Translational Bioinformatics

Faculty: Charles Elkan, James Fowler, Kelly Frazer, Terry Gaasterland, Trey Ideker, Yu-Tsueng Liu, Lucila Ohno-Machado, Pavel Pevzner, Sergei Pond, Shankar Subramaniam, Christopher Woelk, Eugene Yeo 

This track links bioinformatics to health informatics through its special focus on methods and techniques that directly relate to the study of human health and disease. Computational methods related to genomics, transcriptomics, proteomics, and metabolomics are all included in this track, which connects molecular findings and phenotypes to characterize disease susceptibility or determine disease markers, and predict response to treatment and prognosis. Faculty from this track overlap with the ones in the Bioinformatics PhD Program who are directly involved with studying human disease using computational methods. Specialized areas are listed below: 

  • Structural and Functional Genomics: emphasize statistical and machine learning methods for molecular profiling of diseases, correlation of common and rare genetic variants to phenotypes, and regulatory elements (e.g., discovery of new microRNAs from mRNA-seq, prediction of their targets, and use of information in machine learning classifiers to predict disease progression).
  • Metagenomics: computational techniques to discover and characterize infectious disease agents and determine their influence in pathogenesis and disease progression (e.g., phylogenetics for drug-resistant HIV variants). 
  • Biological networks: techniques from systems biology and social network analysis are combined to study interactions among genes and their regulatory elements, proteins, metabolites, signal propagation, and integration of information across different biological levels.

Health Care and Clinical Research Informatics

Faculty: Aziz Boxwala, Kamalika Chaudhuri, James Chen, Anders Dale, Robert El-Kareh, Mark Ellisman, Christine Fennema-Notestine, Amilcare Gentili, Steve Jiang, Grace Kuo, Maryann Martone, Thomas Nelson, 

 The study of health care informatics grounds students in the intersection of clinical medicine, clinical research, cognitive science, and information science. Students learn how the organization of health care delivery, human cognition, data complexity and uncertainty, and access to information affect optimal delivery of care, and how proper analysis, management, and presentation of information can help in this delivery process. Students become familiar with aggregation and sharing of data to facilitate knowledge discovery and clinical research informatics. Specializations within healthcare informatics include imaging informatics, standardized data representation, clinical decision support, pharmacy informatics, and clinical research informatics. 

  • Imaging Informatics: Students specializing in imaging informatics acquire a solid foundation in the medical imaging information chain, from the physical and mathematical principles defining the nature of the image information to the use of image information in clinical decision-making. Research in imaging informatics will leverage the multiple on-campus resources, such as many basic science imaging laboratories on campus, the cientific and data visualization resources at SDSC and CalIT2, and clinical imaging at affiliated hospitals. 
  • Electronic Health Records and Clinical Decision Support: Students specializing in clinical decision support acquire a strong foundation in the effective design, implementation, and rigorous evaluation of systems that enable improved medical decision making for clinicians. Students will study current clinical decision support systems (CDSS), evidence-based medical decision-making, human-computer interface design, knowledge generation and representation, integration of systems into clinical workflow, and the ethical and legal considerations involving these systems, with a strong emphasis on privacy technology. 
  • Pharmacy Informatics: The study of pharmacy informatics focuses on using informatics to improve the efficacy and safety of drug therapy through prescription tools (e.g., integration of intelligent medication selection and dosing applications), dispensing tools (e.g. bedside bar coding technology), and adverse drug events monitoring, reporting, and discovery through data mining, statistical process control, and other techniques. 
  • Clinical Research Informatics: Students in this track explore the management and analysis of data for clinical research purposes. Research projects will leverage the multiple clinical research informatics projects currently underway at UCSD.

Public Health Informatics

Faculty: Sanjoy Dasgupta, James Fowler, Richard Garfein, William Griswold, Gregory Norman, Lucila Ohno-Machado, Kevin Patrick, Steffanie Strathdee 

Public health informatics explores the collection and dissemination of health information outside of traditional clinical settings. Representative public health informatics efforts at UCSD include: 

  • Behavioral and environmental health and monitoring: focuses on the use of information and telecommunications technology to measure and improve health-related behaviors of individuals and populations. BMI faculty collaborate with computer scientists, geneticists, preventive medicine clinicians, and environmental scientists to understand the relationships between physical activity energy expenditure, the environment, and health-related factors at the individual and population level. Innovative techniques such as social network analysis are used as early sensors for public health issues, such as obesity and contagious outbreaks. 
  • Syndromic surveillance: integrates information about individuals’ pre-diagnostic symptoms with other data sources to detect and characterize concerning patterns within a population. With the upcoming focus on meaningful use, public health will acquire more clinical data, which can be useful not only for epidemiology of infectious diseases but also of chronic diseases.
  • Global health: a strong component of our program at UCSD, which has funding for informatics training within DBMI (Biomedical Research Informatics for Global Health Training (BRIGHT) Program) and the Division of Global Public Health in the School of Medicine. Informatics research involves geographical information systems, development, implementation, and evaluation of systems in resource-poor settings, and behavior change through informatics tools and mobile devices.