Compressive sensing DNA microarrays.
Compressive sensing DNA microarrays.
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DOI：
10.1155/2009/162824
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发表时间：
2009
期刊：
影响因子：
--
通讯作者：
Baraniuk RG
中科院分区：
文献类型：
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作者：
Dai W;Sheikh MA;Milenkovic O;Baraniuk RG
压缩传感微阵列(CSMS)是基于DNA的传感器，使用组测试和压缩传感(CS)原理运行。与传统的DNA微阵列不同，在CSM中，每个遗传传感器被设计为对单个目标做出反应，而在CSM中，每个传感器对一组目标做出反应。我们研究了同时考虑CS理论和探针-靶DNA杂交生物化学约束的CSMS的设计问题。提出了一种适合于CSMS的杂交模型，并基于该模型提出了几种用于探针设计和CS信号恢复的方法。实验室实验表明，为了实现准确的杂交图谱，一致的探针序列需要与所有要检测的目标具有至少80%的序列同源性。此外，非平衡数据集通常与从平衡条件获得的数据集一样准确。因此，人们可以在只允许较短杂交时间的应用中使用CSMS。
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.