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Challenges in short oligonucleotide microarray normalisation.
"... Gene expression microarrays have now become a major technique in the toolset of modern biology. But despite their remarkable success, the physico-chemical details of the hybridisation of target mRNA on these arrays are still incompletely understood, and are still an active subject of research, see f ..."
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Gene expression microarrays have now become a major technique in the toolset of modern biology. But despite their remarkable success, the physico-chemical details of the hybridisation of target mRNA on these arrays are still incompletely understood, and are still an active subject of research, see
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach
- Nucleic Acids Res
, 2003
"... There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally speci®c t ..."
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Cited by 133 (5 self)
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There is a substantial interest in implementing bioinformatics technologies that allow the design of oligonucleotides to support the development of microarrays made from short synthetic DNA fragments spotted or in situ synthesized on slides. Ideally, such oligonucleotides should be totally speci
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
- Nat. Biotechnol
, 2009
"... Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA “baits ” to “fish ” targets out of a “pond ” of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides or ..."
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Cited by 158 (7 self)
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originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target>15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About
Custom Design and Analysis of High-Density Oligonucleotide Bacterial Tiling Microarrays
- HAFEMEISTER ET AL.: SELECTING OLIGONUCLEOTIDE PROBES FOR WHOLE-GENOME TILING ARRAYS WITH A CROSS-HYBRIDIZATION... 1651
, 2009
"... Background: High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, several genome dependent variables, such as the genome’s complexity and sequence c ..."
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Cited by 2 (0 self)
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methods or create novel tools. Principal Findings: Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays. We introduce a novel design method to make two 280,000 feature microarrays
Clinically validated benchmarking of normalisation techniques for two-colour oligonucleotide spotted microarray slides
- Appl. Bioinform
, 2003
"... Abstract: Acquisition of microarray data is prone to systematic errors. A correction, called normalisation, must be applied to the data before further analysis is performed. With many normalisation techniques published and in use, the best way of executing this correction remains an open question. I ..."
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Cited by 4 (2 self)
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Abstract: Acquisition of microarray data is prone to systematic errors. A correction, called normalisation, must be applied to the data before further analysis is performed. With many normalisation techniques published and in use, the best way of executing this correction remains an open question
An improved algorithm for the detection of genomic variation using short oligonucleotide
, 2012
"... expression microarrays ..."
Stochastic Models Based on Molecular Hybridization Theory for Short Oligonucleotide Microarrays
- Hopkins University. Dept. of Biostatistics Working Papers
, 2004
"... copyright holder. Copyright © 2011 by the authors ..."
Cross-Platform Microarray Data Normalisation for Regulatory Network Inference
, 2010
"... Background: Inferring Gene Regulatory Networks (GRNs) from time course microarray data suffers from the dimensionality problem created by the short length of available time series compared to the large number of genes in the network. To overcome this, data integration from diverse sources is mandato ..."
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Cited by 2 (2 self)
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Background: Inferring Gene Regulatory Networks (GRNs) from time course microarray data suffers from the dimensionality problem created by the short length of available time series compared to the large number of genes in the network. To overcome this, data integration from diverse sources
Results 1 - 10
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