Algorithms for the Analysis of Data from Massively-parallel Genome Sequencing
Start Date: April 1, 2009
Expires: March 31, 2011
Awarded Amount to Date: $379,919
Principal Investigator: Mihai Pop
Sponsor: University of Maryland College Park
This project is developing parallel algorithms for analyzing new generation sequencing data, with a specific focus on the Map-Reduce paradigm implemented on a highly-distributed computing cluster supported by Google and IBM. The project is primarily focused on developing algorithms for sequence alignment and sequence assembly — critical tasks in the analysis of genomic data — and involves the adaptation of string matching and graph algorithms to the Map-Reduce paradigm. The work will potentially lead to parallelism-enabled genomic analysis software that will allow researchers to analyze new generation sequencing data through web-scale computational resources, thereby obviating the need for establishing and maintaining a local high-performance computing infrastructure. The software developed during this project is being made available under an open-source license in order to encourage broad use and to enable future research.
Sequencing and Analysis of Centrosomal RNAs
Start Date: March 1, 2009
Expires: February 28, 2010
Awarded Amount to Date: $119,988
Principal Investigator: Mark Alliegro
Sponsor: Marine Biological Laboratory, Woods Hole
Centrosomes may contain their own complement of nucleic acids, possibly representing an organellar genome as has been described for mitochondria and chloroplasts. Until recently, the only consensus developed during the past 50 years is that centrosomes do not contain DNA. The existence of centrosomal RNA (cnRNA) remained an open possibility. Research by Mark Alliegro and others has now found cnRNA, although the source and function of cnRNAs remain unknown and controversial. In this project, high throughput sequencing technology and informatics will be used to characterize cnRNAs from the surf clam, Spisula solidissima, and identify related molecules in other species. This will open the way for future phylogenetic and functional analyses to help determine the evolutionary origin and physiological roles of cnRNAs.
Investigation of chemical reactions in femtoliter-volume droplets
Start Date: February 15, 2009
Expires: January 31, 2010
Awarded Amount to Date: $149,575
Principal Investigator: Daniel Chiu
Sponsor: University of Washington
Surfactants with varying concentrations, immiscible oils, and interior solute ionic strength will be varied and tested to determine their exact effects on droplets. The experimental information obtained will be used to synthesize a model to allow prediction of droplet-confined chemical reactions, and how they are affected by the choice of surfactant and immiscible oil as well as the concentration and ionic strength of the solutes contained within the droplet. While droplet microfluidics are beginning to find broad use in diverse areas, such as biological assays, protein crystallization, DNA sequencing, and chemical synthesis, the fundamentals of chemistry in droplets, in particular, how the high surface-to-volume ratio environment affects the chemistry, is still relatively unexplored. The predictive model and associated software will be made available on the PI's laboratory website.