The rapidly diminishing cost of genome sequencing is driving renewed interest in large scale genome sequencing programs such as <i>Genome 10K</i> (G10K). Despite renewed interest the assembly of large genomes from short reads is still an extremely resource intensive process. This work presents a scalable algorithms to create scaffolds, or ordered and… (More)
Power's central role in international relations theory is unsurpassed, yet considerable debate persists over the quality of its most commonly used indicator, the Correlates of War project's Composite Indicator of National Capabilities (CINC). At issue is whether CINC's main feature, its ability to measure a nation's power relative to other nations' power… (More)
NASA and the international community are investing in the development of a commercial transportation infrastructure that includes the increased use of rotorcraft, specifically helicopters and civil tilt rotors. However, there is significant concern over the impact of noise on the communities surrounding the transportation facilities. One way to address the… (More)
—Scaffolding is the important stage of genome assembly consisting of orienting and ordering contigs based on read pairs. We present a scalable scaffolding algorithm that finds most likely contig orientation using integer linear program solved by a non-serial dynamic programming approach. We then formulate the problem of finding most likely contig ordering… (More)
—We propose a Monte-Carlo Regression based method for isoform frequency estimation from RNA-Seq reads.
—Obtaining whole-transcriptome expression profiles of closely related cell types is a daunting task faced by stem-cell biologists. Here we present an approach that utilizes single-cell qPCR probing of a small number of genes to aid in the deconvolution of whole-transcriptome profiles of mixed samples.
The precipitous drop in sequencing costs has generated much enthusiasm for very large scale genome sequenc-ing initiatives. However, assembling high-quality genome sequences from the short reads currently generated by high-throughput sequencing (HTS) technologies represents a formidable computational challenge that has yet to be met. In this work we address… (More)
Molecular biological enquiry has entered a new age in the last few years with the development of high-throughput, massively parallel data acquisition platforms. Since it's advent with the introduction of gene microarrays early in this century, the technology has continued to evolve at an astonishing pace into sequencers capable of millions to billions of… (More)