“To unlock the
value of ‘big data’ in the life sciences and healthcare, we need to
invent computational and statistical tools and methods that will yield
significant, reproducible insights.”
-Andrea Foulkes
-Andrea Foulkes
Biostatistician Andrea Foulkes is
one of the faculty members at UMass Amherst analyzing ‘big’ life
science data in the pursuit of new discoveries. As Director of the Institute for Computational Biology, Biostatistics, and Bioinformatics (ICB3),
Foulkes is creating a multidisciplinary community of computational,
biomedical and translational researchers. The ICB3 team is focused on
developing innovative analytical approaches and enabling discoveries
that help clinicians improve and individualize clinical practices. By
making it easier for interdisciplinary researchers to find one another
and to secure common resources, the institute inspires and facilitates
new, synergistic work.
“As we are faced with more and more complex data than ever before, we
have the opportunity through collaboration to better understand our
personal health” Foulkes explains.
Foulkes, whose research is supported by the National Institutes of
Health (NIH), recently spearheaded a project that resulted in the
“prediction-based classification” system—a new method for monitoring
HIV-infected individuals that can link blood-level indicators to other
patient data (such as height and weight). In resource-limited countries
the method could be a way to more efficiently allocate those scarce
resources by using simpler, inexpensive ways to predict which patients
will need them most.
“To unlock the value of ‘big data’ in the life sciences and
healthcare, we need to invent computational and statistical tools and
methods that will yield significant, reproducible insights. Just as
microscopes reveal to biologists the inner structure of cells, the tools
and methods we are creating act as lenses that bring data into
meaningful focus. These techniques are essential to the development of
personalized medicine with its promise of individual risk assessment and
tailored treatments,” says Foulkes.
Biostatistics faculty member and ICB3 affiliate Raji Balasubramanian is
the Principal Investigator on another NIH project that combines data
from several international cohorts to gain a better understanding of the
characteristics of HIV-1 diagnostic assays. A better understanding of
the timing of mother-to-child transmission will inform strategies to
improve HIV diagnostic testing in infants and the best approaches for
scheduling preventive treatment (particularly in situations where
resources are limited).
As the lead biostatistician on a Johns Hopkins Children’s Center-led
infection prevention trial in over 4,000 critically ill children, ICB3
affiliate and UMass faculty member Nicholas Reich implemented
a “crossover” design to ensure that results were as strong as possible.
The study, which spanned across five pediatric hospitals, showed that
children bathed daily with an antiseptic soap were at a 36 percent lower
risk of bloodstream infection when compared to children bathed with
ordinary soap and water. The results suggest a potentially low-cost
approach to reducing the prevalence of life threatening complications.
Foulkes and two other School of Public Health and Health Sciences
researchers, Gregory Matthews and Ujwall Das, partnered with
cardiologist Muredach Reilly at the University of Pennsylvania to reveal
new information about genes linked to high cholesterol and heart
disease. To accomplish this, the team developed a new analytic approach
called “MixMAP” (Mixed modeling of Meta-Analysis P-values), and applied
it to existing large databases. The method enabled researchers to
identify genetic signals that are too subtle to be recognized by
established methods.
In addition to their research activities, the ICB3 team is taking the
lead in developing initiatives that will equip undergraduate and
graduate students with the skills and knowledge increasingly demanded by
‘big data’ challenges. Two of these initiatives are the Summer Training Institute for Reproducible Research with R (STIRRR) and the Open Source Software Innovation (OSSI) competition.
STIRRR is being offered at the Massachusetts Green High Performance
Computing Center (MGHPCC) as a one-day course for university faculty,
postdoctoral fellows, students, as well as industry scientists. The OSSI
competition is open to members of the UMass Amherst community who
develop and apply new open source software packages to life science
data. There are a number of competition prizes, including a first-place
award of $5,000. The broader purpose of the competition is to foster
cross-disciplinary collaboration and disseminate novel open source tools
that enable new discoveries and insights.
“With the excellent faculty and students at UMass Amherst, there is
remarkable potential for us to make significant contributions to the
challenges posed by ‘big data’ in the life sciences and healthcare on a
number of fronts, including data visualization, health monitoring, and
personalized medicine,” says Foulkes. “The ICB3’s purpose is to help
realize that potential and we look forward to doing our part in these
ambitious efforts.”
Post a Comment
Thanks for reading my blog.
Note: only a member of this blog may post a comment.