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 simultaneously account for
both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization
model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model.
Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have
sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate
as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization
times are allowed.