ArticleEURASIP journal on bioinformatics & systems biology2009
Compressive sensing DNA microarrays.
Article in EURASIP journal on bioinformatics & systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed.
- New insights into binocular rivalry from the reconstruction of evolving percepts using model network dynamics.Frontiers in computational neuroscience · 2023Article
- To Petabytes and beyond: recent advances in probabilistic and signal processing algorithms and their application to metagenomics.Nucleic acids research · 2020Article
- Collaborative representation-based classification of microarray gene expression data.PloS one · 2017Article
- Universal microbial diagnostics using random DNA probes.Science advances · 2016Article
- Improved Compressive Sensing of Natural Scenes Using Localized Random Sampling.Scientific reports · 2016Article
- Sparsity and compressed coding in sensory systems.PLoS computational biology · 2014Article
- Efficient route to high-bandwidth nanoscale magnetometry using single spins in diamond.Scientific reports · 2014Article
- A computational model for compressed sensing RNAi cellular screening.BMC bioinformatics · 2012Article
- Linear program relaxation of sparse nonnegative recovery in compressive sensing microarrays.Computational and mathematical methods in medicine · 2012Article
- A compressed sensing based approach for subtyping of leukemia from gene expression data.Journal of bioinformatics and computational biology · 2011Article
- Open-target sparse sensing of biological agents using DNA microarray.BMC bioinformatics · 2011Article
- Identification of rare alleles and their carriers using compressed se(que)nsing.Nucleic acids research · 2010Article
- poolMC: smart pooling of mRNA samples in microarray experiments.BMC bioinformatics · 2010Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.