Curriculum
UCSF offers PhD training in Clinical and Translational informatics (CTI) as a pathway of the Program in Biological and Medical Informatics. We emphasize foundational training in core informatics theories and methods complemented by coursework and experiences in two major application domains:
- Clinical and translational research
- Quality and safety of evidence-based care
The driving principles underlying the design of the curriculum include a focus on scientific principles, an explicit commitment to high-quality evidence-based practice as the primary motivation, and the recognition that the best informatics work is a combination of the "hard" and "soft" sciences. These principles are reflected throughout the core curriculum as well as in the experiential and research offerings in our application domains.
The full listing of UCSF classes and their descriptions can be found at the UCSF Course Catalog.
Note: class offerings may vary from academic year to year
Via inter-university agreements, students can also take computer science and related classes at either Stanford University or the University of California Berkeley.
Requirements: Required classes include BMI 200, BMI 202, and BMI 283. Students are also required to take at least three Informatics Rotations (BMI 221) in the first year. The purpose of these rotations is to identify a research advisor. Rotations are approved by the student's academic advisor, with the intention of promoting the student's broad exposure to research methods and topics.
Students will review their coursework plans each quarter with their academic advisors. PhD students will take BMI 250 units for their research projects until they advance to candidacy, at which time they will enroll in BMI 299 to complete their research.
Other Core Competencies
Students will either enter the program with the following competencies, or are strongly encouraged to receive formal training in areas in which their backgrounds may be weak. Some of these skills will be learned in practicum, others through class work and seminars.
Programming
Proficiency in a programming language, PC 204 or equivalent
Epi / Biostatistics
Biostat 183 or equivalent
Mathematics
One year of college calculus including an introduction to differential equations
Biomedical & Clinical Science
- Clinical research design, Epi 202 or equivalent
- One upper division course on organismal biology (e.g., human physiology, vertebrate zoology), Physiology 121, Physiology 120 & 125 or equivalent
- One upper division course in biology at the molecular level (e.g., cellular biology, genetics, microbiology, pharmacology): Biochem 246/Cell Biol 245, Immunology 204, Physiology 121, Chemistry 243, Biochem 110 A/B, Pharmacol 100A or equivalent
Research Methods
Design, project management, evaluation, verbal and written communication of results
Familiarity with the biomedical research environment
Structure of NIH, NSF; grantsmanship; the biomedical informatics scholarly community; structure of the health care marketplace and of the biotech and pharmaceutical industries.
| Informatics | |
| BMI 200 | Fundamentals of Clinical and Translational Informatics (5 units, Fa) Staff. Introduction to fundamental computing methods that are being used to improve clinical knowledge and research. Topics include vocabularies, ontologies, data interchange, knowledge base systems, human-computer interaction, simulation and modeling. |
| BMI 202 | Decision Making in the Health Sciences (3 units, Spr) Hudson, Cohen. Introduction to principles and techniques for computer-assisted decision making in the health sciences. Topics include rules-based systems, neural networks and other statistical approaches to decision support. |
| Epi 206 | Medical Informatics for Clinical Researchers (1 unit, Win) Sim. Introduction to the most important technical, clinical, and social aspects of health information technology as they relate to clinical research. |
| CP 123 | Health Policy (3 units, Win) Lipton. An introductory course in health policy analysis with special emphasis on health care reform and its implications and opportunities. |
| BMI 206 | Introduction to Bioinformatics (3 units, Win) Babbitt. Broad survey of bioinformatics. Topics include genome annotation, database design, database searching, family/superfamily analysis, structural genomics, complex systems, genetic circuits, microarray analysis, and protein-protein interactions. |
| BMI 283 (Sociology 211) | Information Technology and Organizational Change (2-3 units, Spr) Miller. An examination of electronic medical records (EMRs) in health care organizations, focusing on: EMR capabilities, use, costs and benefits; factors affecting costs and benefits; theories of innovation diffusion; the relationship between IT and organizational changes; EMR health policy options. |
| Epi 218 | Data Management for Clinical Research (1 unit, Win) Kohn. Instruction in choosing the appropriate data management system, design of research data bases, options in data entry, form and report generation, computer security, and budgeting for data management personnel and equipment. |
| Related Classes and Electives | |
| Epi 211 | Outcomes Research (1.5 units, Spr) |
| Epi 213 | Decision and Cost-Effectiveness Analysis (2 units, Win Spr) |
| Biostats 183 | Introduction to Statistical Methods (4 units, Fa) |
| Biostats 212 | Introduction to Statistical Computing in Clinical Research (1 unit, Sum) |
| Biomed Sci 255 | Basic Genetics and Genomics (4 units, Win) |
| Epi 202 | Designing Clinical Research (2 units, Sum) |
| Pharm Chem 204 | Introduction to Computer Programming (3 units, Fa) |
| Biophys 297 | Modeling Complex Biological Systems (1 unit, Spr) |
| Clin Pharm 156 | Decision Analysis (3 units, Fa Win Spr) |
| Epi 217 | Molecular Methods in Clinical Research (1.5 units, Win) |
| Clin Pharm 123 | Health Policy (3 units, Win) |
| Nurs 211B | Managing Change in Health Care Systems (1-6 units, Sum Fa Win Spr) |
| Grant Writing Workshop (Fa) | |
| Programmatic | |
| BMI 220 | Faculty Informatics Research Seminar |
| BMI 221 | Informatics Research Rotation |
| BMI 222 | Student Informatics Research Seminar |
| BMI 223 | Critical Research Topics in Bioinformatics/Medical Informatics (Journal Club) |
| BMI 224 | Graduate Research Opportunities Seminar |
| BMI 225/250 | Masters/Ph.D. research project |
| BMI 299 | Dissertation Research |
| Epi 201 | Responsible Conduct of Research (0.5 units, Sum) |
