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A viral population can contain a large and diverse collection of viral haplotypes which play important roles in maintaining the viral population. We present an algorithm for reconstructing viral haplotypes in a population from paired-end Next Generation Sequencing (NGS) data. We propose a novel polynomial time dynamic programming based approximation(More)
We examined the actions of exendin-4, a new peptide isolated from Heloderma suspectum venom, on dispersed acini from rat pancreas. Exendin-4 caused a 3-fold increase in cAMP but did not alter cellular calcium concentration. Exendin-4-induced increases in cAMP were inhibited by an exendin-receptor antagonist, exendin (9-39)NH2, but not by VIP-receptor(More)
High genetic variability in viral populations plays an important role in disease progression, pathogenesis, and drug resistance. The last few years has seen significant progress in the development of methods for reconstruction of viral populations using data from next-generation sequencing technologies. These methods identify the differences between(More)
Despite studies indicating the presence of specific pancreatic acinar receptors for PACAP-38, a peptide that was recently isolated from ovine hypothalamus, the actions of the new peptide on pancreatic enzyme secretion have not been examined. The present study demonstrates that in terms of cAMP production and amylase release from dispersed acini from rat(More)
We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related genomes. Frames are sets of non-orthogonal basis functions, traditionally used in signal processing for noise removal. We define a frame for genomes and sequenced reads to consist(More)
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the analyses of targeted sequencing data, for example polymorphic structural variation caused by mobile elements is(More)
Infection with feline immunodeficiency virus (FIV) causes an immunosuppressive disease whose consequences are less severe if cats are co-infected with an attenuated FIV strain (PLV). We use virus diversity measurements, which reflect replication ability and the virus response to various conditions, to test whether diversity of virulent FIV in lymphoid(More)
Metagenomics involves the analysis of genomes of microorganisms sampled directly from their environment. Next Generation Sequencing (NGS) technologies allow a high-throughput sampling of small segments from genomes in the metagenome to generate a large number of reads. In order to study the properties and relationships of the microorganisms present,(More)