Brown CS News

Two members of Brown University’s Department of Computer Science (Brown CS), Professors Michael Littman and Ben Raphael (also Director of the Center for Computational Molecular Biology) have received Seed Awards from Brown University’s Office of the Vice President for Research (OVPR) to help them compete more successfully for large-scale, interdisciplinary, multi-investigator grants. They join multiple previous Brown CS recipients of OVPR Seed Awards, including (most recently) Ugur Cetintemel, Sorin Istrail, Chad Jenkins, and Tim Kraska.

Michael and Ben describe their projects in brief as follows:

Exploring Innovative Delivery Methods for Brief Alcohol Interventions: The Electronic Mobile Alcohol Interventionist (EMAI)

We seek to prototype and evaluate an Electronic Mobile Alcohol Interventionist (EMAI), a robotic system that interacts with college students and helps them consider decreasing unhealthy drinking behaviors. The work is motivated by existing studies that show that robotic systems engender greater compliance than their on-screen counterparts and, at the same time, greater cost-effectiveness than therapies that require face-to-face interactions with trained experts. As a pilot study, we hope to replicate these results in an important concrete therapeutic context, specifically alcohol intervention. If successful, the project will open up opportunities for the team to seek grants at the boundary between the behavioral sciences and robotics, where novel behavioral therapies are joined with powerful new autonomous decision making algorithms to help improve health in a cost-effective manner.

PI: Michael Littman, Professor, Computer Science
Co-PI: Christopher Kahler, Professor, Behavioral and Social Sciences
Funded: $60,000

Assembling Complete Genomes Through Early Access to Nanopore DNA Sequencing

Despite the declining cost and increasing volume of high­throughput gene sequencing, it is still difficult and expensive to sequence and assemble genomes. Recently, we won competitive access to the initial release of a new nanopore sequencing technology (MinION) that has the promise to cost-­effectively read ultra­long DNA fragments. These longer fragments are critical to successfully assembling complete genomes from scratch, and individual reads could potentially capture entire chromosomes. Leveraging this early access, we will research both the DNA preparation methods and data analysis methods needed to realize this promise, with immediate applications to our existing genomics projects. This interdisciplinary research will draw on expertise in biochemistry, computation, and statistics to tackle three key challenges: preserving ultra­long DNA sequences so that they can be sequenced in their entirety by nanopore devices; characterizing the signal space of the nanopore device and developing statistical methods that align and assemble these signals; and testing hybrid assembly methods that combine nanopore sequence data with other high­throughput sequence data to assemble larger metazoan genomes.

The preliminary methods and data generated by this work will enable new proposals for external funding in our groups and respective departments and strengthen pending proposals. The new computational methods developed here could result in a patent for Brown. Moreover, this work will establish a new DNA sequencing resource at Brown that will complement the existing Genomics Core Facility, can be shared by other labs with similar genomics projects, and will lead to further collaborations and funding opportunities.

PI: Susan A. Gerbi, Professor, Molecular Biology, Cell Biology and Biochemistry

Co­PIs: Mark Howison, Director of Data Science, Computing and Information Services
Charles Lawrence, Professor, Division of Applied Mathematics
Benjamin J. Raphael, Associate Professor, Computer Science
Funded: $30,000

Reached for comment, Michael Littman highlights the intention of the awards to support integrated collaboration among a team of researchers. “I'm really excited,” he says, “to get the chance to do cross-disciplinary work with Chris Kahler, Chair of Behavioral and Social Sciences from the School of Public Health. We're learning about how technology can help people with addictions and whether engaging with robots could make interventions even more effective.”

Ben echoes the importance of collaboration, saying, “Our project combines expertise across multiple units at Brown. Such interdisciplinary collaborations are increasingly important in biology, and we’re grateful to OVPR for supporting these initiatives.”