Collaborative Research: Design and Analysis of Compressed Sensing DNA Microarrays

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The diverse functions performed by a living cell during her life cycle are controlled and regulated through complicated gene- and protein- interaction networks. Any pattern of irregular behavior of genes in the network can lead to cell malfunctioning, cell death, or the emergence of diseases like cancer. It is therefore of crucial importance to recognize erroneous gene interaction patterns and compare them to those in healthy cells. For this type of study, one of the most frequently used bioengineering systems is the well known DNA microarray device. DNA microarrays consist of grids of spots containing unique genetic identifiers for each of the tested genes, capable of generating snapshots of gene activity in terms of selective DNA sequence annealing. Microarrays have also found many other applications in the field of molecular biology, most notably for the purpose of detecting hostile microbial agents in food, water, and in the air. One of the main drawbacks of current microarray designs is that they are, for the purpose of whole genome studies, severely underutilized; similarly, for biosensing applications, existing microarray systems cannot be used for simultaneous identification of a large number of microorganisms and their strains due to technological limitations.The investigators study novel array architectures, termed compressed sensing DNA microarrays. The research involves finding DNA probes that serve as group identifiers for classes of microorganisms; designing sparse sensing matrices for DNA group identifiers; developing compressed sensing reconstruction algorithms capable of handling saturation effects arising due to high agent concentration levels; characterizing the fundamental trade-offs between distortion and sensor dimension for non-linear arrays; and, analyzing the complexity of integrating compressed sensing microarrays into existing biosensor networks.