Xiaohu Shen

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Next-generation sequencing systems are capable of rapid and cost-effective DNA sequencing, thus enabling routine sequencing tasks and taking us one step closer to personalized medicine. Accuracy and lengths of their reads, however, are yet to surpass those provided by the conventional Sanger sequencing method. This motivates the search for computationally(More)
Gene regulatory networks are highly complex dynamical systems of biomolecular components - genes, mRNA, proteins. These components interact with each other and through those interactions determine gene expression levels, i.e., determine the rate of gene transcription to mRNA and, consequently, the rate of mRNA translation to proteins. In this paper, a(More)
Computational models of gene regulatory networks (GRNs) well describe the behavior of interactions among molecular species over time. For larger networks, the problem of state-space explosions makes such approaches practically unsound. D. T. Gillespie discovered a statistically identical way of simulating the time evolution of species populations,(More)
ABSTRACT Recent development of next-generation DNA sequencing platforms has dramatically increased the efficiency of sequencing genomes or targeted regions of interest within genomes. Identification of genetic variants is an important downstream application of such platforms. In this paper, we present a novel framework for processing short reads generated(More)
In order to determine an individual's DNA sequence, sequencing platforms often employ shotgun sequencing where multiple identical copies of the DNA strand of interest are randomly fragmented and then the nucleotide content of the short fragments is determined. Assembly of the long DNA strand from short fragments is a computationally challenging task that(More)
Affinity biosensors rely on chemical attraction between targets of interest (mRNA and DNA sequences, proteins) and their molecular complements, probes, which serve as biological sensing elements. The attraction between complementary sequences leads to binding, in which probes capture target molecules. Molecular binding is a stochastic process and hence the(More)
Recent development of next-generation sequencing platforms has dramatically increased the efficiency of obtaining genomic data. Their accuracy, reliability, and achievable read-lengths, however, often lag behind those of the conventional Sanger sequencing method. In this paper, we consider the Illumina sequencing platform and propose a novel DNA(More)
Estimation of the amounts of target molecules in real-time affinity-based biosensors is studied. The problem is mapped to inferring the parameters of a temporally sampled diffusion process. To solve it, we rely on a sequential Monte Carlo algorithm which generates particles using transition density of the diffusion process. The transition density is not(More)
Recent emergence of next-generation DNA sequencing technology has enabled acquisition of genetic information at unprecedented scales. In order to determine the genetic blueprint of an organism, sequencing platforms typically employ the shotgun sequencing strategy to oversample the target genome with a library of relatively short overlapping reads. The order(More)
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