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Emerging next-generation sequencing technologies have revolutionized the collection of genomic data for applications in bioforensics, biosurveillance, and for use in clinical settings. However, to make the most of these new data, new methodology needs to be developed that can accommodate large volumes of genetic data in a computationally efficient manner.(More)
BACKGROUND Recent innovations in sequencing technologies have provided researchers with the ability to rapidly characterize the microbial content of an environmental or clinical sample with unprecedented resolution. These approaches are producing a wealth of information that is providing novel insights into the microbial ecology of the environment and human(More)
Quality control and read preprocessing are critical steps in the analysis of data sets generated from high-throughput genomic screens. In the most extreme cases, improper preprocessing can negatively affect downstream analyses and may lead to incorrect biological conclusions. Here, we present PathoQC, a streamlined toolkit that seamlessly combines the(More)
Understanding the categorization of human diseases is critical for reliably identifying disease causal genes. Recently, genome-wide studies of abnormal chromosomal locations related to diseases have mapped >2000 phenotype-gene relations, which provide valuable information for classifying diseases and identifying candidate genes as drug targets. In this(More)
With ever increasing storage demands and management costs, object based storage is on the verge of becoming the next standard storage interface. The American National Standards Institute (ANSI) ratified the object based storage interface standard (also referred to as OSD T-10) in January 2005. In this paper we present our experiences building a reference(More)
Recent studies hint that endogenous dsRNA plays an unexpected role in cellular signaling. However, a complete understanding of endogenous dsRNA signaling is hindered by an incomplete annotation of dsRNA-producing genes. To identify dsRNAs expressed in Caenorhabditis elegans, we developed a bioinformatics pipeline that identifies dsRNA by detecting clustered(More)
With ever increasing storage demands and management costs, object based storage is on the verge of becoming the next standard storage interface. The American National Standards Institute (ANSI) ratified the object based storage interface standard (also referred to as OSD T-10) in January 2005. In this paper we present our experiences building a reference(More)
We present a novel approach for reducing the computational complexity of updating homologies produced by a wide class of popular state-of-the-art algorithms in comparative computational biology. The algorithms that we consider use hidden Markov models (HMMs) and a Viterbi recursion to evaluate matches between sequences, or between a sequence and models.(More)
Sequence alignment or decoding in molecular biology is mostly done via computationally expensive dynamic programming (DP) based approaches. Unfortunately, as sequencing errors are discovered frequently, researchers must repeat all previous similarity analysis for the erroneous sequence. This can take hours or days. In this work, we derive relative tolerance(More)
Malaria causes over one million deaths annually, posing an enormous health and economic burden in endemic regions. The completion of genome sequencing of the causative agents, a group of parasites in the genus Plasmodium, revealed potential drug and vaccine candidates. However, genomics-driven target discovery has been significantly hampered by our limited(More)