Mona A. Sheikh

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All Rights Reserved ii iii This thesis is dedicated to my mother, iv Acknowledgements During my six years at Tech, I often felt I was leading multiple lives: the life my mom and relatives were familiar with, the life I had in Avery House, and the life of the Mayo lab. I did not mean for my stay to turn out this way, but I am grateful nonetheless. Each life(More)
Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that(More)
We propose a signal recovery method using Belief Propagation (BP) for nonlinear Compressed Sensing (CS) and demonstrate its utility in DNA array decoding. In a CS DNA microarray, the array spots identify DNA sequences that are shared between multiple organisms, thereby reducing the number of spots required. The sparsity in DNA sequence commonality between(More)
—Compressive Sensing Microarrays (CSM) are DNA-based sensors that operate using group testing and compres-sive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM each sensor responds to a group of targets. We study the problem of designing CS probes that(More)
Spike sorting refers to the detection and classification of electric potentials (spikes) from multi-neuron recordings, a difficult but essential pre-processing step before neural data can be analyzed for information content. While several spike sorting algorithms have been proposed, our goal is to determine the ultimate limits of spike classification and to(More)
Early identification of pathogens is essential for limiting development of therapy-resistant pathogens and mitigating infectious disease outbreaks. Most bacterial detection schemes use target-specific probes to differentiate pathogen species, creating time and cost inefficiencies in identifying newly discovered organisms. We present a novel universal(More)