Rashi Gupta

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BACKGROUND MicroRNAs are a class of small non-coding RNAs that regulate mRNA expression at the post - transcriptional level and thereby many fundamental biological processes. A number of methods, such as multiplex polymerase chain reaction, microarrays have been developed for profiling levels of known miRNAs. These methods lack the ability to identify novel(More)
Pixel saturation occurs when the pixel intensity exceeds the scanner upper threshold of detection and the recorded pixel intensity is then truncated at the threshold. Truncation of the pixel intensity causes the estimates of gene expression (i.e., intensity) to be biased. Microarray experiments are commonly affected by saturated pixels; as a result all(More)
RNA-Seq is increasingly being used for gene expression profiling. In this approach, next-generation sequencing (NGS) platforms are used for sequencing. Due to highly parallel nature, millions of reads are generated in a short time and at low cost. Therefore analysis of the data is a major challenge and development of statistical and computational methods is(More)
We propose a method for improving the quality of signal from DNA microarrays by using several scans at varying scanner sensitivities. A Bayesian latent intensity model is introduced for the analysis of such data. The method improves the accuracy at which expressions can be measured in all ranges and extends the dynamic range of measured gene expression at(More)
BACKGROUND DNA microarrays provide an efficient method for measuring activity of genes in parallel and even covering all the known transcripts of an organism on a single array. This has to be balanced against that analyzing data emerging from microarrays involves several consecutive steps, and each of them is a potential source of errors. Errors tend to(More)
Bioinoculants are commonly used for enhancing crop productivity but little information is available on their effect on key microbial communities such as those involved in the cycling of nitrogen, a major plant nutrient. Here we developed a formulation combining different bioinoculants (Bacillus megaterium, Pseudomonas fluorescens and Trichoderma harzianum)(More)
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