Informatics
• For the fourth core class, choose one of the following:
  • CSE 280A: Algorithms in Computational Biology
  • CSE 284: Personal Genomics for Bioinformaticians
  • ECE 208: Computational Evolutionary Biology
  • ECE 213: Parallel Computing in Bioinformatics
  • BNFO 286/MED 283: Network Biology and Biomedicine
  • BENG 203/CSE 283: Genomics, Proteomics, and Network Biology

Other Required Courses

• MED 262: Current Trends in Biomedical Informatics in fall, winter, spring quarters of the first and second year
• BNFO 283: Bioinformatics Student Research Talks in fall, winter, and spring quarters of the first and second year
• BNFO 294: Scientific Ethics (previously SOMI 226 or BIOM 219) must be taken by spring of the second year
• BNFO 298: Research Rotations in the fall, winter, and spring quarters of the first year
• BNFO 299: Graduate Research, for year two and above
• BNFO 500: Teaching Assistantship (or an equivalent course code in another department), for two quarters

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

• MATH 283: Statistical Methods in Bioinformatics
• BENG 202/CSE 282: Introduction to Bioinformatics Algorithms
• BENG 203/CSE 283: Genomics, Proteomics, and Network Biology
• For the fourth core class, choose one of the following:
  • CSE 280A: Algorithms in Computational Biology
  • CSE 284: Personal Genomics for Bioinformaticians
  • ECE 208: Computational Evolutionary Biology
  • ECE 213: Parallel Computing in Bioinformatics
  • BNFO 286/MED 283: Network Biology and Biomedicine

Colloquia

• BNFO 281: Seminar in Bioinformatics and Systems Biology in fall, winter, and spring quarters of the first year
• PHYS 254: QBIO Seminar in fall, winter, and spring quarters of the second year

Student Seminars

• PHYS 255: QBIO Research Talks. Three quarters within the first two years, concurrent with lab courses PHYS 270B or BNFO 299
• PHYS 256: Critical Reading in Quantitative Biology in fall, winter, and spring quarters of the second year

Lab Training

• PHYS 270A: Experimental Techniques for Quantitative Biology in fall quarter of the first year
• PHYS 270B: Quantitative Biology Laboratory in the winter and spring quarters of the first year

Other Required Courses

• BNFO 294: Scientific Ethics (previously SOMI 226 or BIOM 219) must be taken by spring of the second year
• BNFO 299: Graduate Research, for year two and above
• BNFO 500: Teaching Assistantship (or an equivalent course code in another department), for two quarters

Elective Courses

Sixteen units of elective courses selected from elective field QBIO-1 (listed below) are required.

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.

Elective BIO-1: Biochemistry

• BENG 230A: Biochemistry (four units)
• CHEM 209: Macromolecular Recognition (four units)
• CHEM 213A: Structure of Biomolecules and Biomolecular Assemblies (four units)
• CHEM 213B: Biophysical Chemistry of Macromolecules (four units)
• CHEM 216: Chemical Biology (four units)

Elective BIO-2: Molecular Genetics

• BICD 100: Genetics (four units)
• BGGN 206A: Concepts of Reasoning and Experimentation (CORE) I (four units)
• BGGN 220: Graduate Molecular Biology (four units)
• BGGN 223: Graduate Genetics (four units)

Elective BIO-3: Cell Biology

• BICD 110: Cell Biology (four units)
• BICD 130: Embryos, Genes, and Development (four units)
• BGGN 222: Graduate Cell Biology (four units)
• CHEM 221/BGGN 230: Signal Transduction (four units)

Elective CS-1: Algorithms

• BENG 203/CSE 283: Genomics, Proteomics, and Network Biology (four units)--Core for BISB and QBIO tracks, elective for BMI track
• CSE 101: Design and Analysis of Algorithms (four units)
• CSE 200: Computability and Complexity (four units)
• CSE 202: Algorithm Design and Analysis (four units)
• CSE 280A: Algorithms in Computational Biology (four units)
• ECE 213: Parallel Computing in Bioinformatics (four units)
• MATH 261A: Probabilistic Combinatorics and Algorithms (four units)

Elective CS-2: Machine Learning and Data Mining

• BNFO 285: Statistical Learning in Bioinformatics (four units)
• CSE 250A: Principles of Artificial Intelligence: Probabilistic Reasoning and Learning (four units)
• CSE 251A: Machine Learning: Learning Algorithms (four units)
• CSE 251B: Deep Learning (four units)
• CSE 255: Data Mining and Predictive Analytics (four units)
• CSE 258: Recommender Systems and Web Mining (four units)
• ECE 208: Computational Evolutionary Biology (four units)

