• Publications
  • Influence
Computational studies of Family A and Family B GPCRs.
A full picture of the similarities between Family A and Family B GPCRs (G-protein coupled receptors) has been frustrated by the lack of clear homology between the respective sequences. Here, weExpand
  • 43
  • 4
  • PDF
G-spots cause incorrect expression measurement in Affymetrix microarrays
BackgroundHigh Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene isExpand
  • 49
  • 4
  • PDF
Similarity between class A and class B G-protein-coupled receptors exemplified through calcitonin gene-related peptide receptor modelling and mutagenesis studies
Modelling class B G-protein-coupled receptors (GPCRs) using class A GPCR structural templates is difficult due to lack of homology. The plant GPCR, GCR1, has homology to both class A and class BExpand
  • 47
  • 3
  • PDF
Probes containing runs of guanines provide insights into the biophysics and bioinformatics of Affymetrix GeneChips
TLDR
We propose a family of thousands of probes that show correlated expression across thousands of GeneChip experiments. Expand
  • 30
  • 3
  • PDF
An overview of image-processing methods for Affymetrix GeneChips
TLDR
We present an overview of image-processing methods for Affymetrix GeneChips. Expand
  • 41
  • 1
  • PDF
A Survey of Spatial Defects in Homo Sapiens Affymetrix GeneChips
TLDR
We show that, even in the best Human GeneChips 1/4 percent of data are affected by spatial noise. Expand
  • 36
  • 1
Normalized Affymetrix expression data are biased by G-quadruplex formation
Probes with runs of four or more guanines (G-stacks) in their sequences can exhibit a level of hybridization that is unrelated to the expression levels of the mRNA that they are intended to measure.Expand
  • 16
  • 1
  • PDF
Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information
We address the problem of detection and correction of spatial flaws in oligonucleotide microarrays. We present two similar procedures, of which one is intended solely for use with replicates and theExpand
  • 10
  • 1
Identifying the impact of G-Quadruplexes on Affymetrix 3' Arrays using Cloud Computing
TLDR
A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. Expand
  • 19
  • 1
  • PDF
Motif effects in Affymetrix GeneChips seriously affect probe intensities
An Affymetrix GeneChip consists of an array of hundreds of thousands of probes (each a sequence of 25 bases) with the probe values being used to infer the extent to which genes are expressed in theExpand
  • 4
  • 1
  • PDF
...
1
2
3
...