Is Bioinformatics in San Diego’s Future? A Chat with UC San Diego Expert Lucila Ohno-Machado

4/9/10

One notion that emerged at Xconomy’s event in San Diego last week was that biomedical informatics might have a promising role to play in the region’s economic future. There is no consensus on this as yet, as Luke discovered when he talked with Illumina CEO Jay Flatley.

Among the true believers is UC San Diego’s Lucila Ohno-Machado. No surprises there—since last year, she has been director of biomedical informatics at the medical school. Before arriving in San Diego, she was director of the Harvard-MIT-Tufts-Boston University biomedical informatics training program.

We caught up with her this week via e-mail to find out more about the technology, what it means for the U.S. health care system, and the role she sees for San Diego’s innovation community.

Xconomy: What is biomedical informatics?

Lucila Ohno-Machado: Biomedical informatics is a scientific discipline focused on the development of new algorithms and/or new approaches to organize, visualize, and interpret health-related data in order to promote health and alleviate the burden of disease. The discipline is placed at the intersection of health sciences, biology, computer science, and statistics.

San Diego is in a unique position due to the accumulation of human talent, high-tech companies, and a collective interest in improving healthcare for all. It has all the ingredients to become the number one biomedical informatics center in the country.

X: How is it different from computational biology, which we’ve also been hearing a lot about?

LOM: Computational biology usually relates to the development and application of algorithms and computational strategies to analyze biological data at the molecular level. In biomedical informatics, we develop new algorithms and systems that relate to the full spectrum of data: from molecular to individual to population levels. We often refer to bio-, clinical- or public health-informatics for algorithmic developments and strategies targeting these biological levels, but the boundaries are fuzzy, and biomedical informatics encompasses them all.

 X: How is biomedical informatics currently used?

LOM: Advanced medical centers use the technology to improve quality of care through real-time data analysis and decision support for patient care as well as clinical research. Some examples of biomedical informatics projects involve pattern recognition algorithms, systems to automate clinical practice guidelines, construction of computational models of disease progression, real-time monitoring of health data, and integration of health information technology.

X: What are the most promising future applications? And how far into the future will we see them?

LOM: The most promising future applications will make use of increasing amounts of data that are becoming available due to new genome-sequencing technologies. These applications will integrate genetic information, phenotypic data from electronic medical records, and other clinical data in order to create multivariate models that can determine which therapy is best for a particular patient, or ultimately to find causal determinants of disease (and clues to their potential cure) by looking at genetic, environmental, and clinical data from a large number of individuals. We can currently see some limited applications that partially do this, but it will take some more years to be able to see comprehensive applications.

X: What needs to happen for this technology to reach its potential?

LOM: These are exciting times: there is increasing recognition of the importance of informatics in health sciences, and great enthusiasm for its implementation in institutions where it never formally existed. The change is more than technological, and represents the realization that 21st century science is about addressing big challenges with interdisciplinary teams producing large amounts of data that need to be integrated and interpreted with new algorithms and computational tools. What needs to happen for biomedical informatics to reach its full potential is further increase in true collaboration across disciplines, by sharing data and sharing tools. This is already happening in some institutions, but the goal is to have it spread across the country and across the globe in a way that promotes new discoveries while preserving individual privacy.

X: Does U.S. health care reform have any implications, positive or negative, for this technology?

LOM: Part of the U.S. health care reform calls for comparative effectiveness research to determine which healthcare interventions result in better health outcomes. This is definitely something that biomedical informatics can help address, as it requires analysis of high quality matched data from large data sets. Biomedical informatics research covers several components of this process, such as how to optimally capture data, how to efficiently structure it for queries, how to adjust for patient mix, how to match patients, how to graphically display significant trends, and so on.

X: How might the technology improve health in general?

LOM: Globally, it is impossible to improve health without infrastructure that involves a complex network of healthcare providers at multiple institutions, pharmacists, patients and their families. With informatics tools, these players can interact to develop and implement the best strategies to improve health for an individual and for the population.

X: What is the role of the San Diego innovation community in advancing this technology? Besides fostering health improvement, can the technology provide jobs and economic growth?

LOM: The San Diego innovation community can play a unique role in advancing biomedical informatics. Here we have a large number of biotechnology companies such as Illumina, Sequenom, and many others, producing new measurement instruments that generate several gigabytes of data. There is an abundance of outstanding basic scientists and bioengineers in our academic centers and local companies. We also have a world class academic medical center generating large amounts of clinical and imaging data with clinicians working side-by-side with scientists and engineers who can translate discoveries into new healthcare interventions. Furthermore, San Diego leaders in telecommunications (Qualcomm and CalIT2) are generating advanced technology products that enable homecare connections for monitoring devices, telemedicine applications, and body sensor networks.

On top of all this, we have a burgeoning software industry for analytics that is well organized in subspecialty groups (e.g., companies and individuals affiliated with the San Diego Software Industry Council BioAnalytics group) and high performance computing at the San Diego Supercomputer Center that allows massive parallel processing for complex analyses. All these groups can, together with biomedical informatics specialists, make sure that data are integrated and analyzed in novel ways to make discoveries that can be delivered locally to improve health and minimize disease, as well as creating jobs and revitalizing the economy.

Denise Gellene is a former Los Angeles Times science writer and regular contributor to Xconomy. You can reach her at dgellene@xconomy.com Follow @

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  • Harika

    hi mam/sir i completed my graduation in bioinformatics.Can you please tell me the job requirements to do a job in your company.

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