Elective CS-3: Mathematics and Statistics

• ECE 271A: Statistical Learning I (four units)
• MATH 274: Numerical Methods for Physical Modeling (four units)
• MATH 280A: Probability Theory (four units)
• MATH 281A: Mathematical Statistics (four units)
• MATH 281B: Mathematical Statistics (four units)
• MATH 281C: Mathematical Statistics (four units)
• MATH 282A: Applied Statistics I (four units)
• MATH 282B: Applied Statistics II (four units)
• MATH 284: Lifetime Data Analysis (four units)
• PHYS 210A: Equilibrium Statistical Mechanics (five units)
• PHYS 210B: Nonequilibrium Statistical Mechanics (four units)

Elective SB-1: Biological Systems

• BENG 211: Systems Biology and Bioengineering I: Biological Components (four units)
• BENG 212: Systems Biology and Bioengineering II: Large-Scale Data Analysis (four units)
• BENG 227: Transport Phenomena in Living Systems (four units)
• BNFO 286/MED 283: Network Biology and Biomedicine (four units)

Elective SB-2: Kinetic Modeling

• BENG 125: Modeling and Computation in Bioengineering (four units)
• BNFO 284: Nonlinear Dynamics in Quantitative Biology (four units)
• PHYS 276: Quantitative Microbiology (four units)
• CHEM 220: Regulatory Circuits in Cells (four units)

Elective BMI-1: Biomedical Informatics

• MED 263: Bioinformatics Applications to Human Disease (four units)
• MED 264: Principles of Biomedical Informatics (four units)--Core for BMI track, elective for other tracks
• MED 265: Informatics in Clinical Environments (four units)
• MED 267: Modeling Clinical Data and Knowledge for Computation (four units)
• MED 268: Statistics Concepts for Biomedical Research (four units)
• MED 276: Grant Proposal Writing Practicum (two units)
• MED 277: Introduction to Biomedical Natural Language Processing (four units)

Elective QBIO-1: Quantitative Biology

• BENG 226: Foundations of Bioengineering I: Tissue and Cell Properties (four units)
• BENG 235: Molecular Imaging and Quantitation in Living Cells (four units)
• BGGN 214: Introduction to Q-Biology (four units) --May be applied to BIO area elective requirement
• BNFO 262: Quantitative Methods in Genetics (four units)
• BNFO 284: Nonlinear Dynamics in Quantitative Biology (four units)
• CHEM 220: Regulatory Circuits in Cells (four units)
• MAE 263: Experimental Methods in Cell Mechanics (four units)
• PHYS 273: Information Theory and Pattern Formation in Biological Systems (four units)
• PHYS 274: Stochastic Processes in Population Genetics (four units)
• PHYS 275: Biological Physics (four units)
• PHYS 276: Quantitative Microbiology (four units)
• PHYS 277: Physics of the Cell (four units)
• SIOB 242C: Marine Biotechnology III: Introduction to Bioinformatics (four units)

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.

Example: Bioinformatics and Systems Biology Track

Year 1

FALL | WINTER | SPRING
---|---|---
Core: MATH 283 | Core: BENG 202/CSE 282 | Core: BENG 203/CSE 283
Fourth Core or Elective | Fourth Core or Elective | Fourth Core or Elective
| | | BNFO 294: Ethics
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 | 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 Assistantship | BNFO 500: Teaching Assistantship | Qualifying Exam

Example: Biomedical Informatics Track

Year 1

FALL | WINTER | SPRING
---|---|---
Core: MATH 283 | Core: BENG 202/CSE 282 |
Core: MED 264 | | BNFO 294: Ethics
Fourth Core or Elective | Fourth Core or Elective | Fourth Core or 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 Assistantship | BNFO 500: Teaching Assistantship | Qualifying Exam

Example: Quantitative Biology Track

Year 1

FALL | WINTER | SPRING
---|---|---
Core: MATH 283 | Core: BENG 202/CSE 282 | Core: BENG 203/CSE 283
| | | BNFO 294: Ethics
Fourth Core or Elective | Fourth Core or Elective | Fourth Core or 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 Assistantship | BNFO 500: Teaching Assistantship | Qualifying Exam

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.

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.

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.

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.

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.

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.

Financial Support

Eligible students admitted into the PhD program in bioinformatics and systems biology will receive financial assistance subject to their continuance and performance in the program.

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.