Raunaq Malhotra

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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)
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)
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)
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)
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)
Endogenous retroviruses (ERVs) are a class of transposable elements found in all vertebrate genomes that contribute substantially to genomic functional and structural OPEN ACCESS Computation 2014, 2 222 diversity. A host species acquires an ERV when an exogenous retrovirus infects a germ cell of an individual and becomes part of the genome inherited by(More)
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